Revert "Added new amber99sb-ildn-bsc0 force field."

This reverts commit 3f7bdff15b41f7e0ffbfd0bf86b9c677ae51db77.

This is a temporary measure, pending testing of this variant
that is comparable with that for other AMBER forcefields, and/or
resolution of questions raised on gmx-developers.

Also removed line from the manual that was generated when this force
field was in the repo.

Change-Id: I1c2269d2ed554b827fb183d54f1db789a5762a8f

diff --git a/manual/topology.tex b/manual/topology.tex
index 42fb7a5ee375f768f0b4c8e5ab118cc28a9c4a47..c6f6fddc38676ce73e3925079f8cc140aff8d8c0 100644 (file)
--- a/manual/topology.tex
+++ b/manual/topology.tex
@@ -1875,7 +1875,6 @@ The force fields included with {\gromacs} are:
  \item AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
  \item AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
  \item AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
- \item AMBER99SB-ILDN-BSC0 protein, nucleic AMBER94 with ParmBSC0 (Perez et al., Biophys J. 2, 3817–29, 2007)
  \item AMBERGS force field (Garcia \& Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  \item CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  \item GROMOS96 43a1 force field

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.arn b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.arn
deleted file mode 100644 (file)
index 5da55ea..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.arn
+++ /dev/null
@@ -1,83 +0,0 @@
-; atom renaming specification
-; residue   gromacs  forcefield
-  NALA      H               H1
-  NGLY      H               H1
-  NSER      H               H1
-  NTHR      H               H1
-  NLEU      H               H1
-  NILE      H               H1
-  NVAL      H               H1
-  NASN      H               H1
-  NGLN      H               H1
-  NARG      H               H1
-  NHID      H               H1
-  NHIE      H               H1
-  NHIP      H               H1
-  NTRP      H               H1
-  NPHE      H               H1
-  NTYR      H               H1
-  NGLU      H               H1
-  NASP      H               H1
-  NLYS      H               H1
-  NPRO      H               H1
-  NCYS      H               H1
-  NCYX      H               H1
-  NMET      H               H1
-  NGLH       H               H1
-  NASP       H               H1
-; This mapping of O->OC2 and OXT->OC1 might look a bit strange,
-; but when we rebuild an oxygen it will be placed directly after C, so
-; this mapping makes sure OC1 comes before OC2. The oxygens are anyway chemically
-; equivalent, and if you already had their coordinates present they will be kept intact.
-  CALA      O               OC2
-  CALA       OXT             OC1
-  CGLY       O               OC2
-  CGLY      OXT             OC1
-  CSER       O               OC2
-  CSER      OXT             OC1
-  CTHR       O               OC2
-  CTHR      OXT             OC1
-  CLEU       O               OC2
-  CLEU      OXT             OC1
-  CILE       O               OC2
-  CILE      OXT             OC1
-  CVAL       O               OC2
-  CVAL      OXT             OC1
-  CASN       O               OC2
-  CASN      OXT             OC1
-  CGLN       O               OC2
-  CGLN      OXT             OC1
-  CARG       O               OC2
-  CARG      OXT             OC1
-  CHID       O               OC2
-  CHID      OXT             OC1
-  CHIE       O               OC2
-  CHIE      OXT             OC1
-  CHIP       O               OC2
-  CHIP      OXT             OC1
-  CTRP       O               OC2
-  CTRP      OXT             OC1
-  CPHE       O               OC2
-  CPHE      OXT             OC1
-  CTYR       O               OC2
-  CTYR      OXT             OC1
-  CGLU       O               OC2
-  CGLU      OXT             OC1
-  CASP       O               OC2
-  CASP      OXT             OC1
-  CLYS       O               OC2
-  CLYS      OXT             OC1
-  CPRO       O               OC2
-  CPRO      OXT             OC1
-  CCYS       O               OC2
-  CCYS      OXT             OC1
-  CCYX       O               OC2
-  CCYX      OXT             OC1
-  CMET       O               OC2
-  CMET       OXT             OC1
-  CGLH       O               OC2
-  CGLH       OXT             OC1
-  CASH       O               OC2
-  CASH       OXT             OC1
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.c.tdb b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.c.tdb
deleted file mode 100644 (file)
index 50d0742..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.c.tdb
+++ /dev/null
@@ -1,3 +0,0 @@
-; empty
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.hdb b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.hdb
deleted file mode 100644 (file)
index 4df9813..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.hdb
+++ /dev/null
@@ -1,518 +0,0 @@
-HOH    1
-2      7       HW      OW      
-HO4    1
-3      10      HW      OW      
-ACE    1
-3      4       HH3     CH3     C       O       
-NME    2
-1      1       H       N       -C      CH3     
-3      4       HH3     CH3     N       -C
-NHE    1
-2      3       H       N       -C      -CA
-NH2    1
-2      3       H       N       -C      -CA
-ALA    3
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-3      4       HB      CB      CA      N       
-GLY    2
-1      1       H       N       -C      CA      
-2      6       HA      CA      N       C       
-SER    4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      OG      
-1      2       HG      OG      CB      CA      
-THR    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     OG1     
-3      4       HG2     CG2     CB      CA      
-1      2       HG1     OG1     CB      CA      
-LEU    6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      5       HG      CG      CB      CD1     CD2     
-3      4       HD1     CD1     CG      CB      
-3      4       HD2     CD2     CG      CB      
-ILE    6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     CG1     
-3      4       HG2     CG2     CB      CA      
-2      6       HG1     CG1     CB      CD      
-3      4       HD      CD      CG1     CB      
-VAL    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG1     CG2     
-3      4       HG1     CG1     CB      CA      
-3      4       HG2     CG2     CB      CA      
-ASN    4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      3       HD2     ND2     CG      CB      
-GLN    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      3       HE2     NE2     CD      CG      
-ARG    8
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      NE      
-1      1       HE      NE      CD      CZ      
-2      3       HH1     NH1     CZ      NE      
-2      3       HH2     NH2     CZ      NE      
-HID    6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HD2     CD2     CG      NE2     
-HIE    6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-HIP    7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-TRP    9
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      NE1     
-1      1       HE1     NE1     CD1     CE2     
-1      1       HZ2     CZ2     CE2     CH2     
-1      1       HH2     CH2     CZ2     CZ3     
-1      1       HZ3     CZ3     CH2     CE3     
-1      1       HE3     CE3     CZ3     CD2     
-PHE    8
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      1       HZ      CZ      CE1     CE2     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-TYR    8
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      2       HH      OH      CZ      CE1     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-GLU    4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-ASP    3
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-LYS    7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      CE      
-2      6       HE      CE      CD      NZ      
-3      4       HZ      NZ      CE      CD      
-ORN    6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      NE      
-3      4       HE      NE      CD      CG      
-DAB    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      ND      
-3      4       HD      ND      CG      CB      
-LYN    7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      CE      
-2      6       HE      CE      CD      NZ      
-2      3       HZ      NZ      CE      CD      
-PRO    4
-2      6       HD      CD      N       CG      
-2      6       HG      CG      CD      CB      
-2      6       HB      CB      CG      CA      
-1      5       HA      CA      N       CB      C       
-HYP    5
-2      6       HD2     CD2     N       CG      
-1      5       HG      CG      CD2     OD1     CB      
-1      2       HD1     OD1     CG      CD2     
-2      6       HB      CB      CG      CA      
-1      5       HA      CA      N       CB      C       
-CYS    4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-1      2       HG      SG      CB      CA      
-CYM    3
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-CYX    3
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-CYS2   3
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-MET    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      SD      
-3      4       HE      CE      SD      CG      
-ASH    4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      2       HD2     OD2     CG      CB      
-GLH    5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-1      2       HE2     OE2     CD      CG      
-CALA   4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-3      4       HB      CB      CA      N       
-1       1       OC1     C       CA      OC2
-CGLY   3
-1      1       H       N       -C      CA      
-2      6       HA      CA      N       C       
-1       1       OC1     C       CA      OC2
-CSER   5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      OG      
-1      2       HG      OG      CB      CA      
-1       1       OC1     C       CA      OC2
-CTHR   6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     OG1     
-3      4       HG2     CG2     CB      CA      
-1      2       HG1     OG1     CB      CA      
-1       1       OC1     C       CA      OC2
-CLEU   7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      5       HG      CG      CB      CD1     CD2     
-3      4       HD1     CD1     CG      CB      
-3      4       HD2     CD2     CG      CB      
-1       1       OC1     C       CA      OC2
-CILE   7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     CG1     
-3      4       HG2     CG2     CB      CA      
-2      6       HG1     CG1     CB      CD      
-3      4       HD      CD      CG1     CB      
-1       1       OC1     C       CA      OC2
-CVAL   6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG1     CG2     
-3      4       HG1     CG1     CB      CA      
-3      4       HG2     CG2     CB      CA      
-1       1       OC1     C       CA      OC2
-CASN   5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      3       HD2     ND2     CG      CB      
-1       1       OC1     C       CA      OC2
-CGLN   6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      3       HE2     NE2     CD      CG      
-1       1       OC1     C       CA      OC2
-CARG   9
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      NE      
-1      1       HE      NE      CD      CZ      
-2      3       HH1     NH1     CZ      NE      
-2      3       HH2     NH2     CZ      NE      
-1       1       OC1     C       CA      OC2
-CHID   7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HD2     CD2     CG      NE2     
-1       1       OC1     C       CA      OC2
-CHIE   7
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-1       1       OC1     C       CA      OC2
-CHIP   8
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-1       1       OC1     C       CA      OC2
-CTRP   10
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      NE1     
-1      1       HE1     NE1     CD1     CE2     
-1      1       HZ2     CZ2     CE2     CH2     
-1      1       HH2     CH2     CZ2     CZ3     
-1      1       HZ3     CZ3     CH2     CE3     
-1      1       HE3     CE3     CZ3     CD2     
-1       1       OC1     C       CA      OC2
-CPHE   9
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      1       HZ      CZ      CE1     CE2     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-1       1       OC1     C       CA      OC2
-CTYR   9
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      2       HH      OH      CZ      CE1     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-1       1       OC1     C       CA      OC2
-CGLU   5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-1       1       OC1     C       CA      OC2
-CASP   4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1       1       OC1     C       CA      OC2
-CLYS   8
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      CE      
-2      6       HE      CE      CD      NZ      
-3      4       HZ      NZ      CE      CD      
-1       1       OC1     C       CA      OC2
-CPRO   5
-2      6       HD      CD      N       CG      
-2      6       HG      CG      CD      CB      
-2      6       HB      CB      CG      CA      
-1      5       HA      CA      N       CB      C       
-1       1       OC1     C       CA      OC2
-CCYS   5
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-1      2       HG      SG      CB      CA      
-1       1       OC1     C       CA      OC2
-CCYX   4
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-1       1       OC1     C       CA      OC2
-CMET   6
-1      1       H       N       -C      CA      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      SD      
-3      4       HE      CE      SD      CG      
-1       1       OC1     C       CA      OC2
-NALA   3
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-3      4       HB      CB      CA      N       
-NGLY   2
-3      4       H       N       CA      C       
-2      6       HA      CA      N       C       
-NSER   4
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      OG      
-1      2       HG      OG      CB      CA      
-NTHR   5
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     OG1     
-3      4       HG2     CG2     CB      CA      
-1      2       HG1     OG1     CB      CA      
-NLEU   6
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      5       HG      CG      CB      CD1     CD2     
-3      4       HD1     CD1     CG      CB      
-3      4       HD2     CD2     CG      CB      
-NILE   6
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG2     CG1     
-3      4       HG2     CG2     CB      CA      
-2      6       HG1     CG1     CB      CD      
-3      4       HD      CD      CG1     CB      
-NVAL   5
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-1      5       HB      CB      CA      CG1     CG2     
-3      4       HG1     CG1     CB      CA      
-3      4       HG2     CG2     CB      CA      
-NASN   4
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      3       HD2     ND2     CG      CB      
-NGLN   5
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      3       HE2     NE2     CD      CG      
-NARG   8
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      NE      
-1      1       HE      NE      CD      CZ      
-2      3       HH1     NH1     CZ      NE      
-2      3       HH2     NH2     CZ      NE      
-NHID   6
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HD2     CD2     CG      NE2     
-NHIE   6
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-NHIP   7
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     ND1     CG      CE1     
-1      1       HE1     CE1     ND1     NE2     
-1      1       HE2     NE2     CE1     CD2     
-1      1       HD2     CD2     CG      NE2     
-NTRP   9
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      NE1     
-1      1       HE1     NE1     CD1     CE2     
-1      1       HZ2     CZ2     CE2     CH2     
-1      1       HH2     CH2     CZ2     CZ3     
-1      1       HZ3     CZ3     CH2     CE3     
-1      1       HE3     CE3     CZ3     CD2     
-NPHE   8
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      1       HZ      CZ      CE1     CE2     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-NTYR   8
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-1      1       HD1     CD1     CG      CE1     
-1      1       HE1     CE1     CD1     CZ      
-1      2       HH      OH      CZ      CE1     
-1      1       HE2     CE2     CZ      CD2     
-1      1       HD2     CD2     CG      CE2     
-NGLU   4
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-NASP   3
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-NLYS   7
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      CD      
-2      6       HD      CD      CG      CE      
-2      6       HE      CE      CD      NZ      
-3      4       HZ      NZ      CE      CD      
-NPRO   5
-2      6       H       N       CA      CD      
-2      6       HD      CD      N       CG      
-2      6       HG      CG      CD      CB      
-2      6       HB      CB      CG      CA      
-1      5       HA      CA      N       CB      C       
-NCYS   4
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-1      2       HG      SG      CB      CA      
-NCYX   3
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      SG      
-NMET   5
-3      4       H       N       CA      CB      
-1      5       HA      CA      N       CB      C       
-2      6       HB      CB      CA      CG      
-2      6       HG      CG      CB      SD      
-3      4       HE      CE      SD      CG      

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.n.tdb b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.n.tdb
deleted file mode 100644 (file)
index 50d0742..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.n.tdb
+++ /dev/null
@@ -1,3 +0,0 @@
-; empty
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.r2b b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.r2b
deleted file mode 100644 (file)
index bba55ba..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.r2b
+++ /dev/null
@@ -1,31 +0,0 @@
-; rtp residue to rtp building block table
-;GMX   Force-field
-;      main  N-ter C-ter 2-ter
-ALA    ALA   NALA  CALA  -
-ARG    ARG   NARG  CARG  -
-ARGN   -     -     -     -
-ASN    ASN   NASN  CASN  -
-ASP    ASP   NASP  CASP  -
-ASPH   ASH   -     -     -
-CYS    CYS   NCYS  CCYS  -
-CYS2   CYX   NCYX  CCYX  -
-GLN    GLN   NGLN  CGLN  -
-QLN    -     -     -     -
-GLU    GLU   NGLU  CGLU  -
-GLY    GLY   NGLY  CGLY  -
-GLUH   GLH   -     -     -
-HISD   HID   NHID  CHID  -
-HISE   HIE   NHIE  CHIE  -
-HISH   HIP   NHIP  CHIP  -
-ILE    ILE   NILE  CILE  -
-LYSN   LYN   -     -     - 
-LYS    LYS   NLYS  CLYS  -
-LEU    LEU   NLEU  CLEU  -
-MET    MET   NMET  CMET  -
-PHE    PHE   NPHE  CPHE  -
-PRO    PRO   NPRO  CPRO  -
-SER    SER   NSER  CSER  -
-THR    THR   NTHR  CTHR  -
-TRP    TRP   NTRP  CTRP  -
-TYR    TYR   NTYR  CTYR  -
-VAL    VAL   NVAL  CVAL  -

