From: Mark Abraham Date: Wed, 12 Mar 2014 15:19:14 +0000 (+0100) Subject: Revert "Added new amber99sb-ildn-bsc0 force field." X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=18dc06fdfacc65a597088b1eba4792f7533ac86f;p=alexxy%2Fgromacs.git 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 42fb7a5ee3..c6f6fddc38 100644 --- 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 index 5da55eabf2..0000000000 --- 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 index 50d0742fd4..0000000000 --- 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 index 4df98139c9..0000000000 --- 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 index 50d0742fd4..0000000000 --- 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 index bba55ba8b6..0000000000 --- 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 index efb9077947..0000000000 --- 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 index fa52c67442..0000000000 --- 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 index 91dcef9832..0000000000 --- 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 index ef4db904f7..0000000000 --- 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 index 09f83f7c57..0000000000 --- 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 index 285ec3b21b..0000000000 --- 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 index 1170a78b01..0000000000 --- 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 index 2b4bdd17cd..0000000000 --- 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> 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> 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 index ce59c3b2c4..0000000000 --- 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 index 84b35d6311..0000000000 --- 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 index 651b851f48..0000000000 --- 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 index 632e8cbe13..0000000000 --- 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 index fe13ab6661..0000000000 --- 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 index ed58c405d2..0000000000 --- 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 index 43aa32d9a1..0000000000 --- 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 index 9893f43345..0000000000 --- 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 index 0b7f8cb663..0000000000 --- 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 index 1e7cae5368..0000000000 --- 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 index 7c97bfea4c..0000000000 --- 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 index ced4ece670..0000000000 --- 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 index 3f926ca831..0000000000 --- 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 index 571bec6444..0000000000 --- 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 index c3120b0ed1..0000000000 --- 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 index 8cb346a1a4..0000000000 --- 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 index 420808db5e..0000000000 --- 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