Fixed incorrection AmberGS force field (redmine #728)

Change-Id: Iec340d97851bc08bc8555667df859cb6effc4378

diff --git a/share/top/amberGS.ff/aminoacids.rtp b/share/top/amberGS.ff/aminoacids.rtp
index 870f50c39c97afbc3ad44453b78d2a5f29a9f2b2..87d6581c7fec2082239a39d73f7335ba2b552d41 100644 (file)
--- a/share/top/amberGS.ff/aminoacids.rtp
+++ b/share/top/amberGS.ff/aminoacids.rtp
@@ -1994,7 +1994,6 @@
    CZ3   CD2   CE3   HE3    
     CG   NE1   CD1   HD1    
    CD1    CG    CB   CD2
-
                         
 [ CPHE ]
  [ atoms ]

diff --git a/share/top/amberGS.ff/ffbonded.itp b/share/top/amberGS.ff/ffbonded.itp
index 1dc47515855fc4c95ad170c786abe02d85f9cf58..9ad1fac9aede1db85639c56c23efe28a4f51e44d 100644 (file)
--- a/share/top/amberGS.ff/ffbonded.itp
+++ b/share/top/amberGS.ff/ffbonded.itp
@@ -1,18 +1,5 @@
 [ 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
@@ -123,51 +110,13 @@
 ;  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
+CT  C   OH           1   117.000    585.760 ; 
 N*  C   NA           1   115.400    585.760 ; 
 N*  C   NC           1   118.600    585.760 ; 
 N*  C   O            1   120.900    669.440 ; 
@@ -177,17 +126,17 @@ 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 ; 
+O   C   OH           1   126.000    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
+CA  CA  HA           1   120.000    292.880 ; 
+CA  CA  H4           1   120.000    292.880 ; 
+CB  CA  HA           1   120.000    292.880 ; 
+CB  CA  H4           1   120.000    292.880 ; 
 CB  CA  N2           1   123.500    585.760 ; 
 CB  CA  NC           1   117.300    585.760 ; 
 CM  CA  N2           1   120.100    585.760 ; 
@@ -195,9 +144,9 @@ 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
+C   CA  HA           1   120.000    292.880 ; AA tyr
 N2  CA  N2           1   120.000    585.760 ; AA arg
-CN  CA  HA           1   120.000    418.400 ; new99 trp
+CN  CA  HA           1   120.000    292.880 ; AA 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 ; 
@@ -210,22 +159,22 @@ 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
+H5  CK  N*           1   123.050    292.880 ; 
+H5  CK  NB           1   123.050    292.880 ; 
 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
+C   CM  HA           1   119.700    292.880 ; 
+C   CM  H4           1   119.700    292.880 ; 
 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
+CA  CM  HA           1   123.300    292.880 ; 
+CA  CM  H4           1   123.300    292.880 ; 
 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  HA           1   119.700    292.880 ; 
+CM  CM  H4           1   119.700    292.880 ; 
 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
+H4  CM  N*           1   119.100    292.880 ; 
+H5  CQ  NC           1   115.450    292.880 ; 
 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 ; 
@@ -275,17 +224,17 @@ 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
+H5  CR  NA           1   120.000    292.880 ; AA his
+H5  CR  NB           1   120.000    292.880 ; AA 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  H4           1   120.000    292.880 ; AA 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
+H4  CV  NB           1   120.000    292.880 ; AA his
+CC  CW  H4           1   120.000    292.880 ; AA 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
+H4  CW  NA           1   120.000    292.880 ; AA his
+C*  CW  H4           1   120.000    292.880 ; AA 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
@@ -294,38 +243,38 @@ 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
+C   N   H            1   120.000    251.040 ; AA general, gln, asn,changed based on NMA nmodes
+CT  N   H            1   118.040    251.040 ; AA 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
+C   N*  H            1   119.200    251.040 ; changed based on NMA nmodes
 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
+CB  N*  H            1   125.800    251.040 ; for unmethylated n.a. bases,chngd bsd NMA nmodes
 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
+CK  N*  H            1   128.800    251.040 ; 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
+CM  N*  H            1   121.200    251.040 ; for unmethylated n.a. bases,chngd bsd NMA nmodes
+CA  N2  H            1   120.000    292.880 ; 
 H   N2  H            1   120.000    292.880 ; 
-CT  N2  H            1   118.400    418.400 ; new99 arg
+CT  N2  H            1   118.400    292.880 ; AA 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
+C   NA  H            1   116.800    251.040 ; changed based on NMA nmodes
+CA  NA  H            1   118.000    251.040 ; changed based on NMA nmodes
 CC  NA  CR           1   120.000    585.760 ; AA his
-CC  NA  H            1   120.000    418.400 ; new99 his
+CC  NA  H            1   120.000    251.040 ; AA his,    changed based on NMA nmodes
 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
+CR  NA  H            1   120.000    251.040 ; AA his,    changed based on NMA nmodes
+CW  NA  H            1   120.000    251.040 ; AA his,    changed based on NMA nmodes
 CN  NA  CW           1   111.600    585.760 ; AA trp
-CN  NA  H            1   123.100    418.400 ; new99 trp
+CN  NA  H            1   123.100    251.040 ; AA trp,    changed based on NMA nmodes
 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
@@ -333,7 +282,7 @@ 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
+C   OH  HO           1   113.000    292.880 ; 
 CT  OH  HO           1   108.500    460.240 ; 
 HO  OH  P            1   108.500    376.560 ; 
 CT  OS  CT           1   109.500    502.080 ; 
@@ -349,42 +298,37 @@ CT  S   S            1   103.700    569.024 ; AA cyx             (SCHERAGA  JPC
 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
+F   CT  H1           1   109.500    292.880 ; JCC,13,(1992),963;
 N   C   N            1   120.000    585.760 ; Added for Urea (same as N2-CA-N2) - EJS
 