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.rtp b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.rtp
deleted file mode 100644 (file)
index efb9077..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.rtp
+++ /dev/null
@@ -1,3530 +0,0 @@
-[ bondedtypes ]
-; Column 1 : default bondtype
-; Column 2 : default angletype
-; Column 3 : default proper dihedraltype
-; Column 4 : default improper dihedraltype
-; Column 5 : This controls the generation of dihedrals from the bonding.
-;            All possible dihedrals are generated automatically. A value of
-;            1 here means that all these are retained. A value of
-;            0 here requires generated dihedrals be removed if
-;              * there are any dihedrals on the same central atoms
-;                specified in the residue topology, or
-;              * there are other identical generated dihedrals
-;                sharing the same central atoms, or
-;              * there are other generated dihedrals sharing the
-;                same central bond that have fewer hydrogen atoms
-; Column 6 : number of neighbors to exclude from non-bonded interactions
-; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
-;            0 = do not generate such
-; Column 8 : 1 = remove proper dihedrals if found centered on the same
-;                bond as an improper dihedral
-;            0 = do not generate such
-; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
-     1       1          9          4        1         3      1     0
-
-; now: water, ions, urea, terminal caps, AA's and terminal AA's
-
-; tip3p
-[ HOH ]
- [ atoms ]
-    OW   OW           -0.834    0
-   HW1   HW            0.417    0
-   HW2   HW            0.417    0
- [ bonds ]
-    OW   HW1
-    OW   HW2
-
-; tip4p
-[ HO4 ]
- [ atoms ]
-    OW   OW_tip4p      0.00     0
-   HW1   HW            0.52     0
-   HW2   HW            0.52     0
-    MW   MW           -1.04     0
- [ bonds ]
-    OW   HW1
-    OW   HW2
-
-[ IB+ ] ; big positive ion
- [ atoms ]
-   IB     IB           1.00000     1
-
-[ CA ]
- [ atoms ]
-   CA     C0           2.00000     1
-
-[ CL ]
- [ atoms ]
-   CL     Cl          -1.00000     1
-
-[ NA ]
- [ atoms ]
-   NA     Na           1.00000     1
-
-[ MG ]
- [ atoms ]
-   MG     MG           2.00000     1
-
-[ K ]
- [ atoms ]
-   K      K            1.00000     1
-
-[ RB ]
- [ atoms ]
-   RB     Rb           1.00000     1
-
-[ CS ]
- [ atoms ]
-   CS     Cs           1.00000     1
-
-[ LI ]
- [ atoms ]
-   LI     Li           1.00000     1 
-
-[ ZN ]
- [ atoms ]
-   ZN     Zn           2.00000     1
-
-[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell
- [ atoms ]
-    C     C            0.880229        1       
-    O     O           -0.613359        2       
-   N1     N           -0.923545        3       
-  H11     H            0.395055        4       
-  H12     H            0.395055        5       
-   N2     N           -0.923545        6       
-  H21     H            0.395055        7       
-  H22     H            0.395055        8       
- [ bonds ]
-    C    N1
-    C    N2
-    C     O
-   N1    H11
-   N1    H12
-   N2    H21
-   N2    H22
- [ impropers ]
-    N1   N2     C     O
-     C  H11    N1   H12
-     C  H21    N2   H22        
-
-[ ACE ]
- [ atoms ]
-  HH31    HC           0.11230     1
-   CH3    CT          -0.36620     2
-  HH32    HC           0.11230     3
-  HH33    HC           0.11230     4
-     C    C            0.59720     5
-     O    O           -0.56790     6
- [ bonds ]
-  HH31   CH3
-   CH3  HH32
-   CH3  HH33
-   CH3     C
-     C     O
- [ impropers ]
-   CH3    +N     C     O
-                        
-[ NME ] 
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-   CH3    CT          -0.14900     3
-  HH31    H1           0.09760     4
-  HH32    H1           0.09760     5
-  HH33    H1           0.09760     6
- [ bonds ]
-     N     H
-     N   CH3
-   CH3  HH31
-   CH3  HH32
-   CH3  HH33
-    -C     N
- [ impropers ]
-    -C   CH3     N     H
-                        
-[ NHE ]
- [ atoms ]
-     N    N           -0.46300     1
-    H1    H            0.23150     2
-    H2    H            0.23150     3
- [ bonds ]
-     N    H1
-     N    H2
-    -C     N
- [ impropers ]
-    -C    H1     N    H2
-
-[ NH2 ]
- [ atoms ]
-     N    N           -0.46300     1
-    H1    H            0.23150     2
-    H2    H            0.23150     3
- [ bonds ]
-     N    H1
-     N    H2
-    -C     N
- [ impropers ]
-    -C    H1     N    H2
-
-; Next are non-terminal AA's
-
-[ ALA ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.03370     3
-    HA    H1           0.08230     4
-    CB    CT          -0.18250     5
-   HB1    HC           0.06030     6
-   HB2    HC           0.06030     7
-   HB3    HC           0.06030     8
-     C    C            0.59730     9
-     O    O           -0.56790    10
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB   HB3
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ GLY ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.02520     3
-   HA1    H1           0.06980     4
-   HA2    H1           0.06980     5
-     C    C            0.59730     6
-     O    O           -0.56790     7
- [ bonds ]
-     N     H
-     N    CA
-    CA   HA1
-    CA   HA2
-    CA     C
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ SER ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.02490     3
-    HA    H1           0.08430     4
-    CB    CT           0.21170     5
-   HB1    H1           0.03520     6
-   HB2    H1           0.03520     7
-    OG    OH          -0.65460     8
-    HG    HO           0.42750     9
-     C    C            0.59730    10
-     O    O           -0.56790    11
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    OG
-    OG    HG
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ THR ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.03890     3
-    HA    H1           0.10070     4
-    CB    CT           0.36540     5
-    HB    H1           0.00430     6
-   CG2    CT          -0.24380     7
-  HG21    HC           0.06420     8
-  HG22    HC           0.06420     9
-  HG23    HC           0.06420    10
-   OG1    OH          -0.67610    11
-   HG1    HO           0.41020    12
-     C    C            0.59730    13
-     O    O           -0.56790    14
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   OG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   OG1   HG1
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ LEU ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.05180     3
-    HA    H1           0.09220     4
-    CB    CT          -0.11020     5
-   HB1    HC           0.04570     6
-   HB2    HC           0.04570     7
-    CG    CT           0.35310     8
-    HG    HC          -0.03610     9
-   CD1    CT          -0.41210    10
-  HD11    HC           0.10000    11
-  HD12    HC           0.10000    12
-  HD13    HC           0.10000    13
-   CD2    CT          -0.41210    14
-  HD21    HC           0.10000    15
-  HD22    HC           0.10000    16
-  HD23    HC           0.10000    17
-     C    C            0.59730    18
-     O    O           -0.56790    19
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG    HG
-    CG   CD1
-    CG   CD2
-   CD1  HD11
-   CD1  HD12
-   CD1  HD13
-   CD2  HD21
-   CD2  HD22
-   CD2  HD23
-     C     O
-    -C     N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult3
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ ILE ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.05970     3
-    HA    H1           0.08690     4
-    CB    CT           0.13030     5
-    HB    HC           0.01870     6
-   CG2    CT          -0.32040     7
-  HG21    HC           0.08820     8
-  HG22    HC           0.08820     9
-  HG23    HC           0.08820    10
-   CG1    CT          -0.04300    11
-  HG11    HC           0.02360    12
-  HG12    HC           0.02360    13
-    CD    CT          -0.06600    14
-   HD1    HC           0.01860    15
-   HD2    HC           0.01860    16
-   HD3    HC           0.01860    17
-     C    C            0.59730    18
-     O    O           -0.56790    19
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   CG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   CG1  HG11
-   CG1  HG12
-   CG1    CD
-    CD   HD1
-    CD   HD2
-    CD   HD3
-     C     O
-    -C     N
- [ dihedrals ]
-     N    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult1
-     N    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult2
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ VAL ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.08750     3
-    HA    H1           0.09690     4
-    CB    CT           0.29850     5
-    HB    HC          -0.02970     6
-   CG1    CT          -0.31920     7
-  HG11    HC           0.07910     8
-  HG12    HC           0.07910     9
-  HG13    HC           0.07910    10
-   CG2    CT          -0.31920    11
-  HG21    HC           0.07910    12
-  HG22    HC           0.07910    13
-  HG23    HC           0.07910    14
-     C    C            0.59730    15
-     O    O           -0.56790    16
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG1
-    CB   CG2
-   CG1  HG11
-   CG1  HG12
-   CG1  HG13
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ ASN ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.01430     3
-    HA    H1           0.10480     4
-    CB    CT          -0.20410     5
-   HB1    HC           0.07970     6
-   HB2    HC           0.07970     7
-    CG    C            0.71300     8
-   OD1    O           -0.59310     9
-   ND2    N           -0.91910    10
-  HD21    H            0.41960    11
-  HD22    H            0.41960    12
-     C    C            0.59730    13
-     O    O           -0.56790    14
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   ND2
-   ND2  HD21
-   ND2  HD22
-     C     O
-    -C     N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult3
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult4
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult5
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult6
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult1
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult2
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult3
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult4
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult5
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult6
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CB   ND2    CG   OD1
-    CG  HD21   ND2  HD22
-                        
-[ GLN ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.00310     3
-    HA    H1           0.08500     4
-    CB    CT          -0.00360     5
-   HB1    HC           0.01710     6
-   HB2    HC           0.01710     7
-    CG    CT          -0.06450     8
-   HG1    HC           0.03520     9
-   HG2    HC           0.03520    10
-    CD    C            0.69510    11
-   OE1    O           -0.60860    12
-   NE2    N           -0.94070    13
-  HE21    H            0.42510    14
-  HE22    H            0.42510    15
-     C    C            0.59730    16
-     O    O           -0.56790    17
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   NE2
-   NE2  HE21
-   NE2  HE22
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   NE2    CD   OE1
-    CD  HE21   NE2  HE22
-                        
-[ ARG ]
- [ atoms ]
-     N    N           -0.34790     1
-     H    H            0.27470     2
-    CA    CT          -0.26370     3
-    HA    H1           0.15600     4
-    CB    CT          -0.00070     5
-   HB1    HC           0.03270     6
-   HB2    HC           0.03270     7
-    CG    CT           0.03900     8
-   HG1    HC           0.02850     9
-   HG2    HC           0.02850    10
-    CD    CT           0.04860    11
-   HD1    H1           0.06870    12
-   HD2    H1           0.06870    13
-    NE    N2          -0.52950    14
-    HE    H            0.34560    15
-    CZ    CA           0.80760    16
-   NH1    N2          -0.86270    17
-  HH11    H            0.44780    18
-  HH12    H            0.44780    19
-   NH2    N2          -0.86270    20
-  HH21    H            0.44780    21
-  HH22    H            0.44780    22
-     C    C            0.73410    23
-     O    O           -0.58940    24
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    NE
-    NE    HE
-    NE    CZ
-    CZ   NH1
-    CZ   NH2
-   NH1  HH11
-   NH1  HH12
-   NH2  HH21
-   NH2  HH22
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    NE   NH1    CZ   NH2
-    CD    CZ    NE    HE
-    CZ  HH11   NH1  HH12
-    CZ  HH21   NH2  HH22
-               
-[ HID ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.01880     3
-    HA    H1           0.08810     4
-    CB    CT          -0.04620     5
-   HB1    HC           0.04020     6
-   HB2    HC           0.04020     7
-    CG    CC          -0.02660     8
-   ND1    NA          -0.38110     9
-   HD1    H            0.36490    10
-   CE1    CR           0.20570    11
-   HE1    H5           0.13920    12
-   NE2    NB          -0.57270    13
-   CD2    CV           0.12920    14
-   HD2    H4           0.11470    15
-     C    C            0.59730    16
-     O    O           -0.56790    17
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   CE1   ND1   HD1
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ HIE ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.05810     3
-    HA    H1           0.13600     4
-    CB    CT          -0.00740     5
-   HB1    HC           0.03670     6
-   HB2    HC           0.03670     7
-    CG    CC           0.18680     8
-   ND1    NB          -0.54320     9
-   CE1    CR           0.16350    10
-   HE1    H5           0.14350    11
-   NE2    NA          -0.27950    12
-   HE2    H            0.33390    13
-   CD2    CW          -0.22070    14
-   HD2    H4           0.18620    15
-     C    C            0.59730    16
-     O    O           -0.56790    17
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB2
-    CB   HB1
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-   CE1   CD2   NE2   HE2
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ HIP ]
- [ atoms ]
-     N    N           -0.34790     1
-     H    H            0.27470     2
-    CA    CT          -0.13540     3
-    HA    H1           0.12120     4
-    CB    CT          -0.04140     5
-   HB1    HC           0.08100     6
-   HB2    HC           0.08100     7
-    CG    CC          -0.00120     8
-   ND1    NA          -0.15130     9
-   HD1    H            0.38660    10
-   CE1    CR          -0.01700    11
-   HE1    H5           0.26810    12
-   NE2    NA          -0.17180    13
-   HE2    H            0.39110    14
-   CD2    CW          -0.11410    15
-   HD2    H4           0.23170    16
-     C    C            0.73410    17
-     O    O           -0.58940    18
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   CE1   ND1   HD1
-   CE1   CD2   NE2   HE2
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ TRP ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.02750     3
-    HA    H1           0.11230     4
-    CB    CT          -0.00500     5
-   HB1    HC           0.03390     6
-   HB2    HC           0.03390     7
-    CG    C*          -0.14150     8
-   CD1    CW          -0.16380     9
-   HD1    H4           0.20620    10
-   NE1    NA          -0.34180    11
-   HE1    H            0.34120    12
-   CE2    CN           0.13800    13
-   CZ2    CA          -0.26010    14
-   HZ2    HA           0.15720    15
-   CH2    CA          -0.11340    16
-   HH2    HA           0.14170    17
-   CZ3    CA          -0.19720    18
-   HZ3    HA           0.14470    19
-   CE3    CA          -0.23870    20
-   HE3    HA           0.17000    21
-   CD2    CB           0.12430    22
-     C    C            0.59730    23
-     O    O           -0.56790    24
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   NE1
-   NE1   HE1
-   NE1   CE2
-   CE2   CZ2
-   CE2   CD2
-   CZ2   HZ2
-   CZ2   CH2
-   CH2   HH2
-   CH2   CZ3
-   CZ3   HZ3
-   CZ3   CE3
-   CE3   HE3
-   CE3   CD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-   CD1   CE2   NE1   HE1
-   CE2   CH2   CZ2   HZ2
-   CZ2   CZ3   CH2   HH2
-   CH2   CE3   CZ3   HZ3
-   CZ3   CD2   CE3   HE3
-    CG   NE1   CD1   HD1
-   CD1    CG    CB   CD2
-                        
-[ PHE ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.00240     3
-    HA    H1           0.09780     4
-    CB    CT          -0.03430     5
-   HB1    HC           0.02950     6
-   HB2    HC           0.02950     7
-    CG    CA           0.01180     8
-   CD1    CA          -0.12560     9
-   HD1    HA           0.13300    10
-   CE1    CA          -0.17040    11
-   HE1    HA           0.14300    12
-    CZ    CA          -0.10720    13
-    HZ    HA           0.12970    14
-   CE2    CA          -0.17040    15
-   HE2    HA           0.14300    16
-   CD2    CA          -0.12560    17
-   HD2    HA           0.13300    18
-     C    C            0.59730    19
-     O    O           -0.56790    20
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    HZ
-    CZ   CE2
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   CE2   CD2   HD2
-    CZ   CD2   CE2   HE2
-   CE1   CE2    CZ    HZ
-   CD1    CZ   CE1   HE1
-    CG   CE1   CD1   HD1
-   CD1   CD2    CG    CB
-                       
-[ TYR ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.00140     3
-    HA    H1           0.08760     4
-    CB    CT          -0.01520     5
-   HB1    HC           0.02950     6
-   HB2    HC           0.02950     7
-    CG    CA          -0.00110     8
-   CD1    CA          -0.19060     9
-   HD1    HA           0.16990    10
-   CE1    CA          -0.23410    11
-   HE1    HA           0.16560    12
-    CZ    C            0.32260    13
-    OH    OH          -0.55790    14
-    HH    HO           0.39920    15
-   CE2    CA          -0.23410    16
-   HE2    HA           0.16560    17
-   CD2    CA          -0.19060    18
-   HD2    HA           0.16990    19
-     C    C            0.59730    20
-     O    O           -0.56790    21
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    OH
-    CZ   CE2
-    OH    HH
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   CE2   CD2   HD2
-    CZ   CD2   CE2   HE2
-   CD1    CZ   CE1   HE1
-    CG   CE1   CD1   HD1
-   CD1   CD2    CG    CB
-   CE1   CE2    CZ    OH
-                        
-[ GLU ]
- [ atoms ]
-     N    N           -0.51630     1
-     H    H            0.29360     2
-    CA    CT           0.03970     3
-    HA    H1           0.11050     4
-    CB    CT           0.05600     5
-   HB1    HC          -0.01730     6
-   HB2    HC          -0.01730     7
-    CG    CT           0.01360     8
-   HG1    HC          -0.04250     9
-   HG2    HC          -0.04250    10
-    CD    C            0.80540    11
-   OE1    O2          -0.81880    12
-   OE2    O2          -0.81880    13
-     C    C            0.53660    14
-     O    O           -0.58190    15
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   OE2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   OE1    CD   OE2
-                        
-[ ASP ]
- [ atoms ]
-     N    N           -0.51630     1
-     H    H            0.29360     2
-    CA    CT           0.03810     3
-    HA    H1           0.08800     4
-    CB    CT          -0.03030     5
-   HB1    HC          -0.01220     6
-   HB2    HC          -0.01220     7
-    CG    C            0.79940     8
-   OD1    O2          -0.80140     9
-   OD2    O2          -0.80140    10
-     C    C            0.53660    11
-     O    O           -0.58190    12
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   OD2
-     C     O
-    -C     N
- [ dihedrals ]
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult1
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult2
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult3
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult4
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult5
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult6
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult6
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult6
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CB   OD1    CG   OD2
-                        
-[ LYS ]
- [ atoms ]
-     N    N           -0.34790     1
-     H    H            0.27470     2
-    CA    CT          -0.24000     3
-    HA    H1           0.14260     4
-    CB    CT          -0.00940     5
-   HB1    HC           0.03620     6
-   HB2    HC           0.03620     7
-    CG    CT           0.01870     8
-   HG1    HC           0.01030     9
-   HG2    HC           0.01030    10
-    CD    CT          -0.04790    11
-   HD1    HC           0.06210    12
-   HD2    HC           0.06210    13
-    CE    CT          -0.01430    14
-   HE1    HP           0.11350    15
-   HE2    HP           0.11350    16
-    NZ    N3          -0.38540    17
-   HZ1    H            0.34000    18
-   HZ2    H            0.34000    19
-   HZ3    H            0.34000    20
-     C    C            0.73410    21
-     O    O           -0.58940    22
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    CE
-    CE   HE1
-    CE   HE2
-    CE    NZ
-    NZ   HZ1
-    NZ   HZ2
-    NZ   HZ3
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-
-[ ORN ] ; charges taken from amber99.prm of tinker 4.0
- [ atoms ]
-     N    N           -0.34790     1
-     H    H            0.27470     2
-    CA    CT          -0.24000     3
-    HA    H1           0.14260     4
-    CB    CT           0.00990     5
-   HB1    HC           0.03620     6
-   HB2    HC           0.03620     7
-    CG    CT          -0.02790     8
-   HG1    HC           0.06210     9
-   HG2    HC           0.06210    10
-    CD    CT          -0.01430    11
-   HD1    HP           0.11350    12
-   HD2    HP           0.11350    13
-    NE    N3          -0.38540    14
-   HE1    H            0.34000    15
-   HE2    H            0.34000    16
-   HE3    H            0.34000    17
-     C    C            0.73410    18
-     O    O           -0.58940    19
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    NE
-    NE   HE1
-    NE   HE2
-    NE   HE3
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-
-[ DAB ] ; sidechain charges fit to maintain heavy atom charge group trend LYS -> ORN -> DAB
- [ atoms ]
-     N    N           -0.34790     1
-     H    H            0.27470     2
-    CA    CT          -0.24000     3
-    HA    H1           0.14260     4
-    CB    CT           0.02920     5
-   HB1    HC           0.07470     6
-   HB2    HC           0.07470     7
-    CG    CT          -0.01430     8
-   HG1    HP           0.11350     9
-   HG2    HP           0.11350    10
-    ND    N3          -0.38540    11
-   HD1    H            0.34000    12
-   HD2    H            0.34000    13
-   HD3    H            0.34000    14
-     C    C            0.73410    15
-     O    O           -0.58940    16
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    ND
-    ND   HD1
-    ND   HD2
-    ND   HD3
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-
-[ LYN ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.07206     3
-    HA    H1           0.09940     4
-    CB    CT          -0.04845     5
-   HB1    HC           0.03400     6
-   HB2    HC           0.03400     7
-    CG    CT           0.06612     8
-   HG1    HC           0.01041     9
-   HG2    HC           0.01041    10
-    CD    CT          -0.03768    11
-   HD1    HC           0.01155    12
-   HD2    HC           0.01155    13
-    CE    CT           0.32604    14
-   HE1    HP          -0.03358    15
-   HE2    HP          -0.03358    16
-    NZ    N3          -1.03581    17
-   HZ1    H            0.38604    18
-   HZ2    H            0.38604    19
-     C    C            0.59730    20
-     O    O           -0.56790    21
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    CE
-    CE   HE1
-    CE   HE2
-    CE    NZ
-    NZ   HZ1
-    NZ   HZ2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ PRO ]
- [ atoms ]
-     N    N           -0.25480     1
-    CD    CT           0.01920     2
-   HD1    H1           0.03910     3
-   HD2    H1           0.03910     4
-    CG    CT           0.01890     5
-   HG1    HC           0.02130     6
-   HG2    HC           0.02130     7
-    CB    CT          -0.00700     8
-   HB1    HC           0.02530     9
-   HB2    HC           0.02530    10
-    CA    CT          -0.02660    11
-    HA    H1           0.06410    12
-     C    C            0.58960    13
-     O    O           -0.57480    14
- [ bonds ]
-     N    CD
-     N    CA
-    CD   HD1
-    CD   HD2
-    CD    CG
-    CG   HG1
-    CG   HG2
-    CG    CB
-    CB   HB1
-    CB   HB2
-    CB    CA
-    CA    HA
-    CA     C
-     C     O
-    -C     N
- [ impropers ]
-    CA    +N     C     O
-    -C    CD     N    CA       
-
-[ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted).
- [ atoms ] 
-     N    N           -0.25480     1
-   CD2    CT           0.05950     2
-  HD21    H1           0.07000     3
-  HD22    H1           0.07000     4
-    CG    CT           0.04000     5
-    HG    H1           0.04160     6
-   OD1    OH          -0.61340     7
-   HD1    HO           0.38510     8
-    CB    CT           0.02030     9
-   HB1    HC           0.04260    10
-   HB2    HC           0.04260    11
-    CA    CT           0.00470    12
-    HA    H1           0.07700    13
-     C    C            0.58960    14
-     O    O           -0.57480    15
- [ bonds ]
-     N   CD2
-     N    CA
-   CD2  HD21
-   CD2  HD22
-   CD2    CG
-    CG    HG
-    CG   OD1
-    CG    CB
-   OD1   HD1
-    CB   HB1
-    CB   HB2
-    CB    CA
-    CA    HA
-    CA     C
-     C     O
-    -C     N
- [ impropers ]
-    CA    +N     C     O
-    -C   CD2     N    CA
-                        
-[ CYS ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.02130     3
-    HA    H1           0.11240     4
-    CB    CT          -0.12310     5
-   HB1    H1           0.11120     6
-   HB2    H1           0.11120     7
-    SG    SH          -0.31190     8
-    HG    HS           0.19330     9
-     C    C            0.59730    10
-     O    O           -0.56790    11
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-    SG    HG
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ CYM ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.03510     3
-    HA    H1           0.05080     4
-    CB    CT          -0.24130     5
-   HB1    H1           0.11220     6
-   HB2    H1           0.11220     7
-    SG    SH          -0.88440     8
-     C    C            0.59730     9
-     O    O           -0.56790    10
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-[ CYX ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.04290     3
-    HA    H1           0.07660     4
-    CB    CT          -0.07900     5
-   HB1    H1           0.09100     6
-   HB2    H1           0.09100     7
-    SG    S           -0.10810     8
-     C    C            0.59730     9
-     O    O           -0.56790    10
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-
-[ MET ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT          -0.02370     3
-    HA    H1           0.08800     4
-    CB    CT           0.03420     5
-   HB1    HC           0.02410     6
-   HB2    HC           0.02410     7
-    CG    CT           0.00180     8
-   HG1    H1           0.04400     9
-   HG2    H1           0.04400    10
-    SD    S           -0.27370    11
-    CE    CT          -0.05360    12
-   HE1    H1           0.06840    13
-   HE2    H1           0.06840    14
-   HE3    H1           0.06840    15
-     C    C            0.59730    16
-     O    O           -0.56790    17
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    SD
-    SD    CE
-    CE   HE1
-    CE   HE2
-    CE   HE3
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-                        
-; non-terminal acidic AA's
-       
-[ ASH ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.03410     3
-    HA    H1           0.08640     4
-    CB    CT          -0.03160     5
-   HB1    HC           0.04880     6
-   HB2    HC           0.04880     7
-    CG    C            0.64620     8
-   OD1    O           -0.55540     9
-   OD2    OH          -0.63760    10
-   HD2    HO           0.47470    11
-     C    C            0.59730    12
-     O    O           -0.56790    13
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   OD2
-   OD2   HD2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CB   OD1    CG   OD2
-                   
-
-[ GLH ]
- [ atoms ]
-     N    N           -0.41570     1
-     H    H            0.27190     2
-    CA    CT           0.01450     3
-    HA    H1           0.07790     4
-    CB    CT          -0.00710     5
-   HB1    HC           0.02560     6
-   HB2    HC           0.02560     7
-    CG    CT          -0.01740     8
-   HG1    HC           0.04300     9
-   HG2    HC           0.04300    10
-    CD    C            0.68010    11
-   OE1    O           -0.58380    12
-   OE2    OH          -0.65110    13
-   HE2    HO           0.46410    14
-     C    C            0.59730    15
-     O    O           -0.56790    16
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   OE2
-   OE2   HE2
-     C     O
-    -C     N
- [ impropers ]
-    -C    CA     N     H
-    CA    +N     C     O
-    CG   OE1    CD   OE2
-
-; C-terminal AA's
-                        
-[ CALA ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.17470     3
-    HA    H1           0.10670     4
-    CB    CT          -0.20930     5
-   HB1    HC           0.07640     6
-   HB2    HC           0.07640     7
-   HB3    HC           0.07640     8
-     C    C            0.77310     9
-   OC1    O2          -0.80550    10
-   OC2    O2          -0.80550    11
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB   HB3
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CGLY ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.24930     3
-   HA1    H1           0.10560     4
-   HA2    H1           0.10560     5
-     C    C            0.72310     6
-   OC1    O2          -0.78550     7
-   OC2    O2          -0.78550     8
- [ bonds ]
-     N     H
-     N    CA
-    CA   HA1
-    CA   HA2
-    CA     C
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CSER ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.27220     3
-    HA    H1           0.13040     4
-    CB    CT           0.11230     5
-   HB1    H1           0.08130     6
-   HB2    H1           0.08130     7
-    OG    OH          -0.65140     8
-    HG    HO           0.44740     9
-     C    C            0.81130    10
-   OC1    O2          -0.81320    11
-   OC2    O2          -0.81320    12
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    OG
-    OG    HG
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CTHR ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.24200     3
-    HA    H1           0.12070     4
-    CB    CT           0.30250     5
-    HB    H1           0.00780     6
-   CG2    CT          -0.18530     7
-  HG21    HC           0.05860     8
-  HG22    HC           0.05860     9
-  HG23    HC           0.05860    10
-   OG1    OH          -0.64960    11
-   HG1    HO           0.41190    12
-     C    C            0.78100    13
-   OC1    O2          -0.80440    14
-   OC2    O2          -0.80440    15
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   OG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   OG1   HG1
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CLEU ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.28470     3
-    HA    H1           0.13460     4
-    CB    CT          -0.24690     5
-   HB1    HC           0.09740     6
-   HB2    HC           0.09740     7
-    CG    CT           0.37060     8
-    HG    HC          -0.03740     9
-   CD1    CT          -0.41630    10
-  HD11    HC           0.10380    11
-  HD12    HC           0.10380    12
-  HD13    HC           0.10380    13
-   CD2    CT          -0.41630    14
-  HD21    HC           0.10380    15
-  HD22    HC           0.10380    16
-  HD23    HC           0.10380    17
-     C    C            0.83260    18
-   OC1    O2          -0.81990    19
-   OC2    O2          -0.81990    20
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG    HG
-    CG   CD1
-    CG   CD2
-   CD1  HD11
-   CD1  HD12
-   CD1  HD13
-   CD2  HD21
-   CD2  HD22
-   CD2  HD23
-     C   OC1
-     C   OC2
-    -C     N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult3
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CILE ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.31000     3
-    HA    H1           0.13750     4
-    CB    CT           0.03630     5
-    HB    HC           0.07660     6
-   CG2    CT          -0.34980     7
-  HG21    HC           0.10210     8
-  HG22    HC           0.10210     9
-  HG23    HC           0.10210    10
-   CG1    CT          -0.03230    11
-  HG11    HC           0.03210    12
-  HG12    HC           0.03210    13
-    CD    CT          -0.06990    14
-   HD1    HC           0.01960    15
-   HD2    HC           0.01960    16
-   HD3    HC           0.01960    17
-     C    C            0.83430    18
-   OC1    O2          -0.81900    19
-   OC2    O2          -0.81900    20
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   CG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   CG1  HG11
-   CG1  HG12
-   CG1    CD
-    CD   HD1
-    CD   HD2
-    CD   HD3
-     C   OC1
-     C   OC2
-    -C     N
- [ dihedrals ]
-     N    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult1
-     B    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult2
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CVAL ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.34380     3
-    HA    H1           0.14380     4
-    CB    CT           0.19400     5
-    HB    HC           0.03080     6
-   CG1    CT          -0.30640     7
-  HG11    HC           0.08360     8
-  HG12    HC           0.08360     9
-  HG13    HC           0.08360    10
-   CG2    CT          -0.30640    11
-  HG21    HC           0.08360    12
-  HG22    HC           0.08360    13
-  HG23    HC           0.08360    14
-     C    C            0.83500    15
-   OC1    O2          -0.81730    16
-   OC2    O2          -0.81730    17
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG1
-    CB   CG2
-   CG1  HG11
-   CG1  HG12
-   CG1  HG13
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CASN ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.20800     3
-    HA    H1           0.13580     4
-    CB    CT          -0.22990     5
-   HB1    HC           0.10230     6
-   HB2    HC           0.10230     7
-    CG    C            0.71530     8
-   OD1    O           -0.60100     9
-   ND2    N           -0.90840    10
-  HD21    H            0.41500    11
-  HD22    H            0.41500    12
-     C    C            0.80500    13
-   OC1    O2          -0.81470    14
-   OC2    O2          -0.81470    15
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   ND2
-   ND2  HD21
-   ND2  HD22
-     C   OC1
-     C   OC2
-    -C     N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult3
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult4
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult5
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult6
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult1
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult2
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult3
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult4
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult5
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult6
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CB   ND2    CG   OD1    
-    CG  HD21   ND2  HD22    
-                        
-[ CGLN ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.22480     3
-    HA    H1           0.12320     4
-    CB    CT          -0.06640     5
-   HB1    HC           0.04520     6
-   HB2    HC           0.04520     7
-    CG    CT          -0.02100     8
-   HG1    HC           0.02030     9
-   HG2    HC           0.02030    10
-    CD    C            0.70930    11
-   OE1    O           -0.60980    12
-   NE2    N           -0.95740    13
-  HE21    H            0.43040    14
-  HE22    H            0.43040    15
-     C    C            0.77750    16
-   OC1    O2          -0.80420    17
-   OC2    O2          -0.80420    18
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   NE2
-   NE2  HE21
-   NE2  HE22
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   NE2    CD   OE1    
-    CD  HE21   NE2  HE22    
-                        
-[ CARG ]
- [ atoms ]
-     N    N           -0.34810     1
-     H    H            0.27640     2
-    CA    CT          -0.30680     3
-    HA    H1           0.14470     4
-    CB    CT          -0.03740     5
-   HB1    HC           0.03710     6
-   HB2    HC           0.03710     7
-    CG    CT           0.07440     8
-   HG1    HC           0.01850     9
-   HG2    HC           0.01850    10
-    CD    CT           0.11140    11
-   HD1    H1           0.04680    12
-   HD2    H1           0.04680    13
-    NE    N2          -0.55640    14
-    HE    H            0.34790    15
-    CZ    CA           0.83680    16
-   NH1    N2          -0.87370    17
-  HH11    H            0.44930    18
-  HH12    H            0.44930    19
-   NH2    N2          -0.87370    20
-  HH21    H            0.44930    21
-  HH22    H            0.44930    22
-     C    C            0.85570    23
-   OC1    O2          -0.82660    24
-   OC2    O2          -0.82660    25
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    NE
-    NE    HE
-    NE    CZ
-    CZ   NH1
-    CZ   NH2
-   NH1  HH11
-   NH1  HH12
-   NH2  HH21
-   NH2  HH22
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    NE   NH1    CZ   NH2    
-    CD    CZ    NE    HE    
-    CZ  HH11   NH1  HH12    
-    CZ  HH21   NH2  HH22    
-                        
-[ CHID ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.17390     3
-    HA    H1           0.11000     4
-    CB    CT          -0.10460     5
-   HB1    HC           0.05650     6
-   HB2    HC           0.05650     7
-    CG    CC           0.02930     8
-   ND1    NA          -0.38920     9
-   HD1    H            0.37550    10
-   CE1    CR           0.19250    11
-   HE1    H5           0.14180    12
-   NE2    NB          -0.56290    13
-   CD2    CV           0.10010    14
-   HD2    H4           0.12410    15
-     C    C            0.76150    16
-   OC1    O2          -0.80160    17
-   OC2    O2          -0.80160    18
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   CD2
-   CD2   HD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   CE1   ND1   HD1    
-    CG   NE2   CD2   HD2    
-   ND1   NE2   CE1   HE1    
-   ND1   CD2    CG    CB    
-                        
-[ CHIE ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.26990     3
-    HA    H1           0.16500     4
-    CB    CT          -0.10680     5
-   HB1    HC           0.06200     6
-   HB2    HC           0.06200     7
-    CG    CC           0.27240     8
-   ND1    NB          -0.55170     9
-   CE1    CR           0.15580    10
-   HE1    H5           0.14480    11
-   NE2    NA          -0.26700    12
-   HE2    H            0.33190    13
-   CD2    CW          -0.25880    14
-   HD2    H4           0.19570    15
-     C    C            0.79160    16
-   OC1    O2          -0.80650    17
-   OC2    O2          -0.80650    18
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-   CE1   CD2   NE2   HE2    
-    CG   NE2   CD2   HD2    
-   ND1   NE2   CE1   HE1    
-   ND1   CD2    CG    CB    
-                        
-[ CHIP ]
- [ atoms ]
-     N    N           -0.34810     1
-     H    H            0.27640     2
-    CA    CT          -0.14450     3
-    HA    H1           0.11150     4
-    CB    CT          -0.08000     5
-   HB1    HC           0.08680     6
-   HB2    HC           0.08680     7
-    CG    CC           0.02980     8
-   ND1    NA          -0.15010     9
-   HD1    H            0.38830    10
-   CE1    CR          -0.02510    11
-   HE1    H5           0.26940    12
-   NE2    NA          -0.16830    13
-   HE2    H            0.39130    14
-   CD2    CW          -0.12560    15
-   HD2    H4           0.23360    16
-     C    C            0.80320    17
-   OC1    O2          -0.81770    18
-   OC2    O2          -0.81770    19
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   CE1   ND1   HD1    
-   CE1   CD2   NE2   HE2    
-    CG   NE2   CD2   HD2    
-   ND1   NE2   CE1   HE1    
-   ND1   CD2    CG    CB    
-                        
-[ CTRP ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.20840     3
-    HA    H1           0.12720     4
-    CB    CT          -0.07420     5
-   HB1    HC           0.04970     6
-   HB2    HC           0.04970     7
-    CG    C*          -0.07960     8
-   CD1    CW          -0.18080     9
-   HD1    H4           0.20430    10
-   NE1    NA          -0.33160    11
-   HE1    H            0.34130    12
-   CE2    CN           0.12220    13
-   CZ2    CA          -0.25940    14
-   HZ2    HA           0.15670    15
-   CH2    CA          -0.10200    16
-   HH2    HA           0.14010    17
-   CZ3    CA          -0.22870    18
-   HZ3    HA           0.15070    19
-   CE3    CA          -0.18370    20
-   HE3    HA           0.14910    21
-   CD2    CB           0.10780    22
-     C    C            0.76580    23
-   OC1    O2          -0.80110    24
-   OC2    O2          -0.80110    25
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   NE1
-   NE1   HE1
-   NE1   CE2
-   CE2   CZ2
-   CE2   CD2
-   CZ2   HZ2
-   CZ2   CH2
-   CH2   HH2
-   CH2   CZ3
-   CZ3   HZ3
-   CZ3   CE3
-   CE3   HE3
-   CE3   CD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-   CD1   CE2   NE1   HE1    
-   CE2   CH2   CZ2   HZ2    
-   CZ2   CZ3   CH2   HH2    
-   CH2   CE3   CZ3   HZ3    
-   CZ3   CD2   CE3   HE3    
-    CG   NE1   CD1   HD1    
-   CD1    CG    CB   CD2
-                        
-[ CPHE ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.18250     3
-    HA    H1           0.10980     4
-    CB    CT          -0.09590     5
-   HB1    HC           0.04430     6
-   HB2    HC           0.04430     7