 [ 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
+;impropers treated as propers in GROMACS to use correct AMBER analytical function
 CB  CK  N*  CT       4      180.00     4.18400     2   ; 
-CK  CB  N*  CT       4      180.00     4.18400     2    ;
+CK  CB  N*  CT       4      180.00     4.18400     2   ; 
+CM  C   N*  CT       4      180.00     4.18400     2    ; dac guess, 9/94
 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   ; 
+C   CM  CM  CT       4      180.00     4.60240     2   ; 
 CT  O   C   OH       4      180.00    43.93200     2   ; 
+CT  CV  CC  NA       4      180.00     4.60240     2   ; 
 NA  CV  CC  CT       4      180.00     4.60240     2   ; 
+CT  CW  CC  NB       4      180.00     4.60240     2   ; 
 NB  CW  CC  CT       4      180.00     4.60240     2   ; 
+CT  CW  CC  NA       4      180.00     4.60240     2    ;
 NA  CW  CC  CT       4      180.00     4.60240     2   ; 
+CB  CT  C*  CW       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
+CM  N2  CA  NC       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  N2  CA  NC       4      180.00     4.60240     2   ; dac, 10/94
 CB  NC  CA  N2       4      180.00     4.60240     2   ; dac, 10/94
+N2  NA  CA  NC       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
@@ -406,94 +350,46 @@ X   X   CA  H5       4      180.00     4.60240     2      ; bsd.on C6H6 nmodes
 