-    CG    CA           0.05520     8
-   CD1    CA          -0.13000     9
-   HD1    HA           0.14080    10
-   CE1    CA          -0.18470    11
-   HE1    HA           0.14610    12
-    CZ    CA          -0.09440    13
-    HZ    HA           0.12800    14
-   CE2    CA          -0.18470    15
-   HE2    HA           0.14610    16
-   CD2    CA          -0.13000    17
-   HD2    HA           0.14080    18
-     C    C            0.76600    19
-   OC1    O2          -0.80260    20
-   OC2    O2          -0.80260    21
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    HZ
-    CZ   CE2
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   CE2   CD2   HD2    
-    CZ   CD2   CE2   HE2    
-   CE1   CE2    CZ    HZ    
-   CD1    CZ   CE1   HE1    
-    CG   CE1   CD1   HD1    
-   CD1   CD2    CG    CB    
-                        
-[ CTYR ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.20150     3
-    HA    H1           0.10920     4
-    CB    CT          -0.07520     5
-   HB1    HC           0.04900     6
-   HB2    HC           0.04900     7
-    CG    CA           0.02430     8
-   CD1    CA          -0.19220     9
-   HD1    HA           0.17800    10
-   CE1    CA          -0.24580    11
-   HE1    HA           0.16730    12
-    CZ    C            0.33950    13
-    OH    OH          -0.56430    14
-    HH    HO           0.40170    15
-   CE2    CA          -0.24580    16
-   HE2    HA           0.16730    17
-   CD2    CA          -0.19220    18
-   HD2    HA           0.17800    19
-     C    C            0.78170    20
-   OC1    O2          -0.80700    21
-   OC2    O2          -0.80700    22
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    OH
-    CZ   CE2
-    OH    HH
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   CE2   CD2   HD2    
-    CZ   CD2   CE2   HE2    
-   CD1    CZ   CE1   HE1    
-    CG   CE1   CD1   HD1    
-   CD1   CD2    CG    CB    
-   CE1   CE2    CZ    OH    
-                        
-[ CGLU ]
- [ atoms ]
-     N    N           -0.51920     1
-     H    H            0.30550     2
-    CA    CT          -0.20590     3
-    HA    H1           0.13990     4
-    CB    CT           0.00710     5
-   HB1    HC          -0.00780     6
-   HB2    HC          -0.00780     7
-    CG    CT           0.06750     8
-   HG1    HC          -0.05480     9
-   HG2    HC          -0.05480    10
-    CD    C            0.81830    11
-   OE1    O2          -0.82200    12
-   OE2    O2          -0.82200    13
-     C    C            0.74200    14
-   OC1    O2          -0.79300    15
-   OC2    O2          -0.79300    16
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   OE2
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CG   OE1    CD   OE2    
-                        
-[ CASP ]
- [ atoms ]
-     N    N           -0.51920     1
-     H    H            0.30550     2
-    CA    CT          -0.18170     3
-    HA    H1           0.10460     4
-    CB    CT          -0.06770     5
-   HB1    HC          -0.02120     6
-   HB2    HC          -0.02120     7
-    CG    C            0.88510     8
-   OD1    O2          -0.81620     9
-   OD2    O2          -0.81620    10
-     C    C            0.72560    11
-   OC1    O2          -0.78870    12
-   OC2    O2          -0.78870    13
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   OD2
-     C   OC1
-     C   OC2
-    -C     N
- [ dihedrals ]
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult1
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult2
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult3
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult4
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult5
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult6
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult6
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult6
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-    CB   OD1    CG   OD2    
-                        
-[ CLYS ]
- [ atoms ]
-     N    N           -0.34810     1
-     H    H            0.27640     2
-    CA    CT          -0.29030     3
-    HA    H1           0.14380     4
-    CB    CT          -0.05380     5
-   HB1    HC           0.04820     6
-   HB2    HC           0.04820     7
-    CG    CT           0.02270     8
-   HG1    HC           0.01340     9
-   HG2    HC           0.01340    10
-    CD    CT          -0.03920    11
-   HD1    HC           0.06110    12
-   HD2    HC           0.06110    13
-    CE    CT          -0.01760    14
-   HE1    HP           0.11210    15
-   HE2    HP           0.11210    16
-    NZ    N3          -0.37410    17
-   HZ1    H            0.33740    18
-   HZ2    H            0.33740    19
-   HZ3    H            0.33740    20
-     C    C            0.84880    21
-   OC1    O2          -0.82520    22
-   OC2    O2          -0.82520    23
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    CE
-    CE   HE1
-    CE   HE2
-    CE    NZ
-    NZ   HZ1
-    NZ   HZ2
-    NZ   HZ3
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CPRO ]
- [ atoms ]
-     N    N           -0.28020     1
-    CD    CT           0.04340     2
-   HD1    H1           0.03310     3
-   HD2    H1           0.03310     4
-    CG    CT           0.04660     5
-   HG1    HC           0.01720     6
-   HG2    HC           0.01720     7
-    CB    CT          -0.05430     8
-   HB1    HC           0.03810     9
-   HB2    HC           0.03810    10
-    CA    CT          -0.13360    11
-    HA    H1           0.07760    12
-     C    C            0.66310    13
-   OC1    O2          -0.76970    14
-   OC2    O2          -0.76970    15
- [ bonds ]
-     N    CD
-     N    CA
-    CD   HD1
-    CD   HD2
-    CD    CG
-    CG   HG1
-    CG   HG2
-    CG    CB
-    CB   HB1
-    CB   HB2
-    CB    CA
-    CA    HA
-    CA     C
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    CA   OC1     C   OC2    
-    -C    CD     N    CA    
-                        
-[ CCYS ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.16350     3
-    HA    H1           0.13960     4
-    CB    CT          -0.19960     5
-   HB1    H1           0.14370     6
-   HB2    H1           0.14370     7
-    SG    SH          -0.31020     8
-    HG    HS           0.20680     9
-     C    C            0.74970    10
-   OC1    O2          -0.79810    11
-   OC2    O2          -0.79810    12
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-    SG    HG
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CCYX ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.13180     3
-    HA    H1           0.09380     4
-    CB    CT          -0.19430     5
-   HB1    H1           0.12280     6
-   HB2    H1           0.12280     7
-    SG    S           -0.05290     8
-     C    C            0.76180     9
-   OC1    O2          -0.80410    10
-   OC2    O2          -0.80410    11
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-                        
-[ CMET ]
- [ atoms ]
-     N    N           -0.38210     1
-     H    H            0.26810     2
-    CA    CT          -0.25970     3
-    HA    H1           0.12770     4
-    CB    CT          -0.02360     5
-   HB1    HC           0.04800     6
-   HB2    HC           0.04800     7
-    CG    CT           0.04920     8
-   HG1    H1           0.03170     9
-   HG2    H1           0.03170    10
-    SD    S           -0.26920    11
-    CE    CT          -0.03760    12
-   HE1    H1           0.06250    13
-   HE2    H1           0.06250    14
-   HE3    H1           0.06250    15
-     C    C            0.80130    16
-   OC1    O2          -0.81050    17
-   OC2    O2          -0.81050    18
- [ bonds ]
-     N     H
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    SD
-    SD    CE
-    CE   HE1
-    CE   HE2
-    CE   HE3
-     C   OC1
-     C   OC2
-    -C     N
- [ impropers ]
-    -C    CA     N     H    
-    CA   OC1     C   OC2    
-
-; N-terminal AA's                        
-
-[ NALA ]
- [ atoms ]
-     N    N3           0.14140     1
-    H1    H            0.19970     2
-    H2    H            0.19970     3
-    H3    H            0.19970     4
-    CA    CT           0.09620     5
-    HA    HP           0.08890     6
-    CB    CT          -0.05970     7
-   HB1    HC           0.03000     8
-   HB2    HC           0.03000     9
-   HB3    HC           0.03000    10
-     C    C            0.61630    11
-     O    O           -0.57220    12
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB   HB3
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NGLY ]
- [ atoms ]
-     N    N3           0.29430     1
-    H1    H            0.16420     2
-    H2    H            0.16420     3
-    H3    H            0.16420     4
-    CA    CT          -0.01000     5
-   HA1    HP           0.08950     6
-   HA2    HP           0.08950     7
-     C    C            0.61630     8
-     O    O           -0.57220     9
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA   HA1
-    CA   HA2
-    CA     C
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NSER ]
- [ atoms ]
-     N    N3           0.18490     1
-    H1    H            0.18980     2
-    H2    H            0.18980     3
-    H3    H            0.18980     4
-    CA    CT           0.05670     5
-    HA    HP           0.07820     6
-    CB    CT           0.25960     7
-   HB1    H1           0.02730     8
-   HB2    H1           0.02730     9
-    OG    OH          -0.67140    10
-    HG    HO           0.42390    11
-     C    C            0.61630    12
-     O    O           -0.57220    13
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    OG
-    OG    HG
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NTHR ]
- [ atoms ]
-     N    N3           0.18120     1
-    H1    H            0.19340     2
-    H2    H            0.19340     3
-    H3    H            0.19340     4
-    CA    CT           0.00340     5
-    HA    HP           0.10870     6
-    CB    CT           0.45140     7
-    HB    H1          -0.03230     8
-   CG2    CT          -0.25540     9
-  HG21    HC           0.06270    10
-  HG22    HC           0.06270    11
-  HG23    HC           0.06270    12
-   OG1    OH          -0.67640    13
-   HG1    HO           0.40700    14
-     C    C            0.61630    15
-     O    O           -0.57220    16
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   OG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   OG1   HG1
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NLEU ]
- [ atoms ]
-     N    N3           0.10100     1
-    H1    H            0.21480     2
-    H2    H            0.21480     3
-    H3    H            0.21480     4
-    CA    CT           0.01040     5
-    HA    HP           0.10530     6
-    CB    CT          -0.02440     7
-   HB1    HC           0.02560     8
-   HB2    HC           0.02560     9
-    CG    CT           0.34210    10
-    HG    HC          -0.03800    11
-   CD1    CT          -0.41060    12
-  HD11    HC           0.09800    13
-  HD12    HC           0.09800    14
-  HD13    HC           0.09800    15
-   CD2    CT          -0.41040    16
-  HD21    HC           0.09800    17
-  HD22    HC           0.09800    18
-  HD23    HC           0.09800    19
-     C    C            0.61230    20
-     O    O           -0.57130    21
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG    HG
-    CG   CD1
-    CG   CD2
-   CD1  HD11
-   CD1  HD12
-   CD1  HD13
-   CD2  HD21
-   CD2  HD22
-   CD2  HD23
-     C     O
-     C    +N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_LEU_C_CA_CB_CG_mult3
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NILE ]
- [ atoms ]
-     N    N3           0.03110     1
-    H1    H            0.23290     2
-    H2    H            0.23290     3
-    H3    H            0.23290     4
-    CA    CT           0.02570     5
-    HA    HP           0.10310     6
-    CB    CT           0.18850     7
-    HB    HC           0.02130     8
-   CG2    CT          -0.37200     9
-  HG21    HC           0.09470    10
-  HG22    HC           0.09470    11
-  HG23    HC           0.09470    12
-   CG1    CT          -0.03870    13
-  HG11    HC           0.02010    14
-  HG12    HC           0.02010    15
-    CD    CT          -0.09080    16
-   HD1    HC           0.02260    17
-   HD2    HC           0.02260    18
-   HD3    HC           0.02260    19
-     C    C            0.61230    20
-     O    O           -0.57130    21
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG2
-    CB   CG1
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-   CG1  HG11
-   CG1  HG12
-   CG1    CD
-    CD   HD1
-    CD   HD2
-    CD   HD3
-     C     O
-     C    +N
- [ dihedrals ]
-     N    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult1
-     B    CA    CB   CG2        torsion_ILE_N_CA_CB_CG2_mult2
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NVAL ]
- [ atoms ]
-     N    N3           0.05770     1
-    H1    H            0.22720     2
-    H2    H            0.22720     3
-    H3    H            0.22720     4
-    CA    CT          -0.00540     5
-    HA    HP           0.10930     6
-    CB    CT           0.31960     7
-    HB    HC          -0.02210     8
-   CG1    CT          -0.31290     9
-  HG11    HC           0.07350    10
-  HG12    HC           0.07350    11
-  HG13    HC           0.07350    12
-   CG2    CT          -0.31290    13
-  HG21    HC           0.07350    14
-  HG22    HC           0.07350    15
-  HG23    HC           0.07350    16
-     C    C            0.61630    17
-     O    O           -0.57220    18
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB    HB
-    CB   CG1
-    CB   CG2
-   CG1  HG11
-   CG1  HG12
-   CG1  HG13
-   CG2  HG21
-   CG2  HG22
-   CG2  HG23
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NASN ]
- [ atoms ]
-     N    N3           0.18010     1
-    H1    H            0.19210     2
-    H2    H            0.19210     3
-    H3    H            0.19210     4
-    CA    CT           0.03680     5
-    HA    HP           0.12310     6
-    CB    CT          -0.02830     7
-   HB1    HC           0.05150     8
-   HB2    HC           0.05150     9
-    CG    C            0.58330    10
-   OD1    O           -0.57440    11
-   ND2    N           -0.86340    12
-  HD21    H            0.40970    13
-  HD22    H            0.40970    14
-     C    C            0.61630    15
-     O    O           -0.57220    16
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   ND2
-   ND2  HD21
-   ND2  HD22
-     C     O
-     C    +N
- [ dihedrals ]
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult1
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult2
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult3
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult4
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult5
-     C    CA    CB    CG        torsion_ASN_C_CA_CB_CG_mult6
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult1
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult2
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult3
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult4
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult5
-    CA    CB    CG   ND2        torsion_ASN_CA_CB_CG_ND2_mult6
- [ impropers ]
-    CA    +N     C     O
-    CB   ND2    CG   OD1
-    CG  HD21   ND2  HD22
-                        
-[ NGLN ]
- [ atoms ]
-     N    N3           0.14930     1
-    H1    H            0.19960     2
-    H2    H            0.19960     3
-    H3    H            0.19960     4
-    CA    CT           0.05360     5
-    HA    HP           0.10150     6
-    CB    CT           0.06510     7
-   HB1    HC           0.00500     8
-   HB2    HC           0.00500     9
-    CG    CT          -0.09030    10
-   HG1    HC           0.03310    11
-   HG2    HC           0.03310    12
-    CD    C            0.73540    13
-   OE1    O           -0.61330    14
-   NE2    N           -1.00310    15
-  HE21    H            0.44290    16
-  HE22    H            0.44290    17
-     C    C            0.61230    18
-     O    O           -0.57130    19
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   NE2
-   NE2  HE21
-   NE2  HE22
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   NE2    CD   OE1
-    CD  HE21   NE2  HE22
-                        
-[ NARG ]
- [ atoms ]
-     N    N3           0.13050     1
-    H1    H            0.20830     2
-    H2    H            0.20830     3
-    H3    H            0.20830     4
-    CA    CT          -0.02230     5
-    HA    HP           0.12420     6
-    CB    CT           0.01180     7
-   HB1    HC           0.02260     8
-   HB2    HC           0.02260     9
-    CG    CT           0.02360    10
-   HG1    HC           0.03090    11
-   HG2    HC           0.03090    12
-    CD    CT           0.09350    13
-   HD1    H1           0.05270    14
-   HD2    H1           0.05270    15
-    NE    N2          -0.56500    16
-    HE    H            0.35920    17
-    CZ    CA           0.82810    18
-   NH1    N2          -0.86930    19
-  HH11    H            0.44940    20
-  HH12    H            0.44940    21
-   NH2    N2          -0.86930    22
-  HH21    H            0.44940    23
-  HH22    H            0.44940    24
-     C    C            0.72140    25
-     O    O           -0.60130    26
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    NE
-    NE    HE
-    NE    CZ
-    CZ   NH1
-    CZ   NH2
-   NH1  HH11
-   NH1  HH12
-   NH2  HH21
-   NH2  HH22
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    NE   NH1    CZ   NH2
-    CD    CZ    NE    HE
-    CZ  HH11   NH1  HH12
-    CZ  HH21   NH2  HH22
-                        
-[ NHID ]
- [ atoms ]
-     N    N3           0.15420     1
-    H1    H            0.19630     2
-    H2    H            0.19630     3
-    H3    H            0.19630     4
-    CA    CT           0.09640     5
-    HA    HP           0.09580     6
-    CB    CT           0.02590     7
-   HB1    HC           0.02090     8
-   HB2    HC           0.02090     9
-    CG    CC          -0.03990    10
-   ND1    NA          -0.38190    11
-   HD1    H            0.36320    12
-   CE1    CR           0.21270    13
-   HE1    H5           0.13850    14
-   NE2    NB          -0.57110    15
-   CD2    CV           0.10460    16
-   HD2    H4           0.12990    17
-     C    C            0.61230    18
-     O    O           -0.57130    19
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   CE1   ND1   HD1
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ NHIE ]
- [ atoms ]
-     N    N3           0.14720     1
-    H1    H            0.20160     2
-    H2    H            0.20160     3
-    H3    H            0.20160     4
-    CA    CT           0.02360     5
-    HA    HP           0.13800     6
-    CB    CT           0.04890     7
-   HB1    HC           0.02230     8
-   HB2    HC           0.02230     9
-    CG    CC           0.17400    10
-   ND1    NB          -0.55790    11
-   CE1    CR           0.18040    12
-   HE1    H5           0.13970    13
-   NE2    NA          -0.27810    14
-   HE2    H            0.33240    15
-   CD2    CW          -0.23490    16
-   HD2    H4           0.19630    17
-     C    C            0.61230    18
-     O    O           -0.57130    19
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-   CE1   CD2   NE2   HE2
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ NHIP ]
- [ atoms ]
-     N    N3           0.25600     1
-    H1    H            0.17040     2
-    H2    H            0.17040     3
-    H3    H            0.17040     4
-    CA    CT           0.05810     5
-    HA    HP           0.10470     6
-    CB    CT           0.04840     7
-   HB1    HC           0.05310     8
-   HB2    HC           0.05310     9
-    CG    CC          -0.02360    10
-   ND1    NA          -0.15100    11
-   HD1    H            0.38210    12
-   CE1    CR          -0.00110    13
-   HE1    H5           0.26450    14
-   NE2    NA          -0.17390    15
-   HE2    H            0.39210    16
-   CD2    CW          -0.14330    17
-   HD2    H4           0.24950    18
-     C    C            0.72140    19
-     O    O           -0.60130    20
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   ND1
-    CG   CD2
-   ND1   HD1
-   ND1   CE1
-   CE1   HE1
-   CE1   NE2
-   NE2   HE2
-   NE2   CD2
-   CD2   HD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   CE1   ND1   HD1
-   CE1   CD2   NE2   HE2
-    CG   NE2   CD2   HD2
-   ND1   NE2   CE1   HE1
-   ND1   CD2    CG    CB
-                        
-[ NTRP ]
- [ atoms ]
-     N    N3           0.19130     1
-    H1    H            0.18880     2
-    H2    H            0.18880     3
-    H3    H            0.18880     4
-    CA    CT           0.04210     5
-    HA    HP           0.11620     6
-    CB    CT           0.05430     7
-   HB1    HC           0.02220     8
-   HB2    HC           0.02220     9
-    CG    C*          -0.16540    10
-   CD1    CW          -0.17880    11
-   HD1    H4           0.21950    12
-   NE1    NA          -0.34440    13
-   HE1    H            0.34120    14
-   CE2    CN           0.15750    15
-   CZ2    CA          -0.27100    16
-   HZ2    HA           0.15890    17
-   CH2    CA          -0.10800    18
-   HH2    HA           0.14110    19
-   CZ3    CA          -0.20340    20
-   HZ3    HA           0.14580    21
-   CE3    CA          -0.22650    22
-   HE3    HA           0.16460    23
-   CD2    CB           0.11320    24
-     C    C            0.61230    25
-     O    O           -0.57130    26
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   NE1
-   NE1   HE1
-   NE1   CE2
-   CE2   CZ2
-   CE2   CD2
-   CZ2   HZ2
-   CZ2   CH2
-   CH2   HH2
-   CH2   CZ3
-   CZ3   HZ3
-   CZ3   CE3
-   CE3   HE3
-   CE3   CD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-   CD1   CE2   NE1   HE1
-   CE2   CH2   CZ2   HZ2
-   CZ2   CZ3   CH2   HH2
-   CH2   CE3   CZ3   HZ3
-   CZ3   CD2   CE3   HE3
-    CG   NE1   CD1   HD1
-   CD1    CG    CB   CD2
-                        
-[ NPHE ]
- [ atoms ]
-     N    N3           0.17370     1
-    H1    H            0.19210     2
-    H2    H            0.19210     3
-    H3    H            0.19210     4
-    CA    CT           0.07330     5
-    HA    HP           0.10410     6
-    CB    CT           0.03300     7
-   HB1    HC           0.01040     8
-   HB2    HC           0.01040     9
-    CG    CA           0.00310    10
-   CD1    CA          -0.13920    11
-   HD1    HA           0.13740    12
-   CE1    CA          -0.16020    13
-   HE1    HA           0.14330    14
-    CZ    CA          -0.12080    15
-    HZ    HA           0.13290    16
-   CE2    CA          -0.16030    17
-   HE2    HA           0.14330    18
-   CD2    CA          -0.13910    19
-   HD2    HA           0.13740    20
-     C    C            0.61230    21
-     O    O           -0.57130    22
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    HZ
-    CZ   CE2
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   CE2   CD2   HD2
-    CZ   CD2   CE2   HE2
-   CE1   CE2    CZ    HZ
-   CD1    CZ   CE1   HE1
-    CG   CE1   CD1   HD1
-   CD1   CD2    CG    CB
-                        
-[ NTYR ]
- [ atoms ]
-     N    N3           0.19400     1
-    H1    H            0.18730     2
-    H2    H            0.18730     3
-    H3    H            0.18730     4
-    CA    CT           0.05700     5
-    HA    HP           0.09830     6
-    CB    CT           0.06590     7
-   HB1    HC           0.01020     8
-   HB2    HC           0.01020     9
-    CG    CA          -0.02050    10
-   CD1    CA          -0.20020    11
-   HD1    HA           0.17200    12
-   CE1    CA          -0.22390    13
-   HE1    HA           0.16500    14
-    CZ    C            0.31390    15
-    OH    OH          -0.55780    16
-    HH    HO           0.40010    17
-   CE2    CA          -0.22390    18
-   HE2    HA           0.16500    19
-   CD2    CA          -0.20020    20
-   HD2    HA           0.17200    21
-     C    C            0.61230    22
-     O    O           -0.57130    23
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   CD1
-    CG   CD2
-   CD1   HD1
-   CD1   CE1
-   CE1   HE1
-   CE1    CZ
-    CZ    OH
-    CZ   CE2
-    OH    HH
-   CE2   HE2
-   CE2   CD2
-   CD2   HD2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   CE2   CD2   HD2
-    CZ   CD2   CE2   HE2
-   CD1    CZ   CE1   HE1
-    CG   CE1   CD1   HD1
-   CD1   CD2    CG    CB
-   CE1   CE2    CZ    OH
-                        
-                        
-[ NGLU ]
- [ atoms ]
-     N    N3           0.00170     1
-    H1    H            0.23910     2
-    H2    H            0.23910     3
-    H3    H            0.23910     4
-    CA    CT           0.05880     5
-    HA    HP           0.12020     6
-    CB    CT           0.09090     7
-   HB1    HC          -0.02320     8
-   HB2    HC          -0.02320     9
-    CG    CT          -0.02360    10
-   HG1    HC          -0.03150    11
-   HG2    HC          -0.03150    12
-    CD    C            0.80870    13
-   OE1    O2          -0.81890    14
-   OE2    O2          -0.81890    15
-     C    C            0.56210    16
-     O    O           -0.58890    17
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   OE1
-    CD   OE2
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-    CG   OE1    CD   OE2
-                        
-[ NASP ]
- [ atoms ]
-     N    N3           0.07820     1
-    H1    H            0.22000     2
-    H2    H            0.22000     3
-    H3    H            0.22000     4
-    CA    CT           0.02920     5
-    HA    HP           0.11410     6
-    CB    CT          -0.02350     7
-   HB1    HC          -0.01690     8
-   HB2    HC          -0.01690     9
-    CG    C            0.81940    10
-   OD1    O2          -0.80840    11
-   OD2    O2          -0.80840    12
-     C    C            0.56210    13
-     O    O           -0.58890    14
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   OD1
-    CG   OD2
-     C     O
-     C    +N
- [ dihedrals ]
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult1
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult2
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult3
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult4
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult5
-     N    CA    CB    CG        torsion_ASP_N_CA_CB_CG_mult6
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD1        torsion_ASP_CA_CB_CG_OD_mult6
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult1
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult2
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult3
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult4
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult5
-    CA    CB    CG   OD2        torsion_ASP_CA_CB_CG_OD_mult6
- [ impropers ]
-    CA    +N     C     O
-    CB   OD1    CG   OD2
-                        
-[ NLYS ]
- [ atoms ]
-     N    N3           0.09660     1
-    H1    H            0.21650     2
-    H2    H            0.21650     3
-    H3    H            0.21650     4
-    CA    CT          -0.00150     5
-    HA    HP           0.11800     6
-    CB    CT           0.02120     7
-   HB1    HC           0.02830     8
-   HB2    HC           0.02830     9
-    CG    CT          -0.00480    10
-   HG1    HC           0.01210    11
-   HG2    HC           0.01210    12
-    CD    CT          -0.06080    13
-   HD1    HC           0.06330    14
-   HD2    HC           0.06330    15
-    CE    CT          -0.01810    16
-   HE1    HP           0.11710    17
-   HE2    HP           0.11710    18
-    NZ    N3          -0.37640    19
-   HZ1    H            0.33820    20
-   HZ2    H            0.33820    21
-   HZ3    H            0.33820    22
-     C    C            0.72140    23
-     O    O           -0.60130    24
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    CD
-    CD   HD1
-    CD   HD2
-    CD    CE
-    CE   HE1
-    CE   HE2
-    CE    NZ
-    NZ   HZ1
-    NZ   HZ2
-    NZ   HZ3
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NPRO ]
- [ atoms ]
-     N    N3          -0.20200     1
-    H1    H            0.31200     2
-    H2    H            0.31200     3
-    CD    CT          -0.01200     4
-   HD1    HP           0.10000     5
-   HD2    HP           0.10000     6
-    CG    CT          -0.12100     7
-   HG1    HC           0.10000     8
-   HG2    HC           0.10000     9
-    CB    CT          -0.11500    10
-   HB1    HC           0.10000    11
-   HB2    HC           0.10000    12
-    CA    CT           0.10000    13
-    HA    HP           0.10000    14
-     C    C            0.52600    15
-     O    O           -0.50000    16
- [ bonds ]
-     N    H1
-     N    H2
-     N    CD
-     N    CA
-    CD   HD1
-    CD   HD2
-    CD    CG
-    CG   HG1
-    CG   HG2
-    CG    CB
-    CB   HB1
-    CB   HB2
-    CB    CA
-    CA    HA
-    CA     C
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NCYS ]
- [ atoms ]
-     N    N3           0.13250     1
-    H1    H            0.20230     2
-    H2    H            0.20230     3
-    H3    H            0.20230     4
-    CA    CT           0.09270     5
-    HA    HP           0.14110     6
-    CB    CT          -0.11950     7
-   HB1    H1           0.11880     8
-   HB2    H1           0.11880     9
-    SG    SH          -0.32980    10
-    HG    HS           0.19750    11
-     C    C            0.61230    12
-     O    O           -0.57130    13
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    SG
-    SG    HG
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NCYX ]
- [ atoms ]
-     N    N3           0.20690     1
-    H1    H            0.18150     2
-    H2    H            0.18150     3
-    H3    H            0.18150     4
-    CA    CT           0.10550     5
-    HA    HP           0.09220     6
-    CB    CT          -0.02770     7
-   HB1    H1           0.06800     8
-   HB2    H1           0.06800     9
-    SG    S           -0.09840    10
-     C    C            0.61230    11
-     O    O           -0.57130    12
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB2
-    CB   HB1
-    CB    SG
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-                        
-[ NMET ]
- [ atoms ]
-     N    N3           0.15920     1
-    H1    H            0.19840     2
-    H2    H            0.19840     3
-    H3    H            0.19840     4
-    CA    CT           0.02210     5
-    HA    HP           0.11160     6
-    CB    CT           0.08650     7
-   HB1    HC           0.01250     8
-   HB2    HC           0.01250     9
-    CG    CT           0.03340    10
-   HG1    H1           0.02920    11
-   HG2    H1           0.02920    12
-    SD    S           -0.27740    13
-    CE    CT          -0.03410    14
-   HE1    H1           0.05970    15
-   HE2    H1           0.05970    16
-   HE3    H1           0.05970    17
-     C    C            0.61230    18
-     O    O           -0.57130    19
- [ bonds ]
-     N    H1
-     N    H2
-     N    H3
-     N    CA
-    CA    HA
-    CA    CB
-    CA     C
-    CB   HB1
-    CB   HB2
-    CB    CG
-    CG   HG1
-    CG   HG2
-    CG    SD
-    SD    CE
-    CE   HE1
-    CE   HE2
-    CE   HE3
-     C     O
-     C    +N
- [ impropers ]
-    CA    +N     C     O
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.vsd b/share/top/amber99sb-ildn-bsc0.ff/aminoacids.vsd
deleted file mode 100644 (file)
index fa52c67..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/aminoacids.vsd
+++ /dev/null
@@ -1,225 +0,0 @@
-
-[ CH3 ]
-; CT         sp3 aliphatic C 
- ;bound to sp2/sp3 carbons
-   CT           C               MCH3
-   CT           CA              MCH3
-   CT           CB              MCH3
-   CT           CC              MCH3
-   CT           CK              MCH3
-   CT           CM              MCH3
-   CT           CN              MCH3
-   CT           CQ              MCH3
-   CT           CR              MCH3
-   CT           CT              MCH3
-   CT           CV              MCH3
-   CT           CW              MCH3
-   CT           C*              MCH3
-   CT           N               MCH3
-   CT           S               MCH3
-
-[ NH3 ]
-; N3         sp3 N for charged amino groups
-   N3           C               MNH3
-   N3           CA              MNH3
-   N3           CB              MNH3
-   N3           CC              MNH3
-   N3           CK              MNH3
-   N3           CM              MNH3
-   N3           CN              MNH3
-   N3           CQ              MNH3
-   N3           CR              MNH3
-   N3           CT              MNH3
-   N3           CV              MNH3
-   N3           CW              MNH3
-   N3           C*              MNH3
-
-[ NH2 ]
-; N          sp2 nitrogen in amide groups
-   N            planar
-   N2           planar
-
-
-; Data for generating dummy aromatic rings.
-; Actually we dont need all these bonds and angles,
-; but by specifying them here it is easier to improve
-; the dummy generation code later.
-[ PHE ]
-  CG   CD1             0.140
-  CG   CD2             0.140
-  CD1   CE1            0.140
-  CD2  CE2             0.140
-  CE1   CZ             0.140
-  CE2  CZ              0.140
-  CD1  HD1             0.108
-  CD2  HD2             0.108
-  CE1  HE1             0.108
-  CE2   HE2            0.108
-  CZ    HZ             0.108
-  CG    CD1   CE1      120.0
-  CD1   CE1   CZ       120.0
-  CE1   CZ    CE2      120.0
-  CZ    CE2   CD2      120.0
-  CE2   CD2   CG       120.0
-  CD2   CG    CD1      120.0
-  CG    CD1   HD1      120.0
-  CG    CD2   HD2      120.0
-  HD1   CD1   CE1      120.0
-  CD1   CE1   HE1      120.0
-  HE1   CE1   CZ       120.0
-  CE1   CZ    HZ       120.0
-  HZ    CZ    CE2      120.0
-  CZ    CE2   HE2      120.0
-  HE2   CE2   CD2      120.0
-  HD2   CD2   CG       120.0
-
-
-[ TYR ]
-  CG   CD1             0.140
-  CG   CD2             0.140
-  CD1   CE1            0.140
-  CD2  CE2             0.140
-  CE1   CZ             0.140
-  CE2  CZ              0.140
-  CD1  HD1             0.108
-  CD2  HD2             0.108
-  CE1  HE1             0.108   
-  CE2   HE2            0.108   
-  CZ    OH             0.1364  
-  OH    HH             0.0945
-  CG    CD1   CE1      120.0
-  CD1   CE1   CZ       120.0
-  CE1   CZ    CE2      120.0
-  CZ    CE2   CD2      120.0
-  CE2   CD2   CG       120.0
-  CD2   CG    CD1      120.0
-  CG    CD1   HD1      120.0
-  CG    CD2   HD2      120.0
-  HD1   CD1   CE1      120.0
-  CD1   CE1   HE1      120.0
-  HE1   CE1   CZ       120.0
-  CE1   CZ    OH       120.0
-  CZ    OH    HH       113.0
-  OH    CZ    CE2      120.0
-  CZ    CE2   HE2      120.0
-  HE2   CE2   CD2      120.0
-  HD2   CD2   CG       120.0
-
-
-[ TRP ] ; angles from MD sim, corrected to be perfectly planar
-  CB    CG             0.1495
-  CG   CD1             0.1352
-  CD1   NE1            0.1381
-  NE1  CE2             0.138
-  CE2   CD2            0.1419
-  CD2   CG             0.1459
-  CE2   CZ2            0.140
-  CZ2   CH2            0.140
-  CH2   CZ3            0.140
-  CZ3   CE3            0.140
-  CE3   CD2            0.1404
-  CD1   HD1            0.108
-  NE1   HE1            0.101
-  CE3   HE3            0.108
-  CZ2   HZ2            0.108
-  CZ3   HZ3            0.108
-  CH2   HH2            0.108
-  CB    CG    CD1       125.6
-  CB    CG    CD2       128.7
-  CG    CD1   NE1      109.7
-  CD1   NE1   CE2      111.7
-  NE1   CE2   CD2      104.3
-  CE2   CD2   CG       108.5
-  CD2   CG    CD1      105.7
-  NE1   CE2   CZ2      135.7
-  CE2   CZ2   CH2      120.0
-  CZ2   CH2   CZ3      120.0
-  CH2   CZ3   CE3      120.0
-  CZ3   CE3   CD2      120.0
-  CE2   CD2   CE3      120.0
-  CD2   CE2   CZ2      120.0
-  CE3   CD2   CG       131.5
-  CG    CD1   HD1      124.6
-  HD1   CD1   NE1      125.7
-  CD1   NE1   HE1      122.7
-  HE1   NE1   CE2      125.6
-  CZ3   CE3   HE3      120.0
-  HE3   CE3   CD2      120.0
-  CE2   CZ2   HZ2      120.0
-  HZ2   CZ2   CH2      120.0
-  CH2   CZ3   HZ3      120.0
-  HZ3   CZ3   CE3      120.0
-  CZ2   CH2   HH2      120.0
-  HH2   CH2   CZ3      120.0   
-
-
-[ HID ] ; angles from MD sim, corrected to be perfectly planar
-  CG    ND1            0.1381
-  ND1   CE1            0.1343
-  CE1   NE2            0.1335
-  NE2  CD2             0.1394
-  CD2   CG             0.137
-  ND1   HD1            0.101
-  CE1   HE1            0.108
-  CD2   HD2            0.108
-  CG    ND1   CE1      107.4
-  ND1   CE1   NE2      113.1
-  CE1   NE2   CD2      104.5
-  NE2   CD2   CG       109.3
-  CD2   CG    ND1      105.7
-  CG    ND1   HD1      127.7
-  HD1   ND1   CE1      124.9
-  ND1   CE1   HE1      122.9
-  HE1   CE1   NE2      124.0
-  CG    CD2   HD2      129.0
-  HD2   CD2   NE2      121.7
-
-
-[ HIE ] ; angles from MD sim, corrected to be perfectly planar
-  CG    ND1            0.1394
-  ND1   CE1            0.1335
-  CE1   NE2            0.1343
-  NE2  CD2             0.1381
-  CD2   CG             0.137
-  CD2   HD2            0.108
-  CE1   HE1            0.108
-  NE2   HE2            0.101
-  CG    ND1   CE1      104.9
-  ND1   CE1   NE2      112.9
-  CE1   NE2   CD2      107.3
-  NE2   CD2   CG       106.4
-  CD2   CG    ND1      108.5
-  NE2   CD2   HD2      122.4
-  HD2   CD2   CG       131.2
-  ND1   CE1   HE1      123.8
-  HE1   CE1   NE2      123.3
-  CE1   NE2   HE2      125.9
-  HE2   NE2   CD2      126.8
-  
-
-[ HIP ] ; angles from MD sim, corrected to be perfectly planar
-  CG    ND1            0.1381
-  ND1   CE1            0.1343
-  CE1   NE2            0.1343
-  NE2  CD2             0.1381
-  CD2   CG             0.137
-  ND1   HD1            0.101
-  CE1   HE1            0.108
-  CD2   HD2            0.108
-  NE2   HE2            0.101
-  CG    ND1   CE1      107.4
-  ND1   CE1   NE2      111.4
-  CE1   NE2   CD2      107.2
-  NE2   CD2   CG       107.4
-  CD2   CG    ND1      106.6
-  CG    ND1   HD1      127.4
-  HD1   ND1   CE1      125.2
-  ND1   CE1   HE1      124.3
-  HE1   CE1   NE2      124.3
-  CE1   NE2   HE2      126.4
-  HE2   NE2   CD2      126.4
-  NE2   CD2   HD2      120.8
-  HD2   CD2   CG       131.8
-
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/atomtypes.atp b/share/top/amber99sb-ildn-bsc0.ff/atomtypes.atp
deleted file mode 100644 (file)
index 91dcef9..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/atomtypes.atp
+++ /dev/null
@@ -1,68 +0,0 @@
-Br                79.90000     ; bromine
-C                 12.01000     ; sp2 C carbonyl group 
-CA                12.01000     ; sp2 C pure aromatic (benzene)
-CB                12.01000     ; sp2 aromatic C, 5&6 membered ring junction
-CC                12.01000     ; sp2 aromatic C, 5 memb. ring HIS
-CK                12.01000     ; sp2 C 5 memb.ring in purines
-CM                12.01000     ; sp2 C  pyrimidines in pos. 5 & 6
-CN                12.01000     ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
-CQ                12.01000     ; sp2 C in 5 mem.ring of purines between 2 N
-CR                12.01000     ; sp2 arom as CQ but in HIS
-CT                12.01000     ; sp3 aliphatic C
-CV                12.01000     ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
-CW                12.01000     ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
-C*                12.01000     ; sp2 arom. 5 memb.ring w/1 subst. (TRP)
-C0                40.08000     ; calcium
-F                 19.00000     ; fluorine
-H                  1.00800     ; H bonded to nitrogen atoms
-HC                 1.00800     ; H aliph. bond. to C without electrwd.group
-H1                 1.00800     ; H aliph. bond. to C with 1 electrwd. group
-H2                 1.00800     ; H aliph. bond. to C with 2 electrwd.groups
-H3                 1.00800     ; H aliph. bond. to C with 3 eletrwd.groups
-HA                 1.00800     ; H arom. bond. to C without elctrwd. groups
-H4                 1.00800     ; H arom. bond. to C with 1 electrwd. group
-H5                 1.00800     ; H arom. bond. to C with 2 electrwd. groups
-HO                 1.00800     ; hydroxyl group
-HS                 1.00800     ; hydrogen bonded to sulphur (pol?)
-HW                 1.00800     ; H in TIP3P water
-HP                 1.00800     ; H bonded to C next to positively charged gr
-I                126.90000     ; iodine  (Applequist)
-Cl                35.45000     ; chlorine  (Applequist)
-Na                22.99000     ; Na+, ions pol:J.PhysC,11,1541,(1978)
-IB               131.00000     ; 'big ion w/ waters' for vacuum (Na+, 6H2O)
-MG                24.30500     ; magnesium
-N                 14.01000     ; sp2 nitrogen in amide groups
-NA                14.01000     ; sp2 N in 5 memb.ring w/H atom (HIS)
-NB                14.01000     ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
-NC                14.01000     ; sp2 N in 6 memb.ring w/LP (ADE,GUA)
-N2                14.01000     ; sp2 N in amino groups
-N3                14.01000     ; sp3 N for charged amino groups (Lys, etc)
-N*                14.01000     ; sp2 N 
-O                 16.00000     ; carbonyl group oxygen
-OW                16.00000     ; oxygen in TIP3P water
-OH                16.00000     ; oxygen in hydroxyl group
-OS                16.00000     ; ether and ester oxygen
-O2                16.00000     ; carboxyl and phosphate group oxygen
-P                 30.97000     ; phosphate,pol:JACS,112,8543,90,K.J.Miller
-S                 32.06000     ; S in disulfide linkage,pol:JPC,102,2399,98
-SH                32.06000     ; S in cystine
-CU                63.55000     ; copper
-FE                55.00000     ; iron
-K                 39.10000     ; potassium
-Rb                85.47000     ; rubidium
-Cs               132.90000     ; cesium
-OW_spc            15.99940      ; SPC Water OW
-HW_spc             1.00800      ; SPC Water HW
-Li                 6.94000      ; lithium, ions pol:J.PhysC,11,1541,(1978)
-Zn                65.40000      ; Zn2+
-HW_tip4pew         1.00800      ; tip4pEW HW
-OW_tip4pew        16.00000      ; tip4pEW OW
-HW_tip4p           1.00800      ; tip4p HW
-OW_tip4p          16.00000      ; tip4p OW
-HW_tip5p           1.00800      ; tip5p HW
-OW_tip5p          16.00000      ; tip5p OW
-MW                 0.00000      ; Virtual site for tip4p/5p water point charge
-MCH3               0.00000      ; Dummy mass in rigid tetrahedral CH3 group
-MNH3               0.00000      ; Dummy mass in rigid tetrahedral NH3 group
-;
-CI                12.01000     ; New DNA/RNA C5' atomtype
\ No newline at end of file

diff --git a/share/top/amber99sb-ildn-bsc0.ff/dna.arn b/share/top/amber99sb-ildn-bsc0.ff/dna.arn
deleted file mode 100644 (file)
index ef4db90..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/dna.arn
+++ /dev/null
@@ -1,8 +0,0 @@
-DNA  OP1  O1P
-DNA  OP2  O2P
-DNA  H2'  H2'1
-DNA  H2'' H2'2
-DNA  H5'  H5'1
-DNA  H5'' H5'2
-DNA  HO5' H5T
-DNA  HO3' H3T

diff --git a/share/top/amber99sb-ildn-bsc0.ff/dna.hdb b/share/top/amber99sb-ildn-bsc0.ff/dna.hdb
deleted file mode 100644 (file)
index 09f83f7..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/dna.hdb
+++ /dev/null
@@ -1,160 +0,0 @@
-DA5    9
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DA     8
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DA3    9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DAN    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DT5    9
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DT     8
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DT3    9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DTN    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DG5    9
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DG     8
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DG3    9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DGN    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DC5    9
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DC     8
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DC3    9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-DCN    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     

diff --git a/share/top/amber99sb-ildn-bsc0.ff/dna.r2b b/share/top/amber99sb-ildn-bsc0.ff/dna.r2b
deleted file mode 100644 (file)
index 285ec3b..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/dna.r2b
+++ /dev/null
@@ -1,6 +0,0 @@
-; rtp residue to rtp building block table
-;GMX   Force-field
-DA    DA       DA5     DA3     DAN
-DG    DG       DG5     DG3     DGN
-DC    DC       DC5     DC3     DCN
-DT    DT       DT5     DT3     DTN