 
 [ dihedraltypes ]
-;i   j   k   l    func 
- CT  CT  OS  CT    9       0.0      1.60247     3  ; 
+;i  j   k  l    func   C0  ...  C5
  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
+ CT  CT  OS  CT    9       0.0      1.60247     3  ; 
+ C   N   CT  C     9       0.0      0.0         1  ; AmberGS
+ N   CT  C   N     9       0.0      0.0         1  ; AmberGS
+ CT  CT  N   C     9       0.0      2.21752     1  ; 
+ CT  CT  N   C     9     180.0      0.62760     3  ; 
+ CT  CT  N   C     9     180.0      2.09200     4  ; 
+ CT  CT  C   N     9       0.0      0.29288     2  ; 
+ CT  CT  C   N     9       0.0      0.41840     4  ; 
  H   N   C   O     9       0.0      8.36800     1  ; J.C.cistrans-NMA DE
+ H   N   C   O     9     180.0     10.46000     2  ; JCC,7,(1986),230
  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
+ OS  CT  CT  OS    9       0.0      4.18400     2  ; pucker anal (93')
+ OS  CT  CT  OS    9       0.0      0.60250     3  ; JCC,7,(1986),230
+ OS  CT  CT  OH    9       0.0      4.18400     2  ; pucker anal (93')
+ OS  CT  CT  OH    9       0.0      0.60250     3  ; JCC,7,(1986),230
+ OH  CT  CT  OH    9       0.0      4.18400     2  ; check glicolWC? puc
+ OH  CT  CT  OH    9       0.0      0.60250     3  ; JCC,7,(1986),230
  OH  P   OS  CT    9       0.0      5.02080     2  ; gg&gt ene.631g*/mp2
- OS  P   OS  CT    9       0.0      1.04600     3  ; JCC,7,(1986),230
+ OH  P   OS  CT    9       0.0      1.04600     3  ; JCC,7,(1986),230
  OS  P   OS  CT    9       0.0      5.02080     2  ; gg&gt ene.631g*/mp2
- OS  CT  N*  CK    9       0.0     10.46000     1  ; parm98, TC,PC,PAK
- OS  CT  N*  CM    9       0.0     10.46000     1  ; parm98, TC,PC,PAK
- H1  CT  C   O     9       0.0      3.34720     1  ; Junmei et al, 1999
- H1  CT  C   O     9     180.0      0.33472     3  ; Junmei et al, 1999
- HC  CT  C   O     9       0.0      3.34720     1  ; Junmei et al, 1999
- HC  CT  C   O     9     180.0      0.33472     3  ; Junmei et al, 1999
- HC  CT  CT  HC    9       0.0      0.62760     3  ; Junmei et al, 1999
- HC  CT  CT  CT    9       0.0      0.66944     3  ; Junmei et al, 1999
- HC  CT  CM  CM    9     180.0      1.58992     3  ; Junmei et al, 1999
- HC  CT  CM  CM    9       0.0      4.81160     1  ; Junmei et al, 1999
- HO  OH  CT  CT    9       0.0      0.66944     3  ; Junmei et al, 1999
- HO  OH  CT  CT    9       0.0      1.04600     1  ; Junmei et al, 1999
- HO  OH  C   O     9     180.0      9.62320     2  ; Junmei et al, 1999
- HO  OH  C   O     9       0.0      7.94960     1  ; Junmei et al, 1999
- CM  CM  C   O     9     180.0      9.10020     2  ; Junmei et al, 1999
- CM  CM  C   O     9       0.0      1.25520     3  ; Junmei et al, 1999
- CT  CM  CM  CT    9     180.0     27.82360     2  ; Junmei et al, 1999
- CT  CM  CM  CT    9     180.0      7.94960     1  ; Junmei et al, 1999
- CT  CT  CT  CT    9       0.0      0.75312     3  ; Junmei et al, 1999
- CT  CT  CT  CT    9     180.0      1.04600     2  ; Junmei et al, 1999
- CT  CT  CT  CT    9     180.0      0.83680     1  ; Junmei et al, 1999
- CT  CT  OS  C     9       0.0      1.60247     3  ; Junmei et al, 1999
- CT  CT  OS  C     9     180.0      3.34720     1  ; Junmei et al, 1999
- CT  OS  CT  OS    9       0.0      0.41840     3  ; Junmei et al, 1999
- CT  OS  CT  OS    9     180.0      3.55640     2  ; Junmei et al, 1999
- CT  OS  CT  OS    9     180.0      5.64840     1  ; Junmei et al, 1999
- O   C   OS  CT    9     180.0     11.29680     2  ; Junmei et al, 1999
- O   C   OS  CT    9     180.0      5.85760     1  ; Junmei et al, 1999
- F   CT  CT  F     9     180.0      5.02080     1  ; Junmei et al, 1999
- Cl  CT  CT  Cl    9     180.0      1.88280     1  ; Junmei et al, 1999
- Br  CT  CT  Br    9       0.0      0.00000     0  ; Junmei et al, 1999
- H1  CT  CT  OS    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  OH    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  F     9       0.0      0.79496     1  ; Junmei et al, 1999
- H1  CT  CT  Cl    9       0.0      1.04600     1  ; Junmei et al, 1999
- H1  CT  CT  Br    9       0.0      2.30120     1  ; Junmei et al, 1999
- HC  CT  CT  OS    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  OH    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  F     9       0.0      0.79496     1  ; Junmei et al, 1999
- HC  CT  CT  Cl    9       0.0      1.04600     1  ; Junmei et al, 1999
- HC  CT  CT  Br    9       0.0      2.30120     1  ; Junmei et al, 1999
- CT  OS  CT  N*    9       0.0      1.60247     3  ; parm98.dat, TC,PC,PAK
- CT  OS  CT  N*    9       0.0      2.71960     2  ; Piotr et al.
- X   C   C   X     9     180.0     15.16700     2  ; Junmei et al, 1999
- X   C   O   X     9     180.0     11.71520     2  ; Junmei et al, 1999
- X   C   OS  X     9     180.0     11.29680     2  ; Junmei et al, 1999
- X   CA  OH  X     9     180.0      3.76560     2  ; Junmei et al, 99
- X   CM  OS  X     9     180.0      4.39320     2  ; Junmei et al, 1999
+ OS  P   OS  CT    9       0.0      1.04600     3  ; JCC,7,(1986),230
+ OS  CT  N*  CK    9       0.0     10.46000     1  ; sugar frag calc (PC)
+ OS  CT  N*  CK    9     180.0      2.09200     2  ; sugar frag calc (PC)
+ OS  CT  N*  CM    9       0.0     10.46000     1  ; sugar frag calc (PC)
+ OS  CT  N*  CM    9     180.0      2.09200     2  ; sugar frag calc (PC)
  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   C   OH  X     9     180.0      3.76560     2  ; JCC,7,(1986),230
+ X   C   CT  X     9       0.0      0.00000     2  ; 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  CT  X     9       0.0      0.00000     2  ; 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
@@ -504,27 +400,27 @@ X   X   CA  H5       4      180.00     4.60240     2      ; bsd.on C6H6 nmodes
  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  CT  X     9       0.0      0.00000     3  ; 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  N   X     9       0.0      0.00000     2  ; JCC,7,(1986),230
+ X   CT  N*  X     9       0.0      0.00000     2  ; JCC,7,(1986),230
+ X   CT  N2  X     9       0.0      0.00000     3  ; 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   C   N   X     9     180.0     10.46000     2  ; AA|check Wendy?&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*  CT  X     9       0.0      0.00000     2  ; 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  CT  X     9       0.0      0.00000     2  ; 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
@@ -534,6 +430,3 @@ X   X   CA  H5       4      180.00     4.60240     2        ; bsd.on C6H6 nmodes
  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
-
-
-

diff --git a/share/top/amberGS.ff/forcefield.itp b/share/top/amberGS.ff/forcefield.itp
index 3a3e597fe490dd5fbd46005f983ea09fe80f3133..38db0dcb316d22380c6c1af68bbec9aee9ef59a7 100644 (file)
--- a/share/top/amberGS.ff/forcefield.itp
+++ b/share/top/amberGS.ff/forcefield.itp
@@ -10,7 +10,7 @@
 ********************************************************************
 
 #define _FF_AMBER
-#define _FF_AMBER96
+#define _FF_AMBER94
 
 [ defaults ]
 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ

diff --git a/share/top/amberGS.ff/gbsa.itp b/share/top/amberGS.ff/gbsa.itp
index f995567fa75f9586413a9876858935d33a0a52b8..e4197c9ab445342b9f41e6528939939ff5bf6651 100644 (file)
--- a/share/top/amberGS.ff/gbsa.itp
+++ b/share/top/amberGS.ff/gbsa.itp
@@ -1,6 +1,7 @@
 [ implicit_genborn_params ]
 
 ; atype      sar      st     pi       gbr       hct
+;H0           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

diff --git a/share/top/amberGS.ff/rna.r2b b/share/top/amberGS.ff/rna.r2b
index 3b6d92f450a075b5b7b99efa9a6a100620bb3cec..9893f43345a5e69401272fc6cc69bbbc8ef08df6 100644 (file)
--- a/share/top/amberGS.ff/rna.r2b
+++ b/share/top/amberGS.ff/rna.r2b
@@ -1,7 +1,6 @@
 ; rtp residue to rtp building block table
 ;GMX   Force-field
 A     RA       RA5     RA3     RAN
-T     RT       RT5     RT3     RTN
 U     RU       RU5     RU3     RUN
 C     RC       RC5     RC3     RCN
 G     RG       RG5     RG3     RGN