diff --git a/share/top/amber99sb-ildn-bsc0.ff/dna.rtp b/share/top/amber99sb-ildn-bsc0.ff/dna.rtp
deleted file mode 100644 (file)
index 1170a78..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/dna.rtp
+++ /dev/null
@@ -1,1223 +0,0 @@
-[ bondedtypes ]
-; Col 1: Type of bond
-; Col 2: Type of angles
-; Col 3: Type of proper dihedrals
-; Col 4: Type of improper dihedrals
-; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
-; Col 6: Number of excluded neighbors for nonbonded interactions
-; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
-; Col 8: Remove impropers over the same bond as a proper if it is 1
-; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
-     1       1          9          4        1         3      1     0
-
-                 
-; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's 
-
-[ DA5 ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.04310     9
-   H1'    H2            0.18380    10
-    N9    N*           -0.02680    11
-    C8    CK            0.16070    12
-    H8    H5            0.18770    13
-    N7    NB           -0.61750    14
-    C5    CB            0.07250    15
-    C6    CA            0.68970    16
-    N6    N2           -0.91230    17
-   H61    H             0.41670    18
-   H62    H             0.41670    19
-    N1    NC           -0.76240    20
-    C2    CQ            0.57160    21
-    H2    H5            0.05980    22
-    N3    NC           -0.74170    23
-    C4    CB            0.38000    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OS           -0.52320    30
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
- [ impropers ]
-    C4    C8    N9   C1'
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1
-                        
-[ DA ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.04310    11
-   H1'    H2            0.18380    12
-    N9    N*           -0.02680    13
-    C8    CK            0.16070    14
-    H8    H5            0.18770    15
-    N7    NB           -0.61750    16
-    C5    CB            0.07250    17
-    C6    CA            0.68970    18
-    N6    N2           -0.91230    19
-   H61    H             0.41670    20
-   H62    H             0.41670    21
-    N1    NC           -0.76240    22
-    C2    CQ            0.57160    23
-    H2    H5            0.05980    24
-    N3    NC           -0.74170    25
-    C4    CB            0.38000    26
-   C3'    CT            0.07130    27
-   H3'    H1            0.09850    28
-   C2'    CT           -0.08540    29
-  H2'1    HC            0.07180    30
-  H2'2    HC            0.07180    31
-   O3'    OS           -0.52320    32
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'  
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1  
-                        
-[ DA3 ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.04310    11
-   H1'    H2            0.18380    12
-    N9    N*           -0.02680    13
-    C8    CK            0.16070    14
-    H8    H5            0.18770    15
-    N7    NB           -0.61750    16
-    C5    CB            0.07250    17
-    C6    CA            0.68970    18
-    N6    N2           -0.91230    19
-   H61    H             0.41670    20
-   H62    H             0.41670    21
-    N1    NC           -0.76240    22
-    C2    CQ            0.57160    23
-    H2    H5            0.05980    24
-    N3    NC           -0.74170    25
-    C4    CB            0.38000    26
-   C3'    CT            0.07130    27
-   H3'    H1            0.09850    28
-   C2'    CT           -0.08540    29
-  H2'1    HC            0.07180    30
-  H2'2    HC            0.07180    31
-   O3'    OH           -0.65490    32
-   H3T    HO            0.43960    33
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'  
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1  
-
-[ DAN ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.04310     9
-   H1'    H2            0.18380    10
-    N9    N*           -0.02680    11
-    C8    CK            0.16070    12
-    H8    H5            0.18770    13
-    N7    NB           -0.61750    14
-    C5    CB            0.07250    15
-    C6    CA            0.68970    16
-    N6    N2           -0.91230    17
-   H61    H             0.41670    18
-   H62    H             0.41670    19
-    N1    NC           -0.76240    20
-    C2    CQ            0.57160    21
-    H2    H5            0.05980    22
-    N3    NC           -0.74170    23
-    C4    CB            0.38000    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OH           -0.65490    30
-   H3T    HO            0.43960    31
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
- [ impropers ]
-    C4    C8    N9   C1'
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1
-
-
-                 
-[ DT5 ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.06800     9
-   H1'    H2            0.18040    10
-    N1    N*           -0.02390    11
-    C6    CM           -0.22090    12
-    H6    H4            0.26070    13
-    C5    CM            0.00250    14
-    C7    CT           -0.22690    15
-   H71    HC            0.07700    16
-   H72    HC            0.07700    17
-   H73    HC            0.07700    18
-    C4    C             0.51940    19
-    O4    O            -0.55630    20
-    N3    NA           -0.43400    21
-    H3    H             0.34200    22
-    C2    C             0.56770    23
-    O2    O            -0.58810    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OS           -0.52320    30
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    C7
-    C5    C4
-    C7   H71
-    C7   H72
-    C7   H73
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
- [ impropers ]
-    C2    C6    N1   C1'
-    C4    C6    C5    C7
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ DT ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.06800    11
-   H1'    H2            0.18040    12
-    N1    N*           -0.02390    13
-    C6    CM           -0.22090    14
-    H6    H4            0.26070    15
-    C5    CM            0.00250    16
-    C7    CT           -0.22690    17
-   H71    HC            0.07700    18
-   H72    HC            0.07700    19
-   H73    HC            0.07700    20
-    C4    C             0.51940    21
-    O4    O            -0.55630    22
-    N3    NA           -0.43400    23
-    H3    H             0.34200    24
-    C2    C             0.56770    25
-    O2    O            -0.58810    26
-   C3'    CT            0.07130    27
-   H3'    H1            0.09850    28
-   C2'    CT           -0.08540    29
-  H2'1    HC            0.07180    30
-  H2'2    HC            0.07180    31
-   O3'    OS           -0.52320    32
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    C7
-    C5    C4
-    C7   H71
-    C7   H72
-    C7   H73
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    C4    C6    C5    C7
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ DT3 ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.06800    11
-   H1'    H2            0.18040    12
-    N1    N*           -0.02390    13
-    C6    CM           -0.22090    14
-    H6    H4            0.26070    15
-    C5    CM            0.00250    16
-    C7    CT           -0.22690    17
-   H71    HC            0.07700    18
-   H72    HC            0.07700    19
-   H73    HC            0.07700    20
-    C4    C             0.51940    21
-    O4    O            -0.55630    22
-    N3    NA           -0.43400    23
-    H3    H             0.34200    24
-    C2    C             0.56770    25
-    O2    O            -0.58810    26
-   C3'    CT            0.07130    27
-   H3'    H1            0.09850    28
-   C2'    CT           -0.08540    29
-  H2'1    HC            0.07180    30
-  H2'2    HC            0.07180    31
-   O3'    OH           -0.65490    32
-   H3T    HO            0.43960    33
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    C7
-    C5    C4
-    C7   H71
-    C7   H72
-    C7   H73
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    C4    C6    C5    C7
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ DTN ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.06800     9
-   H1'    H2            0.18040    10
-    N1    N*           -0.02390    11
-    C6    CM           -0.22090    12
-    H6    H4            0.26070    13
-    C5    CM            0.00250    14
-    C7    CT           -0.22690    15
-   H71    HC            0.07700    16
-   H72    HC            0.07700    17
-   H73    HC            0.07700    18
-    C4    C             0.51940    19
-    O4    O            -0.55630    20
-    N3    NA           -0.43400    21
-    H3    H             0.34200    22
-    C2    C             0.56770    23
-    O2    O            -0.58810    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OH           -0.65490    30
-   H3T    HO            0.43960    31
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    C7
-    C5    C4
-    C7   H71
-    C7   H72
-    C7   H73
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
- [ impropers ]
-    C2    C6    N1   C1'
-    C4    C6    C5    C7
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-
-                     
-
-[ DG5 ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.03580     9
-   H1'    H2            0.17460    10
-    N9    N*            0.05770    11
-    C8    CK            0.07360    12
-    H8    H5            0.19970    13
-    N7    NB           -0.57250    14
-    C5    CB            0.19910    15
-    C6    C             0.49180    16
-    O6    O            -0.56990    17
-    N1    NA           -0.50530    18
-    H1    H             0.35200    19
-    C2    CA            0.74320    20
-    N2    N2           -0.92300    21
-   H21    H             0.42350    22
-   H22    H             0.42350    23
-    N3    NC           -0.66360    24
-    C4    CB            0.18140    25
-   C3'    CT            0.07130    26
-   H3'    H1            0.09850    27
-   C2'    CT           -0.08540    28
-  H2'1    HC            0.07180    29
-  H2'2    HC            0.07180    30
-   O3'    OS           -0.52320    31
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ DG ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.03580    11
-   H1'    H2            0.17460    12
-    N9    N*            0.05770    13
-    C8    CK            0.07360    14
-    H8    H5            0.19970    15
-    N7    NB           -0.57250    16
-    C5    CB            0.19910    17
-    C6    C             0.49180    18
-    O6    O            -0.56990    19
-    N1    NA           -0.50530    20
-    H1    H             0.35200    21
-    C2    CA            0.74320    22
-    N2    N2           -0.92300    23
-   H21    H             0.42350    24
-   H22    H             0.42350    25
-    N3    NC           -0.66360    26
-    C4    CB            0.18140    27
-   C3'    CT            0.07130    28
-   H3'    H1            0.09850    29
-   C2'    CT           -0.08540    30
-  H2'1    HC            0.07180    31
-  H2'2    HC            0.07180    32
-   O3'    OS           -0.52320    33
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ DG3 ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT            0.03580    11
-   H1'    H2            0.17460    12
-    N9    N*            0.05770    13
-    C8    CK            0.07360    14
-    H8    H5            0.19970    15
-    N7    NB           -0.57250    16
-    C5    CB            0.19910    17
-    C6    C             0.49180    18
-    O6    O            -0.56990    19
-    N1    NA           -0.50530    20
-    H1    H             0.35200    21
-    C2    CA            0.74320    22
-    N2    N2           -0.92300    23
-   H21    H             0.42350    24
-   H22    H             0.42350    25
-    N3    NC           -0.66360    26
-    C4    CB            0.18140    27
-   C3'    CT            0.07130    28
-   H3'    H1            0.09850    29
-   C2'    CT           -0.08540    30
-  H2'1    HC            0.07180    31
-  H2'2    HC            0.07180    32
-   O3'    OH           -0.65490    33
-   H3T    HO            0.43960    34
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ DGN ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT            0.03580     9
-   H1'    H2            0.17460    10
-    N9    N*            0.05770    11
-    C8    CK            0.07360    12
-    H8    H5            0.19970    13
-    N7    NB           -0.57250    14
-    C5    CB            0.19910    15
-    C6    C             0.49180    16
-    O6    O            -0.56990    17
-    N1    NA           -0.50530    18
-    H1    H             0.35200    19
-    C2    CA            0.74320    20
-    N2    N2           -0.92300    21
-   H21    H             0.42350    22
-   H22    H             0.42350    23
-    N3    NC           -0.66360    24
-    C4    CB            0.18140    25
-   C3'    CT            0.07130    26
-   H3'    H1            0.09850    27
-   C2'    CT           -0.08540    28
-  H2'1    HC            0.07180    29
-  H2'2    HC            0.07180    30
-   O3'    OH           -0.65490    31
-   H3T    HO            0.43960    32
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                      
-[ DC5 ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT           -0.01160     9
-   H1'    H2            0.19630    10
-    N1    N*           -0.03390    11
-    C6    CM           -0.01830    12
-    H6    H4            0.22930    13
-    C5    CM           -0.52220    14
-    H5    HA            0.18630    15
-    C4    CA            0.84390    16
-    N4    N2           -0.97730    17
-   H41    H             0.43140    18
-   H42    H             0.43140    19
-    N3    NC           -0.77480    20
-    C2    C             0.79590    21
-    O2    O            -0.65480    22
-   C3'    CT            0.07130    23
-   H3'    H1            0.09850    24
-   C2'    CT           -0.08540    25
-  H2'1    HC            0.07180    26
-  H2'2    HC            0.07180    27
-   O3'    OS           -0.52320    28
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
- [ impropers ]
-   C1'    N1    C6    C2
-    N1    N3    C2    O2 
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-[ DC ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT           -0.01160    11
-   H1'    H2            0.19630    12
-    N1    N*           -0.03390    13
-    C6    CM           -0.01830    14
-    H6    H4            0.22930    15
-    C5    CM           -0.52220    16
-    H5    HA            0.18630    17
-    C4    CA            0.84390    18
-    N4    N2           -0.97730    19
-   H41    H             0.43140    20
-   H42    H             0.43140    21
-    N3    NC           -0.77480    22
-    C2    C             0.79590    23
-    O2    O            -0.65480    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OS           -0.52320    30
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2 
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-[ DC3 ]
- [ atoms ]
-     P    P             1.16590     1
-   O1P    O2           -0.77610     2
-   O2P    O2           -0.77610     3
-   O5'    OS           -0.49540     4
-   C5'    CI           -0.00690     5
-  H5'1    H1            0.07540     6
-  H5'2    H1            0.07540     7
-   C4'    CT            0.16290     8
-   H4'    H1            0.11760     9
-   O4'    OS           -0.36910    10
-   C1'    CT           -0.01160    11
-   H1'    H2            0.19630    12
-    N1    N*           -0.03390    13
-    C6    CM           -0.01830    14
-    H6    H4            0.22930    15
-    C5    CM           -0.52220    16
-    H5    HA            0.18630    17
-    C4    CA            0.84390    18
-    N4    N2           -0.97730    19
-   H41    H             0.43140    20
-   H42    H             0.43140    21
-    N3    NC           -0.77480    22
-    C2    C             0.79590    23
-    O2    O            -0.65480    24
-   C3'    CT            0.07130    25
-   H3'    H1            0.09850    26
-   C2'    CT           -0.08540    27
-  H2'1    HC            0.07180    28
-  H2'2    HC            0.07180    29
-   O3'    OH           -0.65490    30
-   H3T    HO            0.43960    31
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-
-[ DCN ]
- [ atoms ]
-   H5T    HO            0.44220     1
-   O5'    OH           -0.63180     2
-   C5'    CI           -0.00690     3
-  H5'1    H1            0.07540     4
-  H5'2    H1            0.07540     5
-   C4'    CT            0.16290     6
-   H4'    H1            0.11760     7
-   O4'    OS           -0.36910     8
-   C1'    CT           -0.01160     9
-   H1'    H2            0.19630    10
-    N1    N*           -0.03390    11
-    C6    CM           -0.01830    12
-    H6    H4            0.22930    13
-    C5    CM           -0.52220    14
-    H5    HA            0.18630    15
-    C4    CA            0.84390    16
-    N4    N2           -0.97730    17
-   H41    H             0.43140    18
-   H42    H             0.43140    19
-    N3    NC           -0.77480    20
-    C2    C             0.79590    21
-    O2    O            -0.65480    22
-   C3'    CT            0.07130    23
-   H3'    H1            0.09850    24
-   C2'    CT           -0.08540    25
-  H2'1    HC            0.07180    26
-  H2'2    HC            0.07180    27
-   O3'    OH           -0.65490    28
-   H3T    HO            0.43960    29
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'  H2'2
-   O3'   H3T
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    N3    C4    N4    C5
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/ffbonded.itp b/share/top/amber99sb-ildn-bsc0.ff/ffbonded.itp
deleted file mode 100644 (file)
index 2b4bdd1..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/ffbonded.itp
+++ /dev/null
@@ -1,632 +0,0 @@
-[ bondtypes ]
-; i    j  func       b0          kb
-  C  C          1     0.1525   259408.0 ; new99
-  C  OS         1     0.1323   376560.0 ; new99
-  C  H4         1     0.1080   307105.6 ; new99
-  C  H5         1     0.1080   307105.6 ; new99
-  CA OH         1     0.1364   376560.0 ; new99
-  CM OS         1     0.1240   401664.0 ; new99
-  Cl CT         1     0.1766   194137.6 ; new99
-  Br CT         1     0.1944   133051.2 ; new99
-  I  CT         1     0.2166   123846.4 ; new99
-  F  CA         1     0.1359   323004.8 ; new99
-  Cl CA         1     0.1727   161502.4 ; new99
-  I  CA         1     0.2075   143092.8 ; new99
-  Br CA         1     0.1890   143929.6 ; new99
-  OW HW         1    0.09572   462750.4 ; P water
-  HW HW         1    0.15136   462750.4 ; P water
-  C  CA         1    0.14090   392459.2 ; 7,(1986),230; TYR
-  C  CB         1    0.14190   374049.6 ; 7,(1986),230; GUA
-  C  CM         1    0.14440   343088.0 ; 7,(1986),230; THY,URA
-  C  CT         1    0.15220   265265.6 ; 7,(1986),230; AA
-  C  N*         1    0.13830   354803.2 ; 7,(1986),230; CYT,URA
-  C  NA         1    0.13880   349782.4 ; 7,(1986),230; GUA.URA
-  C  NC         1    0.13580   382417.6 ; 7,(1986),230; CYT
-  C  O          1    0.12290   476976.0 ; 7,(1986),230; AA,CYT,GUA,THY,URA
-  C  O2         1    0.12500   548940.8 ; 7,(1986),230; GLU,ASP
-  C  OH         1    0.13640   376560.0 ; 7,(1986),230; TYR
-  CA CA         1    0.14000   392459.2 ; 7,(1986),230; BENZENE,PHE,TRP,TYR
-  CA CB         1    0.14040   392459.2 ; 7,(1986),230; ADE,TRP
-  CA CM         1    0.14330   357313.6 ; 7,(1986),230; CYT
-  CA CT         1    0.15100   265265.6 ; 7,(1986),230; PHE,TYR
-  CA HA         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
-  CA H4         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; no assigned
-  CA N2         1    0.13400   402500.8 ; 7,(1986),230; ARG,CYT,GUA
-  CA NA         1    0.13810   357313.6 ; 7,(1986),230; GUA
-  CA NC         1    0.13390   404174.4 ; 7,(1986),230; ADE,CYT,GUA
-  CB CB         1    0.13700   435136.0 ; 7,(1986),230; ADE,GUA
-  CB N*         1    0.13740   364844.8 ; 7,(1986),230; ADE,GUA
-  CB NB         1    0.13910   346435.2 ; 7,(1986),230; ADE,GUA
-  CB NC         1    0.13540   385764.8 ; 7,(1986),230; ADE,GUA
-  CK H5         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE,GUA
-  CK N*         1    0.13710   368192.0 ; 7,(1986),230; ADE,GUA
-  CK NB         1    0.13040   442667.2 ; 7,(1986),230; ADE,GUA
-  CM CM         1    0.13500   459403.2 ; 7,(1986),230; CYT,THY,URA
-  CM CT         1    0.15100   265265.6 ; 7,(1986),230; THY
-  CM HA         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA
-  CM H4         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA
-  CM H5         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; not assigned
-  CM N*         1    0.13650   374886.4 ; 7,(1986),230; CYT,THY,URA
-  CQ H5         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE
-  CQ NC         1    0.13240   420073.6 ; 7,(1986),230; ADE
-  CT CT         1    0.15260   259408.0 ; 7,(1986),230; AA, SUGARS
-  CT HC         1    0.10900   284512.0 ; ged from 331 bsd on NMA nmodes; AA, SUGARS
-  CT H1         1    0.10900   284512.0 ; ged from 331 bsd on NMA nmodes; AA, RIBOSE
-  CT H2         1    0.10900   284512.0 ; ged from 331 bsd on NMA nmodes; SUGARS
-  CT H3         1    0.10900   284512.0 ; ged from 331 bsd on NMA nmodes; not assigned
-  CT HP         1    0.10900   284512.0 ; nged from 331; AA-lysine, methyl ammonium cation
-  CT N*         1    0.14750   282001.6 ; 7,(1986),230; ADE,CYT,GUA,THY,URA
-  CT N2         1    0.14630   282001.6 ; 7,(1986),230; ARG
-  CT OH         1    0.14100   267776.0 ; 7,(1986),230; SUGARS
-  CT OS         1    0.14100   267776.0 ; 7,(1986),230; NUCLEIC ACIDS
-  H  N2         1    0.10100   363171.2 ; 7,(1986),230; ADE,CYT,GUA,ARG
-  H  N*         1    0.10100   363171.2 ; plain unmethylated bases ADE,CYT,GUA,ARG
-  H  NA         1    0.10100   363171.2 ; 7,(1986),230; GUA,URA,HIS
-  HO OH         1    0.09600   462750.4 ; 7,(1986),230; SUGARS,SER,TYR
-  HO OS         1    0.09600   462750.4 ; 7,(1986),230; NUCLEOTIDE ENDS
-  O2 P          1    0.14800   439320.0 ; 7,(1986),230; NA PHOSPHATES
-  OH P          1    0.16100   192464.0 ; 7,(1986),230; NA PHOSPHATES
-  OS P          1    0.16100   192464.0 ; 7,(1986),230; NA PHOSPHATES
-  C* HC         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes, not needed AA
-  C  N          1    0.13350   410032.0 ; 7,(1986),230; AA
-  C* CB         1    0.14590   324678.4 ; 7,(1986),230; TRP
-  C* CT         1    0.14950   265265.6 ; 7,(1986),230; TRP
-  C* CW         1    0.13520   456892.8 ; 7,(1986),230; TRP
-  CA CN         1    0.14000   392459.2 ; 7,(1986),230; TRP
-  CB CN         1    0.14190   374049.6 ; 7,(1986),230; TRP
-  CC CT         1    0.15040   265265.6 ; 7,(1986),230; HIS
-  CC CV         1    0.13750   428441.6 ; 7,(1986),230; HIS(delta)
-  CC CW         1    0.13710   433462.4 ; 7,(1986),230; HIS(epsilon)
-  CC NA         1    0.13850   353129.6 ; 7,(1986),230; HIS
-  CC NB         1    0.13940   343088.0 ; 7,(1986),230; HIS
-  CN NA         1    0.13800   358150.4 ; 7,(1986),230; TRP
-  CR H5         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS
-  CR NA         1    0.13430   399153.6 ; 7,(1986),230; HIS
-  CR NB         1    0.13350   408358.4 ; 7,(1986),230; HIS
-  CT N          1    0.14490   282001.6 ; 7,(1986),230; AA
-  CT N3         1    0.14710   307105.6 ; 7,(1986),230; LYS
-  CT S          1    0.18100   189953.6 ; ged from 222.0 based on dimethylS nmodes
-  CT SH         1    0.18100   198321.6 ; ged from 222.0 based on methanethiol nmodes
-  CV H4         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; HIS
-  CV NB         1    0.13940   343088.0 ; 7,(1986),230; HIS
-  CW H4         1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
-  CW NA         1    0.13810   357313.6 ; 7,(1986),230; HIS,TRP
-  H  N          1    0.10100   363171.2 ; 7,(1986),230; AA
-  H  N3         1    0.10100   363171.2 ; 7,(1986),230; LYS    
-  HS SH         1    0.13360   229283.2 ; 7,(1986),230; CYS
-  S  S          1    0.20380   138908.8 ; 7,(1986),230; CYX   (SCHERAGA)
-  CT F          1    0.13800   307105.6 ; 13,(1992),963;CF4; R0=1.332 FOR CHF3
-;
-; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT) 
-;
-  CI H1         1    0.10900   284512.0
-  CI CT         1    0.15260   259408.0
-  CI OH         1    0.14100   267776.0
-  CI OS         1    0.14100   267776.0
-
-
-[ constrainttypes ]
-; this section is implemented manually from bond & angle values
-
-; constraints for rigid CH3 groups
- MCH3   CT      2    0.166426
- MCH3   S       2    0.193875
- MCH3   MCH3    2    0.092163
-; constraints for rigid NH3 groups
- MNH3   CT      2    0.158254
- MNH3   MNH3    2    0.080229
-
-; angle-derived constraints for OH and SH groups in proteins
-; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.
-  C     HO      2    0.195074
-  CA    HO      2    0.195074
-  CT    HO      2    0.194132
-  CT    HS      2    0.235935
-
-
-
-[ angletypes ]
-;  i    j    k  func       th0       cth
-HW  OW  HW           1   104.520    836.800 ; TIP3P water
-HW  HW  OW           1   127.740      0.000 ; (found in crystallographic water with 3 bonds)
-C   C   O            1   120.000    669.440 ; new99
-C   C   OH           1   120.000    669.440 ; new99
-CT  C   CT           1   117.000    527.184 ; new99
-CT  C   OS           1   115.000    669.440 ; new99
-O   C   OS           1   125.000    669.440 ; new99
-H4  C   C            1   120.000    418.400 ; new99
-H4  C   CM           1   115.000    418.400 ; new99
-H4  C   CT           1   115.000    418.400 ; new99
-H4  C   O            1   120.000    418.400 ; new99
-H4  C   OH           1   120.000    418.400 ; new99
-H5  C   N            1   120.000    418.400 ; new99
-H5  C   O            1   119.000    418.400 ; new99
-H5  C   OH           1   107.000    418.400 ; new99
-H5  C   OS           1   107.000    418.400 ; new99
-CA  CA  OH           1   120.000    585.760 ; new99
-CA  OH  HO           1   113.000    418.400 ; new99
-F   CA  CA           1   121.000    585.760 ; new99
-Cl  CA  CA           1   118.800    585.760 ; new99
-Br  CA  CA           1   118.800    585.760 ; new99
-I   CA  CA           1   118.800    585.760 ; new99
-CM  CM  OS           1   125.000    669.440 ; new99
-H4  CM  OS           1   113.000    418.400 ; new99
-HA  CM  HA           1   120.000    292.880 ; new99
-HA  CM  CT           1   120.000    418.400 ; new99
-H1  CT  CM           1   109.500    418.400 ; new99
-HC  CT  CM           1   109.500    418.400 ; new99
-C   CT  OS           1   109.500    502.080 ; new99
-CM  CT  CT           1   111.000    527.184 ; new99
-CM  CT  OS           1   109.500    418.400 ; new99
-CT  CT  CA           1   114.000    527.184 ; new99
-OS  CT  OS           1   101.000    502.080 ; new99
-F   CT  CT           1   109.000    418.400 ; new99
-F   CT  H2           1   109.500    418.400 ; new99
-Cl  CT  CT           1   108.500    418.400 ; new99
-Cl  CT  H1           1   108.500    418.400 ; new99
-Br  CT  CT           1   108.000    418.400 ; new99
-Br  CT  H1           1   106.500    418.400 ; new99
-I   CT  CT           1   106.000    418.400 ; new99
-CB  C   NA           1   111.300    585.760 ; NA
-CB  C   O            1   128.800    669.440 ; 
-CM  C   NA           1   114.100    585.760 ; 
-CM  C   O            1   125.300    669.440 ; 
-CT  C   O            1   120.400    669.440 ; 
-CT  C   O2           1   117.000    585.760 ; 
-CT  C   OH           1   110.000    669.440 ; new99
-N*  C   NA           1   115.400    585.760 ; 
-N*  C   NC           1   118.600    585.760 ; 
-N*  C   O            1   120.900    669.440 ; 
-NA  C   O            1   120.600    669.440 ; 
-NC  C   O            1   122.500    669.440 ; 
-CT  C   N            1   116.600    585.760 ; AA general
-N   C   O            1   122.900    669.440 ; AA general
-O   C   O            1   126.000    669.440 ; AA COO- terminal residues
-O2  C   O2           1   126.000    669.440 ; AA GLU            (SCH JPC 79,2379)
-O   C   OH           1   120.000    669.440 ; 
-CA  C   CA           1   120.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA tyr
-CA  C   OH           1   120.000    585.760 ; AA tyr
-C   CA  CA           1   120.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes
-CA  CA  CA           1   120.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes
-CA  CA  CB           1   120.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes
-CA  CA  CT           1   120.000    585.760 ; 
-CA  CA  HA           1   120.000    418.400 ; new99
-CA  CA  H4           1   120.000    418.400 ; new99
-CB  CA  HA           1   120.000    418.400 ; new99
-CB  CA  H4           1   120.000    418.400 ; new99
-CB  CA  N2           1   123.500    585.760 ; 
-CB  CA  NC           1   117.300    585.760 ; 
-CM  CA  N2           1   120.100    585.760 ; 
-CM  CA  NC           1   121.500    585.760 ; 
-N2  CA  NA           1   116.000    585.760 ; 
-N2  CA  NC           1   119.300    585.760 ; 
-NA  CA  NC           1   123.300    585.760 ; 
-C   CA  HA           1   120.000    418.400 ; new99 tyr
-N2  CA  N2           1   120.000    585.760 ; AA arg
-CN  CA  HA           1   120.000    418.400 ; new99 trp
-CA  CA  CN           1   120.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-C   CB  CB           1   119.200    527.184 ; changed from 85.0  bsd on C6H6 nmodes; NA gua
-C   CB  NB           1   130.000    585.760 ; 
-CA  CB  CB           1   117.300    527.184 ; changed from 85.0  bsd on C6H6 nmodes; NA ade
-CA  CB  NB           1   132.400    585.760 ; 
-CB  CB  N*           1   106.200    585.760 ; 
-CB  CB  NB           1   110.400    585.760 ; 
-CB  CB  NC           1   127.700    585.760 ; 
-N*  CB  NC           1   126.200    585.760 ; 
-C*  CB  CA           1   134.900    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-C*  CB  CN           1   108.800    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-CA  CB  CN           1   116.200    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-H5  CK  N*           1   123.050    418.400 ; new99
-H5  CK  NB           1   123.050    418.400 ; new99
-N*  CK  NB           1   113.900    585.760 ; 
-C   CM  CM           1   120.700    527.184 ; changed from 85.0  bsd on C6H6 nmodes; NA thy
-C   CM  CT           1   119.700    585.760 ; 
-C   CM  HA           1   119.700    418.400 ; new99
-C   CM  H4           1   119.700    418.400 ; new99
-CA  CM  CM           1   117.000    527.184 ; changed from 85.0  bsd on C6H6 nmodes; NA cyt
-CA  CM  HA           1   123.300    418.400 ; new99
-CA  CM  H4           1   123.300    418.400 ; new99
-CM  CM  CT           1   119.700    585.760 ; 
-CM  CM  HA           1   119.700    418.400 ; new99
-CM  CM  H4           1   119.700    418.400 ; new99
-CM  CM  N*           1   121.200    585.760 ; 
-H4  CM  N*           1   119.100    418.400 ; new99
-H5  CQ  NC           1   115.450    418.400 ; new99
-NC  CQ  NC           1   129.100    585.760 ; 
-CM  CT  HC           1   109.500    418.400 ; changed based on NMA nmodes
-CT  CT  CT           1   109.500    334.720 ; 
-CT  CT  HC           1   109.500    418.400 ; changed based on NMA nmodes
-CT  CT  H1           1   109.500    418.400 ; changed based on NMA nmodes
-CT  CT  H2           1   109.500    418.400 ; changed based on NMA nmodes
-CT  CT  HP           1   109.500    418.400 ; changed based on NMA nmodes
-CT  CT  N*           1   109.500    418.400 ; 
-CT  CT  OH           1   109.500    418.400 ; 
-CT  CT  OS           1   109.500    418.400 ; 
-HC  CT  HC           1   109.500    292.880 ; 
-H1  CT  H1           1   109.500    292.880 ; 
-HP  CT  HP           1   109.500    292.880 ; AA lys, ch3nh4+
-H2  CT  N*           1   109.500    418.400 ; changed based on NMA nmodes
-H1  CT  N*           1   109.500    418.400 ; changed based on NMA nmodes
-H1  CT  OH           1   109.500    418.400 ; changed based on NMA nmodes 
-H1  CT  OS           1   109.500    418.400 ; changed based on NMA nmodes 
-H2  CT  OS           1   109.500    418.400 ; changed based on NMA nmodes
-N*  CT  OS           1   109.500    418.400 ; 
-H1  CT  N            1   109.500    418.400 ; AA general  changed based on NMA nmodes
-C   CT  H1           1   109.500    418.400 ; AA general  changed based on NMA nmodes
-C   CT  HP           1   109.500    418.400 ; AA zwitterion  changed based on NMA nmodes
-H1  CT  S            1   109.500    418.400 ; AA cys     changed based on NMA nmodes
-H1  CT  SH           1   109.500    418.400 ; AA cyx     changed based on NMA nmodes
-CT  CT  S            1   114.700    418.400 ; AA cyx            (SCHERAGA  JPC 79,1428)
-CT  CT  SH           1   108.600    418.400 ; AA cys
-H2  CT  H2           1   109.500    292.880 ; AA lys
-H1  CT  N2           1   109.500    418.400 ; AA arg     changed based on NMA nmodes
-HP  CT  N3           1   109.500    418.400 ; AA lys, ch3nh3+, changed based on NMA nmodes
-CA  CT  CT           1   114.000    527.184 ; AA phe tyr          (SCH JPC  79,2379)
-C   CT  HC           1   109.500    418.400 ; AA gln      changed based on NMA nmodes
-C   CT  N            1   110.100    527.184 ; AA general
-CT  CT  N2           1   111.200    669.440 ; AA arg             (JCP 76, 1439)
-CT  CT  N            1   109.700    669.440 ; AA ala, general    (JACS 94, 2657)
-C   CT  CT           1   111.100    527.184 ; AA general
-CA  CT  HC           1   109.500    418.400 ; AA tyr     changed based on NMA nmodes
-CT  CT  N3           1   111.200    669.440 ; AA lys             (JCP 76, 1439)
-CC  CT  CT           1   113.100    527.184 ; AA his
-CC  CT  HC           1   109.500    418.400 ; AA his     changed based on NMA nmodes
-C   CT  N3           1   111.200    669.440 ; AA amino terminal residues
-C*  CT  CT           1   115.600    527.184 ; AA trp
-C*  CT  HC           1   109.500    418.400 ; AA trp    changed based on NMA nmodes
-CT  CC  NA           1   120.000    585.760 ; AA his
-CT  CC  CV           1   120.000    585.760 ; AA his
-CT  CC  NB           1   120.000    585.760 ; AA his
-CV  CC  NA           1   120.000    585.760 ; AA his
-CW  CC  NA           1   120.000    585.760 ; AA his
-CW  CC  NB           1   120.000    585.760 ; AA his
-CT  CC  CW           1   120.000    585.760 ; AA his
-H5  CR  NA           1   120.000    418.400 ; new99 his
-H5  CR  NB           1   120.000    418.400 ; new99 his
-NA  CR  NA           1   120.000    585.760 ; AA his
-NA  CR  NB           1   120.000    585.760 ; AA his
-CC  CV  H4           1   120.000    418.400 ; new99 his
-CC  CV  NB           1   120.000    585.760 ; AA his
-H4  CV  NB           1   120.000    418.400 ; new99 his
-CC  CW  H4           1   120.000    418.400 ; new99 his
-CC  CW  NA           1   120.000    585.760 ; AA his
-H4  CW  NA           1   120.000    418.400 ; new99 his
-C*  CW  H4           1   120.000    418.400 ; new99 trp
-C*  CW  NA           1   108.700    585.760 ; AA trp
-CT  C*  CW           1   125.000    585.760 ; AA trp
-CB  C*  CT           1   128.600    585.760 ; AA trp
-CB  C*  CW           1   106.400    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-CA  CN  NA           1   132.800    585.760 ; AA trp
-CB  CN  NA           1   104.400    585.760 ; AA trp
-CA  CN  CB           1   122.700    527.184 ; changed from 85.0  bsd on C6H6 nmodes; AA trp
-C   N   CT           1   121.900    418.400 ; AA general
-C   N   H            1   120.000    418.400 ; new99 general, gln, asn,changed based on NMA nmodes
-CT  N   H            1   118.040    418.400 ; new99 general,     changed based on NMA nmodes
-CT  N   CT           1   118.000    418.400 ; AA pro             (DETAR JACS 99,1232)
-H   N   H            1   120.000    292.880 ; ade,cyt,gua,gln,asn     **
-C   N*  CM           1   121.600    585.760 ; 
-C   N*  CT           1   117.600    585.760 ; 
-C   N*  H            1   119.200    418.400 ; new99
-CB  N*  CK           1   105.400    585.760 ; 
-CB  N*  CT           1   125.800    585.760 ; 
-CB  N*  H            1   125.800    418.400 ; new99
-CK  N*  CT           1   128.800    585.760 ; 
-CK  N*  H            1   128.800    418.400 ; new99  for unmethylated n.a. bases,chngd bsd NMA nmodes
-CM  N*  CT           1   121.200    585.760 ; 
-CM  N*  H            1   121.200    418.400 ; new99  for unmethylated n.a. bases,chngd bsd NMA nmodes
-CA  N2  H            1   120.000    418.400 ; new99
-H   N2  H            1   120.000    292.880 ; 
-CT  N2  H            1   118.400    418.400 ; new99 arg
-CA  N2  CT           1   123.200    418.400 ; AA arg
-CT  N3  H            1   109.500    418.400 ; AA lys,     changed based on NMA nmodes
-CT  N3  CT           1   109.500    418.400 ; AA pro/nt
-H   N3  H            1   109.500    292.880 ; AA lys, AA(end)
-C   NA  C            1   126.400    585.760 ; 
-C   NA  CA           1   125.200    585.760 ; 
-C   NA  H            1   116.800    418.400 ; new99
-CA  NA  H            1   118.000    418.400 ; new99
-CC  NA  CR           1   120.000    585.760 ; AA his
-CC  NA  H            1   120.000    418.400 ; new99 his
-CR  NA  CW           1   120.000    585.760 ; AA his
-CR  NA  H            1   120.000    418.400 ; new99 his
-CW  NA  H            1   120.000    418.400 ; new99 his
-CN  NA  CW           1   111.600    585.760 ; AA trp
-CN  NA  H            1   123.100    418.400 ; new99 trp
-CB  NB  CK           1   103.800    585.760 ; 
-CC  NB  CR           1   117.000    585.760 ; AA his
-CR  NB  CV           1   117.000    585.760 ; AA his
-C   NC  CA           1   120.500    585.760 ; 
-CA  NC  CB           1   112.200    585.760 ; 
-CA  NC  CQ           1   118.600    585.760 ; 
-CB  NC  CQ           1   111.000    585.760 ; 
-C   OH  HO           1   113.000    418.400 ; new99
-CT  OH  HO           1   108.500    460.240 ; 
-HO  OH  P            1   108.500    376.560 ; 
-CT  OS  CT           1   109.500    502.080 ; 
-CT  OS  P            1   120.500    836.800 ; 
-P   OS  P            1   120.500    836.800 ; 
-O2  P   OH           1   108.230    376.560 ; 
-O2  P   O2           1   119.900   1171.520 ; 
-O2  P   OS           1   108.230    836.800 ; 
-OH  P   OS           1   102.600    376.560 ; 
-OS  P   OS           1   102.600    376.560 ; 
-CT  S   CT           1    98.900    518.816 ; AA met
-CT  S   S            1   103.700    569.024 ; AA cyx             (SCHERAGA  JPC 79,1428)
-CT  SH  HS           1    96.000    359.824 ; changed from 44.0 based on methanethiol nmodes
-HS  SH  HS           1    92.070    292.880 ; AA cys
-F   CT  F            1   109.100    644.336 ; JCC,13,(1992),963;
-F   CT  H1           1   109.500    418.400 ; new99
-N   C   N            1   120.000    585.760 ; Added for Urea (same as N2-CA-N2) - EJS
-;
-; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT) 
-;
-CT  CI  H1           1   109.500    418.400
-H1  CI  H1           1   109.500    292.880
-CI  CT  H1           1   109.500    418.400
-CI  CT  OS           1   109.500    418.400
-CI  CT  CT           1   109.500    334.720
-H1  CI  OS           1   109.500    418.400
-CT  CI  OS           1   109.500    418.400
-CI  OS  P            1   120.500    836.800
-H1  CI  OH           1   109.500    418.400
-CT  CI  OH           1   109.500    418.400
-CI  OH  HO           1   108.500    460.240
-
-[ dihedraltypes ]
-;i  j   k  l    func      phase      kd      pn
-CA  CA  CA  OH       4      180.00     4.60240     2   ; new99
-H5  O   C   OH       4      180.00     4.60240     2   ; new99
-H5  O   C   OS       4      180.00     4.60240     2   ; new99
-CM  CT  CM  HA       4      180.00     4.60240     2   ; new99
-CA  CA  CA  Br       4      180.00     4.60240     2   ; new99
-CM  H4  C   O        4      180.00     4.60240     2   ; new99
-C   CT  N   H        4      180.00     4.60240     2   ; new99
-C   CT  N   O        4      180.00     4.60240     2    ; new99
-CB  CK  N*  CT       4      180.00     4.18400     2   ; 
-CK  CB N*  CT       4      180.00     4.18400     2    ;
-C   CM  N*  CT       4      180.00     4.18400     2   ; dac guess, 9/94
-CT  N*  C   CM       4      180.00     4.18400     2    ; 
-CM  C   CM  CT       4      180.00     4.60240     2   ; 
-CT  O   C   OH       4      180.00    43.93200     2   ; 
-NA  CV  CC  CT       4      180.00     4.60240     2   ; 
-NB  CW  CC  CT       4      180.00     4.60240     2   ; 
-NA  CW  CC  CT       4      180.00     4.60240     2   ; 
-CW  CB  C*  CT       4      180.00     4.60240     2   ; 
-CA  CA  CA  CT       4      180.00     4.60240     2   ; 
-C   CM  CM  CT       4      180.00     4.60240     2   ; dac guess, 9/94
-NC  CM  CA  N2       4      180.00     4.60240     2   ; dac guess, 9/94
-CB  NC  CA  N2       4      180.00     4.60240     2   ; dac, 10/94
-NA  NC  CA  N2       4      180.00     4.60240     2   ; dac, 10/94
-CA  CA  C   OH       4      180.00     4.60240     2   ; 
-CT  CV  CC  NA       4      180.00     4.60240     2   ; 
-CT  CW  CC  NB       4      180.00     4.60240     2   ; 
-CT  CW  CC  NA       4      180.00     4.60240     2   ; 
-CB  CT  C*  CW       4      180.00     4.60240     2   ; 
-CM  N2  CA  NC       4      180.00     4.60240     2   ; 
-CB  N2  CA  NC       4      180.00     4.60240     2   ; 
-N2  NA  CA  NC       4      180.00     4.60240     2   ; 
-N   N   C   O        4      180.00    43.93200     2   ; urea
-X   O2  C   O2       4      180.00    43.93200     2   ; JCC,7,(1986),230
-X   N2  CA  N2       4      180.00    43.93200     2   ; JCC,7,(1986),230
-X   CT  N   CT       4      180.00     4.18400     2   ; JCC,7,(1986),230
-X   X   C   O        4      180.00    43.93200     2   ; JCC,7,(1986),230
-X   X   N   H        4      180.00     4.18400     2   ; JCC,7,(1986),230
-X   X   N2  H        4      180.00     4.18400     2   ; JCC,7,(1986),230
-X   X   NA  H        4      180.00     4.18400     2   ; JCC,7,(1986),230
-X   X   CA  HA       4      180.00     4.60240     2   ; bsd.on C6H6 nmodes
-X   X   CW  H4       4      180.00     4.60240     2   ; 
-X   X   CR  H5       4      180.00     4.60240     2   ; 
-X   X   CV  H4       4      180.00     4.60240     2   ; 
-X   X   CQ  H5       4      180.00     4.60240     2   ; 
-X   X   CK  H5       4      180.00     4.60240     2   ; 
-X   X   CM  H4       4      180.00     4.60240     2   ; 
-X   X   CM  HA       4      180.00     4.60240     2   ; 
-X   X   CA  H4       4      180.00     4.60240     2   ; bsd.on C6H6 nmodes 
-X   X   CA  H5       4      180.00     4.60240     2   ; bsd.on C6H6 nmodes
-
-
-[ dihedraltypes ]
-;i   j   k   l    func 
-;
-; New dihedrals for C5' in DNA/RNA 
-;
- CT  OS  CT  CI           9       0.0      1.60247     3
- CT  OS  CT  CI           9     180.0      0.41840     2
- H1  CI         CT  OS    9       0.0      1.04600     1
- H1  CI         CT  OH    9       0.0      1.04600     1
- H1  CT         CI  OS    9       0.0      1.04600     1
- H1  CT         CI  OH    9       0.0      1.04600     1
- CI  CT         CT  CT    9       0.0      0.75312     3
- CI  CT         CT  CT    9     180.0      1.04600     2  
- CI  CT         CT  CT    9     180.0      0.83680     1
-;
- OS  P  OS  CI    9    31.795      0.774797    1  ; alpha (6DP after conversion, as 6DP given in paper)
- OS  P  OS  CI    9  351.9596      5.257326    2  ; alpha
- OS  P  OS  CI    9 357.24748      1.484726    3  ; alpha
- OH  P  OS  CI    9    31.795      0.774797    1  ; alpha
- OH  P  OS  CI    9  351.9596      5.257326    2  ; alpha
- OH  P  OS  CI    9 357.24748      1.484726    3  ; alpha
- CT  CT         CI  OS    9 190.97653      4.928919    1  ; gamma
- CT  CT         CI  OS    9 295.63279      0.385355    2  ; gamma
- CT  CT         CI  OS    9 348.09535      4.028481    3  ; gamma
- CT  CT         CI  OH    9 190.97653      4.928919    1  ; gamma
- CT  CT         CI  OH    9 295.63279      0.385355    2  ; gamma
- CT  CT         CI  OH    9 348.09535      4.028481    3  ; gamma
-;
- X   CI  OS  X    9       0.0      1.60387     3
- X   CI  OH  X     9       0.0      0.69733     3
- X   CI  CT  X     9       0.0      0.65084     3
-;
-; Back to normal dihedrals
-;
- CT  CT  OS  CT    9       0.0      1.60247     3  ; 
- CT  CT  OS  CT    9     180.0      0.41840     2  ; 
- C   N   CT  C     9       0.0      1.12968     2  ; new for 99sb
- C   N   CT  C     9       0.0      1.75728     3  ; new for 99sb
- N   CT  C   N     9     180.0      1.88280     1  ; new for 99sb
- N   CT  C   N     9     180.0      6.61072     2  ; new for 99sb
- N   CT  C   N     9     180.0      2.30120     3  ; new for 99sb
- CT  CT  N   C     9       0.0      8.36800     1  ; new for 99sb
- CT  CT  N   C     9       0.0      8.36800     2  ; new for 99sb
- CT  CT  N   C     9       0.0      1.67360     3  ; new for 99sb
- CT  CT  C   N     9       0.0      0.83680     1  ; new for 99sb
- CT  CT  C   N     9       0.0      0.83680     2  ; new for 99sb
- CT  CT  C   N     9       0.0      1.67360     3  ; new for 99sb
- H   N   C   O     9     180.0     10.46000     2  ; JCC,7,(1986),230
- H   N   C   O     9       0.0      8.36800     1  ; J.C.cistrans-NMA DE
- CT  S   S   CT    9       0.0     14.64400     2  ; JCC,7,(1986),230
- CT  S   S   CT    9       0.0      2.51040     3  ; JCC,7,(1986),230
- OS  CT  CT  OS    9       0.0      0.60250     3  ; parm98, TC,PC,PAK
- OS  CT  CT  OS    9       0.0      4.91620     2  ; Piotr et al.
- OS  CT  CT  OH    9       0.0      0.60250     3  ; parm98, TC,PC,PAK
- OS  CT  CT  OH    9       0.0      4.91620     2  ; parm98, TC,PC,PAK
- OH  CT  CT  OH    9       0.0      0.60250     3  ; parm98, TC,PC,PAK
- OH  CT  CT  OH    9       0.0      4.91620     2  ; parm98, TC,PC,PAK
- OH  P   OS  CT    9       0.0      1.04600     3  ; JCC,7,(1986),230
- OH  P   OS  CT    9       0.0      5.02080     2  ; gg&gt ene.631g*/mp2
- OS  P   OS  CT    9       0.0      1.04600     3  ; JCC,7,(1986),230
- OS  P   OS  CT    9       0.0      5.02080     2  ; gg&gt ene.631g*/mp2
- OS  CT  N*  CK    9       0.0     10.46000     1  ; parm98, TC,PC,PAK
- OS  CT  N*  CM    9       0.0     10.46000     1  ; parm98, TC,PC,PAK
- H1  CT  C   O     9       0.0      3.34720     1  ; Junmei et al, 1999
- H1  CT  C   O     9     180.0      0.33472     3  ; Junmei et al, 1999
- HC  CT  C   O     9       0.0      3.34720     1  ; Junmei et al, 1999
- HC  CT  C   O     9     180.0      0.33472     3  ; Junmei et al, 1999
- HC  CT  CT  HC    9       0.0      0.62760     3  ; Junmei et al, 1999
- HC  CT  CT  CT    9       0.0      0.66944     3  ; Junmei et al, 1999
- HC  CT  CM  CM    9     180.0      1.58992     3  ; Junmei et al, 1999
- HC  CT  CM  CM    9       0.0      4.81160     1  ; Junmei et al, 1999
- HO  OH  CT  CT    9       0.0      0.66944     3  ; Junmei et al, 1999
- HO  OH  CT  CT    9       0.0      1.04600     1  ; Junmei et al, 1999
- HO  OH  C   O     9     180.0      9.62320     2  ; Junmei et al, 1999
- HO  OH  C   O     9       0.0      7.94960     1  ; Junmei et al, 1999
- CM  CM  C   O     9     180.0      9.10020     2  ; Junmei et al, 1999
- CM  CM  C   O     9       0.0      1.25520     3  ; Junmei et al, 1999
- CT  CM  CM  CT    9     180.0     27.82360     2  ; Junmei et al, 1999
- CT  CM  CM  CT    9     180.0      7.94960     1  ; Junmei et al, 1999
- CT  CT  CT  CT    9       0.0      0.75312     3  ; Junmei et al, 1999
- CT  CT  CT  CT    9     180.0      1.04600     2  ; Junmei et al, 1999
- CT  CT  CT  CT    9     180.0      0.83680     1  ; Junmei et al, 1999
- CT  CT  OS  C     9       0.0      1.60247     3  ; Junmei et al, 1999
- CT  CT  OS  C     9     180.0      3.34720     1  ; Junmei et al, 1999
- CT  OS  CT  OS    9       0.0      0.41840     3  ; Junmei et al, 1999
- CT  OS  CT  OS    9     180.0      3.55640     2  ; Junmei et al, 1999
- CT  OS  CT  OS    9     180.0      5.64840     1  ; Junmei et al, 1999
- O   C   OS  CT    9     180.0     11.29680     2  ; Junmei et al, 1999
- O   C   OS  CT    9     180.0      5.85760     1  ; Junmei et al, 1999
- F   CT  CT  F     9     180.0      5.02080     1  ; Junmei et al, 1999
- Cl  CT  CT  Cl    9     180.0      1.88280     1  ; Junmei et al, 1999
- Br  CT  CT  Br    9       0.0      0.00000     0  ; Junmei et al, 1999
- H1  CT  CT  OS    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  OH    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  F     9       0.0      0.79496     1  ; Junmei et al, 1999
- H1  CT  CT  Cl    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  Br    9       0.0      2.30120     1  ; Junmei et al, 1999
- HC  CT  CT  OS    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  OH    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  F     9       0.0      0.79496     1  ; Junmei et al, 1999
- HC  CT  CT  Cl    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  Br    9       0.0      2.30120     1  ; Junmei et al, 1999
- CT  OS  CT  N*    9       0.0      1.60247     3  ; parm98.dat, TC,PC,PAK
- CT  OS  CT  N*    9       0.0      2.71960     2  ; Piotr et al.
- X   C   C   X     9     180.0     15.16700     2  ; Junmei et al, 1999
- X   C   O   X     9     180.0     11.71520     2  ; Junmei et al, 1999
- X   C   OS  X     9     180.0     11.29680     2  ; Junmei et al, 1999
- X   CA  OH  X     9     180.0      3.76560     2  ; Junmei et al, 99
- X   CM  OS  X     9     180.0      4.39320     2  ; Junmei et al, 1999
- X   C   CA  X     9     180.0     15.16700     2  ; intrpol.bsd.on C6H6
- X   C   CB  X     9     180.0     12.55200     2  ; intrpol.bsd.on C6H6
- X   C   CM  X     9     180.0      9.10020     2  ; intrpol.bsd.on C6H6
- X   C   N*  X     9     180.0      6.06680     2  ; JCC,7,(1986),230
- X   C   NA  X     9     180.0      5.64840     2  ; JCC,7,(1986),230
- X   C   NC  X     9     180.0     16.73600     2  ; JCC,7,(1986),230
- X   C   OH  X     9     180.0      9.62320     2  ; Junmei et al, 1999
- X   C   CT  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CA  CA  X     9     180.0     15.16700     2  ; intrpol.bsd.on C6H6
- X   CA  CB  X     9     180.0     14.64400     2  ; intrpol.bsd.on C6H6
- X   CA  CM  X     9     180.0     10.66920     2  ; intrpol.bsd.on C6H6
- X   CA  CT  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CA  N2  X     9     180.0     10.04160     2  ; reinterpolated 93'
- X   CA  NA  X     9     180.0      6.27600     2  ; JCC,7,(1986),230
- X   CA  NC  X     9     180.0     20.08320     2  ; JCC,7,(1986),230
- X   CB  CB  X     9     180.0     22.80280     2  ; intrpol.bsd.on C6H6
- X   CB  N*  X     9     180.0      6.90360     2  ; JCC,7,(1986),230
- X   CB  NB  X     9     180.0     10.66920     2  ; JCC,7,(1986),230
- X   CB  NC  X     9     180.0     17.36360     2  ; JCC,7,(1986),230
- X   CK  N*  X     9     180.0      7.11280     2  ; JCC,7,(1986),230
- X   CK  NB  X     9     180.0     41.84000     2  ; JCC,7,(1986),230
- X   CM  CM  X     9     180.0     27.82360     2  ; intrpol.bsd.on C6H6
- X   CM  CT  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CM  N*  X     9     180.0      7.74040     2  ; JCC,7,(1986),230
- X   CQ  NC  X     9     180.0     28.45120     2  ; JCC,7,(1986),230
- X   CT  CT  X     9       0.0      0.65084     3  ; JCC,7,(1986),230
- X   CT  N   X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CT  N*  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CT  N2  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CT  OH  X     9       0.0      0.69733     3  ; JCC,7,(1986),230
- X   CT  OS  X     9       0.0      1.60387     3  ; JCC,7,(1986),230
- X   OH  P   X     9       0.0      1.04600     3  ; JCC,7,(1986),230
- X   OS  P   X     9       0.0      1.04600     3  ; JCC,7,(1986),230
- X   C   N   X     9     180.0     10.46000     2  ; AA,NMA
- X   CT  N3  X     9       0.0      0.65084     3  ; JCC,7,(1986),230
- X   CT  S   X     9       0.0      1.39467     3  ; JCC,7,(1986),230
- X   CT  SH  X     9       0.0      1.04600     3  ; JCC,7,(1986),230
- X   C*  CB  X     9     180.0      7.00820     2  ; intrpol.bsd.onC6H6aa
- X   C*  CT  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   C*  CW  X     9     180.0     27.30060     2  ; intrpol.bsd.on C6H6
- X   CA  CN  X     9     180.0     15.16700     2  ; reinterpolated 93'
- X   CB  CN  X     9     180.0     12.55200     2  ; reinterpolated 93'
- X   CC  CT  X     9       0.0      0.00000     0  ; JCC,7,(1986),230
- X   CC  CV  X     9     180.0     21.54760     2  ; intrpol.bsd.on C6H6
- X   CC  CW  X     9     180.0     22.48900     2  ; intrpol.bsd.on C6H6
- X   CC  NA  X     9     180.0      5.85760     2  ; JCC,7,(1986),230
- X   CC  NB  X     9     180.0     10.04160     2  ; JCC,7,(1986),230
- X   CN  NA  X     9     180.0      6.38060     2  ; reinterpolated 93'
- X   CR  NA  X     9     180.0      9.72780     2  ; JCC,7,(1986),230
- X   CR  NB  X     9     180.0     20.92000     2  ; JCC,7,(1986),230
- X   CV  NB  X     9     180.0     10.04160     2  ; JCC,7,(1986),230
- X   CW  NA  X     9     180.0      6.27600     2  ; JCC,7,(1986),230
-; Modified amino acid torsions in Amber99SB-ILDN
-; These should not override the general torsion for the atom types,
-; so to avoid introducing extra new atom types we list them explicitly for
-; the residues in question:
-
-#define torsion_ILE_N_CA_CB_CG2_mult1          0.0        0.8158800        1  ; Proteins 78, 1950 (2010)
-#define torsion_ILE_N_CA_CB_CG2_mult2          0.0       -3.5396640        2  ; Proteins 78, 1950 (2010)
-
-#define torsion_LEU_C_CA_CB_CG_mult1           0.0        2.3890640        1  ; Proteins 78, 1950 (2010)
-#define torsion_LEU_C_CA_CB_CG_mult2           0.0       -1.4978720        2  ; Proteins 78, 1950 (2010)
-#define torsion_LEU_C_CA_CB_CG_mult3           0.0        0.5648400        3  ; Proteins 78, 1950 (2010)
-
-#define torsion_ASP_N_CA_CB_CG_mult1           0.0       -11.024840        1  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_N_CA_CB_CG_mult2           0.0        -4.978960        2  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_N_CA_CB_CG_mult3           0.0        -0.029288        3  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_N_CA_CB_CG_mult4           0.0         1.769832        4  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_N_CA_CB_CG_mult5           0.0         0.970688        5  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_N_CA_CB_CG_mult6           0.0        -0.891192        6  ; Proteins 78, 1950 (2010)
-
-#define torsion_ASP_CA_CB_CG_OD_mult1          0.0         0.0             1  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_CA_CB_CG_OD_mult2          0.0        -1.853512        2  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_CA_CB_CG_OD_mult3          0.0         0.0             3  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_CA_CB_CG_OD_mult4          0.0        -0.577392        4  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_CA_CB_CG_OD_mult5          0.0         0.0             5  ; Proteins 78, 1950 (2010)
-#define torsion_ASP_CA_CB_CG_OD_mult6          0.0        -0.054392        6  ; Proteins 78, 1950 (2010)
-
-#define torsion_ASN_C_CA_CB_CG_mult1           0.0         2.389064        1  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_C_CA_CB_CG_mult2           0.0        -2.493664        2  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_C_CA_CB_CG_mult3           0.0         0.493712        3  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_C_CA_CB_CG_mult4           0.0        -1.744728        4  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_C_CA_CB_CG_mult5           0.0         0.435136        5  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_C_CA_CB_CG_mult6           0.0        -0.422584        6  ; Proteins 78, 1950 (2010)
-
-#define torsion_ASN_CA_CB_CG_ND2_mult1         0.0        -4.376464        1  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_CA_CB_CG_ND2_mult2         0.0        -0.757304        2  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_CA_CB_CG_ND2_mult3         0.0        -0.146440        3  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_CA_CB_CG_ND2_mult4         0.0         0.418400        4  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_CA_CB_CG_ND2_mult5         0.0         0.543920        5  ; Proteins 78, 1950 (2010)
-#define torsion_ASN_CA_CB_CG_ND2_mult6         0.0        -0.443504        6  ; Proteins 78, 1950 (2010)
-
-
- 
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/ffnonbonded.itp b/share/top/amber99sb-ildn-bsc0.ff/ffnonbonded.itp
deleted file mode 100644 (file)
index ce59c3b..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/ffnonbonded.itp
+++ /dev/null
@@ -1,79 +0,0 @@
-[ atomtypes ]
-; name      at.num  mass     charge ptype  sigma      epsilon
-Br          35      79.90    0.0000  A   0.00000e+00  0.00000e+00
-C            6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CA           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CB           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CC           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CK           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CM           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CN           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CQ           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CR           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CT           6      12.01    0.0000  A   3.39967e-01  4.57730e-01
-CV           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-CW           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-C*           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
-C0          20      40.08    0.0000  A   3.05240e-01  1.92376e+00
-F            9      19.00    0.0000  A   3.11815e-01  2.55224e-01
-H            1       1.008   0.0000  A   1.06908e-01  6.56888e-02
-HC           1       1.008   0.0000  A   2.64953e-01  6.56888e-02
-H1           1       1.008   0.0000  A   2.47135e-01  6.56888e-02
-H2           1       1.008   0.0000  A   2.29317e-01  6.56888e-02
-H3           1       1.008   0.0000  A   2.11499e-01  6.56888e-02
-HA           1       1.008   0.0000  A   2.59964e-01  6.27600e-02
-H4           1       1.008   0.0000  A   2.51055e-01  6.27600e-02
-H5           1       1.008   0.0000  A   2.42146e-01  6.27600e-02
-HO           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
-HS           1       1.008   0.0000  A   1.06908e-01  6.56888e-02
-HW           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
-HP           1       1.008   0.0000  A   1.95998e-01  6.56888e-02
-I           53     126.9     0.0000  A   4.18722e-01  1.67360e+00
-Cl          17      35.45    0.0000  A   4.40104e-01  4.18400e-01
-Na          11      22.99    0.0000  A   3.32840e-01  1.15897e-02
-IB           0     131.0     0.0000  A   8.90899e-01  4.18400e-01
-MG          12      24.305   0.0000  A   1.41225e-01  3.74342e+00
-N            7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-NA           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-NB           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-NC           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-N2           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-N3           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-N*           7      14.01    0.0000  A   3.25000e-01  7.11280e-01
-O            8      16.00    0.0000  A   2.95992e-01  8.78640e-01
-OW           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
-OH           8      16.00    0.0000  A   3.06647e-01  8.80314e-01
-OS           8      16.00    0.0000  A   3.00001e-01  7.11280e-01
-O2           8      16.00    0.0000  A   2.95992e-01  8.78640e-01
-P           15      30.97    0.0000  A   3.74177e-01  8.36800e-01
-S           16      32.06    0.0000  A   3.56359e-01  1.04600e+00
-SH          16      32.06    0.0000  A   3.56359e-01  1.04600e+00
-CU          29      63.55    0.0000  A   3.39967e-01  3.59824e-01
-FE          26      55.00    0.0000  A   0.00000e+00  0.00000e+00
-K           19      39.10    0.0000  A   4.73602e-01  1.37235e-03
-Rb          37      85.47    0.0000  A   5.26699e-01  7.11280e-04
-Cs          55     132.91    0.0000  A   6.04920e-01  3.37230e-04
-; spc water - use only with spc.itp & settles
-OW_spc       8      15.9994  0.0000  A   3.16557e-01  6.50629e-01
-HW_spc       1       1.0080  0.0000  A   0.00000e+00  0.00000e+00
-Li           3       6.94    0.0000  A   2.02590e-01  7.65672e-02
-Zn          30      65.4     0.0000  A   1.95998e-01  5.23000e-02
-;tip4p-EW
-HW_tip4pew   1       1.008   0.0000  A   0.00000e+00  0.00000e+00
-OW_tip4pew   8      16.00    0.0000  A   3.16435e-01  6.80946e-01
-; tip4p
-HW_tip4p     1       1.008   0.0000  A   0.00000e+00  0.00000e+00
-OW_tip4p     8      16.00    0.0000  A   3.15365e-01  6.48520e-01
-;tip5p
-HW_tip5p     1       1.008   0.0000  A   0.00000e+00  0.00000e+00
-OW_tip5p     8      16.00    0.0000  A   3.12000e-01  6.69440e-01
-; dummy defs
-; MW=Dummy mass for tip4p/EW/5p water extra point charge
-MW           0       0.0000  0.0000  A   0.00000e+00  0.00000e+00
-; Dummy masses for rigid CH3 and NH3 groups
-MCH3         0       0.0000  0.0000  A   0.00000e+00  0.00000e+00
-MNH3         0       0.0000  0.0000  A   0.00000e+00  0.00000e+00
-;
-; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT) 
-;
-CI           6      12.01    0.0000  A   3.39967e-01  4.57730e-01

diff --git a/share/top/amber99sb-ildn-bsc0.ff/forcefield.doc b/share/top/amber99sb-ildn-bsc0.ff/forcefield.doc
deleted file mode 100644 (file)
index 84b35d6..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/forcefield.doc
+++ /dev/null
@@ -1,25 +0,0 @@
-AMBER99SB-ILDN-BSC0 protein, nucleic AMBER94 with ParmBSC0 (Perez et al., Biophys J. 2, 3817–29, 2007)
-
-********************************************************************
-* The original ffamber ports were written by Eric J. Sorin,        *
-* CSU Long Beach, Dept. of Chem & Biochem, and have now been       *
-* integrated with the standard gromacs distribution.               *
-* (Please don't blame Eric for errors we might have introduced.)   *
-* For the implementation/validation, please read/cite:             * 
-* Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493.              *
-* For related material and updates, please consult                 *
-* http://chemistry.csulb.edu/ffamber/                              *
-********************************************************************
-
-AMBER99SB-ILDN FF: Lindorff-Larsen et al., Proteins 78, 1950-58, 2010
-ParmBSC0: Perez et al., Biophys J. 2(11), 3817–3829, 2007
-
-Added the new atomtpye CI plus the bonds, angles (which are the same as CT) and dihedrals for the ParmBSC0 dihedrals, based on work by Thomas Piggot, May 2011, for the AMBER99SB force field.
-
-If you use these parameters please cite, in addition to the original publications of the force fields (AMBER99SB-ILDN and/or ParmBSC0), the following work:
-
-Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study
-Andrew T. Guy, Thomas J. Piggot, and Syma Khalid
-Biophysical Journal Volume 103, Issue 5, 5 September 2012, Pages 1028–1036
-http://dx.doi.org/10.1016/j.bpj.2012.08.012
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/forcefield.itp b/share/top/amber99sb-ildn-bsc0.ff/forcefield.itp
deleted file mode 100644 (file)
index 651b851..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/forcefield.itp
+++ /dev/null
@@ -1,23 +0,0 @@
-********************************************************************
-* The original ffamber ports were written by Eric J. Sorin,        *
-* CSU Long Beach, Dept. of Chem & Biochem, and have now been       *
-* integrated with the standard gromacs distribution.               *
-* (Please don't blame Eric for errors we might have introduced.)   *
-* For the implementation/validation, please read/cite:             * 
-* Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493.              *
-* For related material and updates, please consult                 *
-* http://chemistry.csulb.edu/ffamber/                              *
-********************************************************************
-
-#define _FF_AMBER
-#define _FF_AMBER99SBILDNBSC0
-
-[ defaults ]
-; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
-1               2               yes             0.5     0.8333
-
-#include "ffnonbonded.itp"
-#include "ffbonded.itp"
-#include "gbsa.itp"
-
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/gbsa.itp b/share/top/amber99sb-ildn-bsc0.ff/gbsa.itp
deleted file mode 100644 (file)
index 632e8cb..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/gbsa.itp
+++ /dev/null
@@ -1,38 +0,0 @@
-[ implicit_genborn_params ]
-
-; atype      sar      st     pi       gbr       hct
-;Br           0.1      1      1        0.125     0.85 ; H
-C            0.172    1      1.554    0.1875    0.72 ; C
-CA           0.18     1      1.037    0.1875    0.72 ; C
-CB           0.172    0.012  1.554    0.1875    0.72 ; C
-CC           0.172    1      1.554    0.1875    0.72 ; C
-CN           0.172    0.012  1.554    0.1875    0.72 ; C
-CR           0.18     1      1.073    0.1875    0.72 ; C
-CT           0.18     1      1.276    0.190     0.72 ; C
-CV           0.18     1      1.073    0.1875    0.72 ; C 
-CW           0.18     1      1.073    0.1875    0.72 ; C
-C*           0.172    0.012  1.554    0.1875    0.72 ; C
-H            0.1      1      1        0.115     0.85 ; H
-HC           0.1      1      1        0.125     0.85 ; H
-H1           0.1      1      1        0.125     0.85 ; H
-HA           0.1      1      1        0.125     0.85 ; H
-H4           0.1      1      1        0.115     0.85 ; H
-H5           0.1      1      1        0.125     0.85 ; H
-HO           0.1      1      1        0.105     0.85 ; H
-HS           0.1      1      1        0.125     0.85 ; H
-HP           0.1      1      1        0.125     0.85 ; H
-N            0.155    1      1.028    0.17063   0.79 ; N
-NA           0.155    1      1.028    0.17063   0.79 ; N
-NB           0.155    1      1.215    0.17063   0.79 ; N
-N2           0.16     1      1.215    0.17063   0.79 ; N
-N3           0.16     1      1.215    0.1625    0.79 ; N
-O            0.15     1      0.926    0.148     0.85 ; O
-OH           0.152    1      1.080    0.1535    0.85 ; O
-O2           0.17     1      0.922    0.148     0.85 ; O
-S            0.18     1      1.121    0.1775    0.96 ; S
-SH           0.18     1      1.121    0.1775    0.96 ; S
-
-; masscenters for vsites do not have gbsa parameters
-
-MNH3         0        0      0        0         0
-MCH3         0        0      0        0         0

diff --git a/share/top/amber99sb-ildn-bsc0.ff/ions.itp b/share/top/amber99sb-ildn-bsc0.ff/ions.itp
deleted file mode 100644 (file)
index fe13ab6..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/ions.itp
+++ /dev/null
@@ -1,88 +0,0 @@
-[ moleculetype ]
-; molname       nrexcl
-IB+             1       ; big positive ion
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       IB              1       IB+             IB       1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-CA              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       C0              1       CA              CA       1      2.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-CL              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Cl              1       CL              CL       1      -1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-NA              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Na              1       NA              NA       1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-MG              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       MG              1       MG              MG       1      2.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-K               1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       K               1       K               K        1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-RB              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Rb              1       RB              RB       1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-CS              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Cs              1       CS              CS       1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-LI              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Li              1       LI              LI       1      1.00000
-
-
-[ moleculetype ]
-; molname       nrexcl
-ZN              1
-
-[ atoms ]
-; id    at type         res nr  residu name     at name  cg nr  charge
-1       Zn              1       ZN              ZN       1      2.00000

diff --git a/share/top/amber99sb-ildn-bsc0.ff/rna.arn b/share/top/amber99sb-ildn-bsc0.ff/rna.arn
deleted file mode 100644 (file)
index ed58c40..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/rna.arn
+++ /dev/null
@@ -1,8 +0,0 @@
-RNA  OP1  O1P
-RNA  OP2  O2P
-RNA  H2'  H2'1
-RNA  H2'' H2'2
-RNA  H5'  H5'1
-RNA  H5'' H5'2
-RNA  HO5' H5T
-RNA  HO3' H3T

diff --git a/share/top/amber99sb-ildn-bsc0.ff/rna.hdb b/share/top/amber99sb-ildn-bsc0.ff/rna.hdb
deleted file mode 100644 (file)
index 43aa32d..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/rna.hdb
+++ /dev/null
@@ -1,205 +0,0 @@
-RA5    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RA     9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RA3    10
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RAN    11
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-2      3       H6      N6      C6      C5      
-1      1       H2      C2      N1      N3      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-DT5    9
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DT     8
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-DT3    9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-3      4       H7      C7      C5      C6      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-2      6       H2'     C2'     C1'     C3'     
-1      2       H3T     O3'     C3'     C4'     
-RU5    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RU     9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RU3    10
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RUN    11
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-1      1       H3      N3      C4      C2      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RG5    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RG     9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RG3    10
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RGN    11
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N9      C2'     
-1      1       H8      C8      N9      N7      
-1      1       H1      N1      C6      C2      
-2      3       H2      N2      C2      N1      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RC5    10
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RC     9
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-RC3    10
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     
-RCN    11
-1      2       H5T     O5'     C5'     C4'     
-2      6       H5'     C5'     O5'     C4'     
-1      5       H4'     C4'     C5'     O4'     C3'     
-1      5       H1'     C1'     O4'     N1      C2'     
-1      1       H6      C6      N1      C5      
-1      1       H5      C5      C6      C4      
-2      3       H4      N4      C4      C5      
-1      5       H3'     C3'     C4'     C2'     O3'     
-1      5       H2'1    C2'     C1'     C3'     O2'     
-1      2       HO'2    O2'     C2'     C1'     
-1      2       H3T     O3'     C3'     C4'     

diff --git a/share/top/amber99sb-ildn-bsc0.ff/rna.r2b b/share/top/amber99sb-ildn-bsc0.ff/rna.r2b
deleted file mode 100644 (file)
index 9893f43..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/rna.r2b
+++ /dev/null
@@ -1,6 +0,0 @@
-; rtp residue to rtp building block table
-;GMX   Force-field
-A     RA       RA5     RA3     RAN
-U     RU       RU5     RU3     RUN
-C     RC       RC5     RC3     RCN
-G     RG       RG5     RG3     RGN

diff --git a/share/top/amber99sb-ildn-bsc0.ff/rna.rtp b/share/top/amber99sb-ildn-bsc0.ff/rna.rtp
deleted file mode 100644 (file)
index 0b7f8cb..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/rna.rtp
+++ /dev/null
@@ -1,1232 +0,0 @@
-[ bondedtypes ]
-; Col 1: Type of bond
-; Col 2: Type of angles
-; Col 3: Type of proper dihedrals
-; Col 4: Type of improper dihedrals
-; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
-; Col 6: Number of excluded neighbors for nonbonded interactions
-; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
-; Col 8: Remove impropers over the same bond as a proper if it is 1
-; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
-     1       1          9          4        1         3      1     0
-
-                 
-; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's 
-                
-                        
-[ RA5 ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.03940     9
-   H1'    H2            0.20070    10
-    N9    N*           -0.02510    11
-    C8    CK            0.20060    12
-    H8    H5            0.15530    13
-    N7    NB           -0.60730    14
-    C5    CB            0.05150    15
-    C6    CA            0.70090    16
-    N6    N2           -0.90190    17
-   H61    H             0.41150    18
-   H62    H             0.41150    19
-    N1    NC           -0.76150    20
-    C2    CQ            0.58750    21
-    H2    H5            0.04730    22
-    N3    NC           -0.69970    23
-    C4    CB            0.30530    24
-   C3'    CT            0.20220    25
-   H3'    H1            0.06150    26
-   C2'    CT            0.06700    27
-  H2'1    H1            0.09720    28
-   O2'    OH           -0.61390    29
-  HO'2    HO            0.41860    30
-   O3'    OS           -0.52460    31
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
- [ impropers ]
-    C4    C8    N9   C1'
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1
-                        
-[ RA ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.03940    11
-   H1'    H2            0.20070    12
-    N9    N*           -0.02510    13
-    C8    CK            0.20060    14
-    H8    H5            0.15530    15
-    N7    NB           -0.60730    16
-    C5    CB            0.05150    17
-    C6    CA            0.70090    18
-    N6    N2           -0.90190    19
-   H61    H             0.41150    20
-   H62    H             0.41150    21
-    N1    NC           -0.76150    22
-    C2    CQ            0.58750    23
-    H2    H5            0.04730    24
-    N3    NC           -0.69970    25
-    C4    CB            0.30530    26
-   C3'    CT            0.20220    27
-   H3'    H1            0.06150    28
-   C2'    CT            0.06700    29
-  H2'1    H1            0.09720    30
-   O2'    OH           -0.61390    31
-  HO'2    HO            0.41860    32
-   O3'    OS           -0.52460    33
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'  
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1  
-                        
-[ RA3 ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.03940    11
-   H1'    H2            0.20070    12
-    N9    N*           -0.02510    13
-    C8    CK            0.20060    14
-    H8    H5            0.15530    15
-    N7    NB           -0.60730    16
-    C5    CB            0.05150    17
-    C6    CA            0.70090    18
-    N6    N2           -0.90190    19
-   H61    H             0.41150    20
-   H62    H             0.41150    21
-    N1    NC           -0.76150    22
-    C2    CQ            0.58750    23
-    H2    H5            0.04730    24
-    N3    NC           -0.69970    25
-    C4    CB            0.30530    26
-   C3'    CT            0.20220    27
-   H3'    H1            0.06150    28
-   C2'    CT            0.06700    29
-  H2'1    H1            0.09720    30
-   O2'    OH           -0.61390    31
-  HO'2    HO            0.41860    32
-   O3'    OH           -0.65410    33
-   H3T    HO            0.43760    34
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'  
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1  
-                        
-[ RAN ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.03940     9
-   H1'    H2            0.20070    10
-    N9    N*           -0.02510    11
-    C8    CK            0.20060    12
-    H8    H5            0.15530    13
-    N7    NB           -0.60730    14
-    C5    CB            0.05150    15
-    C6    CA            0.70090    16
-    N6    N2           -0.90190    17
-   H61    H             0.41150    18
-   H62    H             0.41150    19
-    N1    NC           -0.76150    20
-    C2    CQ            0.58750    21
-    H2    H5            0.04730    22
-    N3    NC           -0.69970    23
-    C4    CB            0.30530    24
-   C3'    CT            0.20220    25
-   H3'    H1            0.06150    26
-   C2'    CT            0.06700    27
-  H2'1    H1            0.09720    28
-   O2'    OH           -0.61390    29
-  HO'2    HO            0.41860    30
-   O3'    OH           -0.65410    31
-   H3T    HO            0.43760    32
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    N6
-    C6    N1
-    N6   H61
-    N6   H62
-    N1    C2
-    C2    H2
-    C2    N3
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
- [ impropers ]
-    C4    C8    N9   C1'
-    C6   H61    N6   H62
-    N9    N7    C8    H8
-    N1    N3    C2    H2
-    C5    N6    C6    N1
-                        
-                        
-[ RU5 ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.06740     9
-   H1'    H2            0.18240    10
-    N1    N*            0.04180    11
-    C6    CM           -0.11260    12
-    H6    H4            0.21880    13
-    C5    CM           -0.36350    14
-    H5    HA            0.18110    15
-    C4    C             0.59520    16
-    O4    O            -0.57610    17
-    N3    NA           -0.35490    18
-    H3    H             0.31540    19
-    C2    C             0.46870    20
-    O2    O            -0.54770    21
-   C3'    CT            0.20220    22
-   H3'    H1            0.06150    23
-   C2'    CT            0.06700    24
-  H2'1    H1            0.09720    25
-   O2'    OH           -0.61390    26
-  HO'2    HO            0.41860    27
-   O3'    OS           -0.52460    28
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
- [ impropers ]
-    C2    C6    N1   C1'
-    C6    C4    C5    H5
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ RU ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.06740    11
-   H1'    H2            0.18240    12
-    N1    N*            0.04180    13
-    C6    CM           -0.11260    14
-    H6    H4            0.21880    15
-    C5    CM           -0.36350    16
-    H5    HA            0.18110    17
-    C4    C             0.59520    18
-    O4    O            -0.57610    19
-    N3    NA           -0.35490    20
-    H3    H             0.31540    21
-    C2    C             0.46870    22
-    O2    O            -0.54770    23
-   C3'    CT            0.20220    24
-   H3'    H1            0.06150    25
-   C2'    CT            0.06700    26
-  H2'1    H1            0.09720    27
-   O2'    OH           -0.61390    28
-  HO'2    HO            0.41860    29
-   O3'    OS           -0.52460    30
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    C6    C4    C5    H5
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ RU3 ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.06740    11
-   H1'    H2            0.18240    12
-    N1    N*            0.04180    13
-    C6    CM           -0.11260    14
-    H6    H4            0.21880    15
-    C5    CM           -0.36350    16
-    H5    HA            0.18110    17
-    C4    C             0.59520    18
-    O4    O            -0.57610    19
-    N3    NA           -0.35490    20
-    H3    H             0.31540    21
-    C2    C             0.46870    22
-    O2    O            -0.54770    23
-   C3'    CT            0.20220    24
-   H3'    H1            0.06150    25
-   C2'    CT            0.06700    26
-  H2'1    H1            0.09720    27
-   O2'    OH           -0.61390    28
-  HO'2    HO            0.41860    29
-   O3'    OH           -0.65410    30
-   H3T    HO            0.43760    31
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2 
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    C6    C4    C5    H5
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-[ RUN ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.06740     9
-   H1'    H2            0.18240    10
-    N1    N*            0.04180    11
-    C6    CM           -0.11260    12
-    H6    H4            0.21880    13
-    C5    CM           -0.36350    14
-    H5    HA            0.18110    15
-    C4    C             0.59520    16
-    O4    O            -0.57610    17
-    N3    NA           -0.35490    18
-    H3    H             0.31540    19
-    C2    C             0.46870    20
-    O2    O            -0.54770    21
-   C3'    CT            0.20220    22
-   H3'    H1            0.06150    23
-   C2'    CT            0.06700    24
-  H2'1    H1            0.09720    25
-   O2'    OH           -0.61390    26
-  HO'2    HO            0.41860    27
-   O3'    OH           -0.65410    28
-   H3T    HO            0.43760    29
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    O4
-    C4    N3
-    N3    H3
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
- [ impropers ]
-    C2    C6    N1   C1'
-    C6    C4    C5    H5
-    N1    N3    C2    O2
-    C5    N3    C4    O4
-    C4    C2    N3    H3  
-    N1    C5    C6    H6
-                        
-              
-[ RG5 ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.01910     9
-   H1'    H2            0.20060    10
-    N9    N*            0.04920    11
-    C8    CK            0.13740    12
-    H8    H5            0.16400    13
-    N7    NB           -0.57090    14
-    C5    CB            0.17440    15
-    C6    C             0.47700    16
-    O6    O            -0.55970    17
-    N1    NA           -0.47870    18
-    H1    H             0.34240    19
-    C2    CA            0.76570    20
-    N2    N2           -0.96720    21
-   H21    H             0.43640    22
-   H22    H             0.43640    23
-    N3    NC           -0.63230    24
-    C4    CB            0.12220    25
-   C3'    CT            0.20220    26
-   H3'    H1            0.06150    27
-   C2'    CT            0.06700    28
-  H2'1    H1            0.09720    29
-   O2'    OH           -0.61390    30
-  HO'2    HO            0.41860    31
-   O3'    OS           -0.52460    32
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ RG ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.01910    11
-   H1'    H2            0.20060    12
-    N9    N*            0.04920    13
-    C8    CK            0.13740    14
-    H8    H5            0.16400    15
-    N7    NB           -0.57090    16
-    C5    CB            0.17440    17
-    C6    C             0.47700    18
-    O6    O            -0.55970    19
-    N1    NA           -0.47870    20
-    H1    H             0.34240    21
-    C2    CA            0.76570    22
-    N2    N2           -0.96720    23
-   H21    H             0.43640    24
-   H22    H             0.43640    25
-    N3    NC           -0.63230    26
-    C4    CB            0.12220    27
-   C3'    CT            0.20220    28
-   H3'    H1            0.06150    29
-   C2'    CT            0.06700    30
-  H2'1    H1            0.09720    31
-   O2'    OH           -0.61390    32
-  HO'2    HO            0.41860    33
-   O3'    OS           -0.52460    34
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ RG3 ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.01910    11
-   H1'    H2            0.20060    12
-    N9    N*            0.04920    13
-    C8    CK            0.13740    14
-    H8    H5            0.16400    15
-    N7    NB           -0.57090    16
-    C5    CB            0.17440    17
-    C6    C             0.47700    18
-    O6    O            -0.55970    19
-    N1    NA           -0.47870    20
-    H1    H             0.34240    21
-    C2    CA            0.76570    22
-    N2    N2           -0.96720    23
-   H21    H             0.43640    24
-   H22    H             0.43640    25
-    N3    NC           -0.63230    26
-    C4    CB            0.12220    27
-   C3'    CT            0.20220    28
-   H3'    H1            0.06150    29
-   C2'    CT            0.06700    30
-  H2'1    H1            0.09720    31
-   O2'    OH           -0.61390    32
-  HO'2    HO            0.41860    33
-   O3'    OH           -0.65410    34
-   H3T    HO            0.43760    35
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-[ RGN ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.01910     9
-   H1'    H2            0.20060    10
-    N9    N*            0.04920    11
-    C8    CK            0.13740    12
-    H8    H5            0.16400    13
-    N7    NB           -0.57090    14
-    C5    CB            0.17440    15
-    C6    C             0.47700    16
-    O6    O            -0.55970    17
-    N1    NA           -0.47870    18
-    H1    H             0.34240    19
-    C2    CA            0.76570    20
-    N2    N2           -0.96720    21
-   H21    H             0.43640    22
-   H22    H             0.43640    23
-    N3    NC           -0.63230    24
-    C4    CB            0.12220    25
-   C3'    CT            0.20220    26
-   H3'    H1            0.06150    27
-   C2'    CT            0.06700    28
-  H2'1    H1            0.09720    29
-   O2'    OH           -0.61390    30
-  HO'2    HO            0.41860    31
-   O3'    OH           -0.65410    32
-   H3T    HO            0.43760    33
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N9
-   C1'   C2'
-    N9    C8
-    N9    C4
-    C8    H8
-    C8    N7
-    N7    C5
-    C5    C6
-    C5    C4
-    C6    O6
-    C6    N1
-    N1    H1
-    N1    C2
-    C2    N2
-    C2    N3
-    N2   H21
-    N2   H22
-    N3    C4
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
- [ impropers ]
-    C4    C8    N9   C1'
-    C5    N1    C6    O6
-    C6    C2    N1    H1
-    C2   H21    N2   H22
-    N9    N7    C8    H8
-    N2    N1    C2    N3
-                        
-                   
-[ RC5 ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.00660     9
-   H1'    H2            0.20290    10
-    N1    N*           -0.04840    11
-    C6    CM            0.00530    12
-    H6    H4            0.19580    13
-    C5    CM           -0.52150    14
-    H5    HA            0.19280    15
-    C4    CA            0.81850    16
-    N4    N2           -0.95300    17
-   H41    H             0.42340    18
-   H42    H             0.42340    19
-    N3    NC           -0.75840    20
-    C2    C             0.75380    21
-    O2    O            -0.62520    22
-   C3'    CT            0.20220    23
-   H3'    H1            0.06150    24
-   C2'    CT            0.06700    25
-  H2'1    H1            0.09720    26
-   O2'    OH           -0.61390    27
-  HO'2    HO            0.41860    28
-   O3'    OS           -0.52460    29
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-[ RC ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.00660    11
-   H1'    H2            0.20290    12
-    N1    N*           -0.04840    13
-    C6    CM            0.00530    14
-    H6    H4            0.19580    15
-    C5    CM           -0.52150    16
-    H5    HA            0.19280    17
-    C4    CA            0.81850    18
-    N4    N2           -0.95300    19
-   H41    H             0.42340    20
-   H42    H             0.42340    21
-    N3    NC           -0.75840    22
-    C2    C             0.75380    23
-    O2    O            -0.62520    24
-   C3'    CT            0.20220    25
-   H3'    H1            0.06150    26
-   C2'    CT            0.06700    27
-  H2'1    H1            0.09720    28
-   O2'    OH           -0.61390    29
-  HO'2    HO            0.41860    30
-   O3'    OS           -0.52460    31
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-[ RC3 ]
- [ atoms ]
-     P    P             1.16620     1
-   O1P    O2           -0.77600     2
-   O2P    O2           -0.77600     3
-   O5'    OS           -0.49890     4
-   C5'    CI            0.05580     5
-  H5'1    H1            0.06790     6
-  H5'2    H1            0.06790     7
-   C4'    CT            0.10650     8
-   H4'    H1            0.11740     9
-   O4'    OS           -0.35480    10
-   C1'    CT            0.00660    11
-   H1'    H2            0.20290    12
-    N1    N*           -0.04840    13
-    C6    CM            0.00530    14
-    H6    H4            0.19580    15
-    C5    CM           -0.52150    16
-    H5    HA            0.19280    17
-    C4    CA            0.81850    18
-    N4    N2           -0.95300    19
-   H41    H             0.42340    20
-   H42    H             0.42340    21
-    N3    NC           -0.75840    22
-    C2    C             0.75380    23
-    O2    O            -0.62520    24
-   C3'    CT            0.20220    25
-   H3'    H1            0.06150    26
-   C2'    CT            0.06700    27
-  H2'1    H1            0.09720    28
-   O2'    OH           -0.61390    29
-  HO'2    HO            0.41860    30
-   O3'    OH           -0.65410    31
-   H3T    HO            0.43760    32
- [ bonds ]
-     P   O1P
-     P   O2P
-     P   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
-  -O3'     P
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-[ RCN ]
- [ atoms ]
-   H5T    HO            0.42950     1
-   O5'    OH           -0.62230     2
-   C5'    CI            0.05580     3
-  H5'1    H1            0.06790     4
-  H5'2    H1            0.06790     5
-   C4'    CT            0.10650     6
-   H4'    H1            0.11740     7
-   O4'    OS           -0.35480     8
-   C1'    CT            0.00660     9
-   H1'    H2            0.20290    10
-    N1    N*           -0.04840    11
-    C6    CM            0.00530    12
-    H6    H4            0.19580    13
-    C5    CM           -0.52150    14
-    H5    HA            0.19280    15
-    C4    CA            0.81850    16
-    N4    N2           -0.95300    17
-   H41    H             0.42340    18
-   H42    H             0.42340    19
-    N3    NC           -0.75840    20
-    C2    C             0.75380    21
-    O2    O            -0.62520    22
-   C3'    CT            0.20220    23
-   H3'    H1            0.06150    24
-   C2'    CT            0.06700    25
-  H2'1    H1            0.09720    26
-   O2'    OH           -0.61390    27
-  HO'2    HO            0.41860    28
-   O3'    OH           -0.65410    29
-   H3T    HO            0.43760    30
- [ bonds ]
-   H5T   O5'
-   O5'   C5'
-   C5'  H5'1
-   C5'  H5'2
-   C5'   C4'
-   C4'   H4'
-   C4'   O4'
-   C4'   C3'
-   O4'   C1'
-   C1'   H1'
-   C1'    N1
-   C1'   C2'
-    N1    C6
-    N1    C2
-    C6    H6
-    C6    C5
-    C5    H5
-    C5    C4
-    C4    N4
-    C4    N3
-    N4   H41
-    N4   H42
-    N3    C2
-    C2    O2
-   C3'   H3'
-   C3'   C2'
-   C3'   O3'
-   C2'  H2'1
-   C2'   O2'
-   O2'  HO'2
-   O3'   H3T
- [ impropers ]
-    C2    C6    N1   C1'
-    N1    N3    C2    O2
-    C4   H41    N4   H42
-    N1    C5    C6    H6
-    C6    C4    C5    H5
-    C5    N4    C4    N3
-                        
-

diff --git a/share/top/amber99sb-ildn-bsc0.ff/spc.itp b/share/top/amber99sb-ildn-bsc0.ff/spc.itp
deleted file mode 100644 (file)
index 1e7cae5..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/spc.itp
+++ /dev/null
@@ -1,33 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW_spc      1       SOL       OW       1      -0.82     15.99940
-  2   HW_spc      1       SOL       HW1      1       0.41      1.00800
-  3   HW_spc      1       SOL       HW2      1       0.41      1.00800
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; OW   funct   doh     dhh
-1       1       0.1     0.16330
-
-[ exclusions ]
-1      2       3
-2      1       3
-3      1       2
-
-#else
-
-[ bonds ]
-; i     j       funct   length  force.c.
-1       2       1       0.1     345000  0.1     345000
-1       3       1       0.1     345000  0.1     345000
-
-[ angles ]
-; i     j       k       funct   angle   force.c.
-2       1       3       1       109.47  383     109.47  383
-
-#endif

diff --git a/share/top/amber99sb-ildn-bsc0.ff/spce.itp b/share/top/amber99sb-ildn-bsc0.ff/spce.itp
deleted file mode 100644 (file)
index 7c97bfe..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/spce.itp
+++ /dev/null
@@ -1,33 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW_spc      1       SOL       OW       1      -0.8476   15.99940
-  2   HW_spc      1       SOL       HW1      1       0.4238    1.00800
-  3   HW_spc      1       SOL       HW2      1       0.4238    1.00800
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; OW   funct   doh     dhh
-1       1       0.1     0.16330
-
-[ exclusions ]
-1      2       3
-2      1       3
-3      1       2
-
-#else
-
-[ bonds ]
-; i     j       funct   length  force.c.
-1       2       1       0.1     345000  0.1     345000
-1       3       1       0.1     345000  0.1     345000
-
-[ angles ]
-; i     j       k       funct   angle   force.c.
-2       1       3       1       109.47  383     109.47  383
-
-#endif

diff --git a/share/top/amber99sb-ildn-bsc0.ff/tip3p.itp b/share/top/amber99sb-ildn-bsc0.ff/tip3p.itp
deleted file mode 100644 (file)
index ced4ece..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/tip3p.itp
+++ /dev/null
@@ -1,34 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW          1       SOL       OW       1      -0.834    16.00000
-  2   HW          1       SOL       HW1      1       0.417     1.00800
-  3   HW          1       SOL       HW2      1       0.417     1.00800
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; OW   funct   doh     dhh
-1       1       0.09572 0.15139
-
-[ exclusions ]
-1      2       3
-2      1       3
-3      1       2
-
-#else
-
-[ bonds ]
-; i     j       funct   length  force_constant
-1       2       1       0.09572 502416.0   0.09572        502416.0 
-1       3       1       0.09572 502416.0   0.09572        502416.0 
-        
-
-[ angles ]
-; i     j       k       funct   angle   force_constant
-2       1       3       1       104.52  628.02      104.52  628.02  
-
-#endif

diff --git a/share/top/amber99sb-ildn-bsc0.ff/tip4p.itp b/share/top/amber99sb-ildn-bsc0.ff/tip4p.itp
deleted file mode 100644 (file)
index 3f926ca..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/tip4p.itp
+++ /dev/null
@@ -1,55 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW_tip4p    1       SOL       OW       1       0        16.00000
-  2   HW_tip4p    1       SOL       HW1      1       0.52      1.00800
-  3   HW_tip4p    1       SOL       HW2      1       0.52      1.00800
-  4   MW          1       SOL       MW       1      -1.04      0.00000
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; i    funct   doh     dhh
-1      1       0.09572 0.15139
-
-#else
-
-[ bonds ]
-; i     j       funct   length  force.c.
-1       2       1       0.09572 502416.0 0.09572        502416.0 
-1       3       1       0.09572 502416.0 0.09572        502416.0 
-        
-[ angles ]
-; i     j       k       funct   angle   force.c.
-2       1       3       1       104.52  628.02  104.52  628.02  
-
-#endif
-
-
-[ virtual_sites3 ]
-; Vsite from                    funct   a               b
-4       1       2       3       1       0.128012065     0.128012065
-
-
-[ exclusions ]
-1      2       3       4
-2      1       3       4
-3      1       2       4
-4      1       2       3
-
-
-; The position of the virtual site is computed as follows:
-;
-;              O
-;            
-;              V
-;        
-;      H               H
-;
-; const = distance (OV) / [ cos (angle(VOH))   * distance (OH) ]
-;        0.015 nm      / [ cos (52.26 deg)     * 0.09572 nm    ]
-;
-; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

diff --git a/share/top/amber99sb-ildn-bsc0.ff/tip4pew.itp b/share/top/amber99sb-ildn-bsc0.ff/tip4pew.itp
deleted file mode 100644 (file)
index 571bec6..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/tip4pew.itp
+++ /dev/null
@@ -1,56 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW_tip4pew  1       SOL       OW       1       0        16.00000
-  2   HW_tip4pew  1       SOL       HW1      1       0.52422   1.00800
-  3   HW_tip4pew  1       SOL       HW2      1       0.52422   1.00800
-  4   MW          1       SOL       MW       1      -1.04844   0.00000
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; i    funct   doh     dhh
-1      1       0.09572 0.15139
-
-#else
-[ bonds ]
-; i     j       funct   length  force.c.
-1       2       1       0.09572 502416.0 0.09572        502416.0 
-1       3       1       0.09572 502416.0 0.09572        502416.0 
-        
-[ angles ]
-; i     j       k       funct   angle   force.c.
-2       1       3       1       104.52  628.02  104.52  628.02  
-
-#endif
-
-
-[ virtual_sites3 ]
-; Vsite from                    funct   a               b
-4       1       2       3       1       0.106676721     0.106676721
-
-
-[ exclusions ]
-1      2       3       4
-2      1       3       4
-3      1       2       4
-4      1       2       3
-
-
-; The position of the virtual site is computed as follows:
-;
-;              O
-;            
-;              V
-;        
-;      H               H
-;
-; Ewald tip4p:
-; const = distance (OV) / [ cos (angle(VOH))   * distance (OH) ]
-;        0.0125 nm     / [ cos (52.26 deg)     * 0.09572 nm    ]
-;      then a = b = 0.5 * const = 0.106676721
-;
-; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

diff --git a/share/top/amber99sb-ildn-bsc0.ff/tip5p.itp b/share/top/amber99sb-ildn-bsc0.ff/tip5p.itp
deleted file mode 100644 (file)
index c3120b0..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/tip5p.itp
+++ /dev/null
@@ -1,69 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-SOL            2
-
-[ atoms ]
-; id  at type     res nr  res name  at name  cg nr  charge    mass
-  1   OW_tip5p    1       SOL       OW       1       0        16.00000
-  2   HW_tip5p    1       SOL       HW1      1       0.241     1.00800
-  3   HW_tip5p    1       SOL       HW2      1       0.241     1.00800
-  4   MW          1       SOL       LP1      1      -0.241     0.00000
-  5   MW          1       SOL       LP2      1      -0.241     0.00000
-
-#ifndef FLEXIBLE
-
-[ settles ]
-; i    funct   doh     dhh
-1      1       0.09572 0.15139
-
-#else
-
-[ bonds ]
-; i     j       funct   length  force.c.
-1       2       1       0.09572 502416.0 0.09572        502416.0 
-1       3       1       0.09572 502416.0 0.09572        502416.0 
-        
-[ angles ]
-; i     j       k       funct   angle   force.c.
-2       1       3       1       104.52  628.02  104.52  628.02  
-
-#endif
-
-
-[ virtual_sites3 ]
-; Vsite from                    funct   a               b               c
-4      1       2       3       4        -0.344908262    -0.34490826     -6.4437903493
-5      1       2       3       4        -0.344908262    -0.34490826     6.4437903493
-
-
-[ exclusions ]
-1      2       3       4       5     
-2      1       3       4       5
-3      1       2       4       5
-4      1       2       3       5
-5      1       2       3       4
-
-
-; The positions of the vsites are computed as follows:
-;
-;           LP1 LP2
-;            
-;              O
-;        
-;      H1              H2
-;
-; angle A (H1-O-H2) = 104.52
-; angle B (M1-O-M2) = 109.47
-; dist C (H-O) = 0.09572 nm
-; dist D (M-O) = 0.070 nm
-;
-;atom  x               y               z               
-;O     0.0             0.0             0.0
-;H1    0.585882276     0.756950327     0.0
-;H2    0.585882276     -0.756950327    0.0
-;M1    -0.404151276    0.0             0.571543301
-;M2    -0.404151276    0.0             -0.571543301
-; Dummy pos x4 = x1 + a4*(x2-x1) + b4*(x3-x1) + c4*((x2-x1) x (x3-x1))
-; Dummy pos x5 = x1 + a5*(x2-x1) + b5*(x3-x1) + c5*((x2-x1) x (x3-x1))
-; a4 = b4 = a5 = b5 = (D*cos(B/2)) / (2*C*cos(A/2))  = -0.34490826
-; c5 = -c4 = (D * sin(B/2))/ (C^2 * sin(A)) = 6.4437903

diff --git a/share/top/amber99sb-ildn-bsc0.ff/urea.itp b/share/top/amber99sb-ildn-bsc0.ff/urea.itp
deleted file mode 100644 (file)
index 8cb346a..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/urea.itp
+++ /dev/null
@@ -1,36 +0,0 @@
-[ moleculetype ]
-; molname      nrexcl
-URE            3
-
-[ atoms ]
-     1  C            1  URE     C      1     0.880229  12.01000       ; amber C  type
-     2  O            1  URE     O      2    -0.613359  16.00000       ; amber O  type
-     3  N            1  URE     N1      3    -0.923545  14.01000       ; amber N  type
-     4  H            1  URE    H11      4     0.395055   1.00800       ; amber H  type
-     5  H            1  URE    H12      5     0.395055   1.00800       ; amber H  type
-     6  N            1  URE     N2      6    -0.923545  14.01000       ; amber N  type
-     7  H            1  URE    H21      7     0.395055   1.00800       ; amber H  type
-     8  H            1  URE    H22      8     0.395055   1.00800       ; amber H  type
-
-[ bonds ]
-    1  2
-    1  3       
-    1   6
-    3  4
-    3  5
-    6  7
-    6  8
-[ dihedrals ] 
-;   ai    aj    ak    al funct  definition
-     2     1     3     4   9     
-     2     1     3     5   9     
-     2     1     6     7   9     
-     2     1     6     8   9     
-     3     1     6     7   9     
-     3     1     6     8   9     
-     6     1     3     4   9     
-     6     1     3     5   9     
-[ dihedrals ] 
-     3     6     1     2   4     
-     1     4     3     5   4    
-     1     7     6     8   4

diff --git a/share/top/amber99sb-ildn-bsc0.ff/watermodels.dat b/share/top/amber99sb-ildn-bsc0.ff/watermodels.dat
deleted file mode 100644 (file)
index 420808d..0000000
--- a/share/top/amber99sb-ildn-bsc0.ff/watermodels.dat
+++ /dev/null
@@ -1,5 +0,0 @@
-tip3p    TIP3P     TIP 3-point, recommended
-tip4p    TIP4P     TIP 4-point
-tip4pew  TIP4P-Ew  TIP 4-point optimized with Ewald
-spc      SPC       simple point charge
-spce     SPC/E     extended simple point charge