/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp is in gromacs-data 4.5.5-2.
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1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 | ; New format introduced in Gromacs 3.1.4.
; Dont use this forcefield with earlier versions.
; This residue database includes new reparameterized sidechain dihedrals
; from Kaminski et al (JPCB, 2001) that override the default atomtype-based
; dihedrals. We use set 2 for SER and THR, set 2 for ASP, and the better
; separate dihedrals for LEU and VAL instead of the combined ones, since we
; can specify them here without using introducing extra atom types.
; (That was the reason they were combined in the paper).
; NB: OPLS chargegroups are not strictly neutral, since we mainly
; use them to optimize the neighborsearching. For accurate simulations
; you should use PME.
[ 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 propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
[ ACE ]
[ atoms ]
CH3 opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
[ impropers ]
CH3 +N C O improper_O_C_X_Y
[ ALA ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_135 -0.180 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
HB3 opls_140 0.060 2
C opls_235 0.500 3
O opls_236 -0.500 3
[ 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 improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ AIB ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_225B 0.200 1
CB1 opls_135 -0.180 2
HB11 opls_140 0.060 2
HB12 opls_140 0.060 2
HB13 opls_140 0.060 2
CB2 opls_135 -0.180 3
HB21 opls_140 0.060 3
HB22 opls_140 0.060 3
HB23 opls_140 0.060 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA CB1
CA CB2
CA C
CB1 HB11
CB1 HB12
CB1 HB13
CB2 HB21
CB2 HB22
CB2 HB23
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ ARG ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_308 -0.050 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_307 0.190 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
NE opls_303 -0.700 5
HE opls_304 0.440 5
CZ opls_302 0.640 5
NH1 opls_300 -0.800 6
HH11 opls_301 0.460 6
HH12 opls_301 0.460 6
NH2 opls_300 -0.800 7
HH21 opls_301 0.460 7
HH22 opls_301 0.460 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ARG_chi1_N_C_C_C
CG CB CA C dih_ARG_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD CZ NE HE improper_Z_N_X_Y
NE NH1 CZ NH2 improper_O_C_X_Y
CZ HH11 NH1 HH12 improper_Z_N_X_Y
CZ HH21 NH2 HH22 improper_Z_N_X_Y
[ ARGN ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_308 -0.050 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_748 0.040 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
NE opls_749 -0.620 5
HE opls_304 0.350 5; guessed charge
CZ opls_752 0.550 6
NH1 opls_750 -0.785 6
HH1 opls_301 0.340 6; guessed charge
NH2 opls_751 -0.785 7
HH21 opls_301 0.360 7; guessed charge
HH22 opls_301 0.360 7; guessed charge
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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 HH1
NH2 HH21
NH2 HH22
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD CZ NE HE improper_Z_N_X_Y
NE NH1 CZ NH2 improper_O_C_X_Y
CZ HH21 NH2 HH22 improper_Z_N_X_Y
[ ASN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_235 0.500 3
OD1 opls_236 -0.500 3
ND2 opls_237 -0.760 4
HD21 opls_240 0.380 4
HD22 opls_240 0.380 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ 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 ] ; override some with residue-specific ones
N CA CB CG dih_ASN_chi1_N_C_C_C
CG CB CA C dih_ASN_chi1_C_C_C_CO
CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB ND2 CG OD1 improper_O_C_X_Y
CG HD21 ND2 HD22 improper_Z_N_X_Y
[ ASP ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_274 -0.220 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_271 0.700 3
OD1 opls_272 -0.800 3
OD2 opls_272 -0.800 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ 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 ] ; override some with residue-specific ones
N CA CB CG dih_ASP_chi1_N_C_C_C
CG CB CA C dih_ASP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB OD1 CG OD2 improper_O_C_X_Y
[ ASPH ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_267 0.520 3
OD1 opls_269 -0.530 3
OD2 opls_268 -0.440 4
HD2 opls_270 0.450 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ASP_chi1_N_C_C_C
CG CB CA C dih_ASP_chi1_C_C_C_CO
CB CG OD2 HD2 dih_sidechain_COOH_C_C_O_H
OD1 CG OD2 HD2 dih_sidechain_COOH_O_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB OD1 CG OD2 improper_O_C_X_Y
[ CYS2 ] ; aka CYX
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_214 0.0975 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
SG opls_203 -0.2175 2
C opls_235 0.500 3
O opls_236 -0.500 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB SG dih_CYS_chi1_N_C_C_S
C CA CB SG dih_CYS_chi1_CO_C_C_S
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ CYSH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_206 0.060 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
SG opls_200 -0.335 3
HG opls_204 0.155 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB SG dih_CYS_chi1_N_C_C_S
C CA CB SG dih_CYS_chi1_CO_C_C_S
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ GLN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_235 0.500 4
OE1 opls_236 -0.500 4
NE2 opls_237 -0.760 5
HE21 opls_240 0.380 5
HE22 opls_240 0.380 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ 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
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB CG dih_GLN_chi1_N_C_C_C
CG CB CA C dih_GLN_chi1_C_C_C_CO
CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG NE2 CD OE1 improper_O_C_X_Y
CD HE21 NE2 HE22 improper_Z_N_X_Y
; Charged Glutamine
; See. Patriksson et al. Int. J. Mass. Spectrom. 248 pp 124-135 (2006)
[ QLN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 0.054 3
HG1 opls_140 0.131 3
HG2 opls_140 0.131 3
CD opls_235 0.544 4
OE1 opls_154 -0.496 4
HE1 opls_155 0.498 4
NE2 opls_237 -0.720 5
HE21 opls_240 0.429 5
HE22 opls_240 0.429 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ 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
OE1 HE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB CG dih_GLN_chi1_N_C_C_C
CG CB CA C dih_GLN_chi1_C_C_C_CO
CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
CG CD OE1 HE1 dih_GLN_chi4_C_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG NE2 CD OE1 improper_O_C_X_Y
CD HE21 NE2 HE22 improper_Z_N_X_Y
HE1 OE1 CD NE2 improper_O_C_X_Y
[ GLU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_274 -0.220 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_271 0.700 4
OE1 opls_272 -0.800 4
OE2 opls_272 -0.800 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG OE1 CD OE2 improper_O_C_X_Y
[ PGLU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_274 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_235 0.500 4
OE opls_236 -0.500 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE
CD N
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
; CG OE1 CD OE2 improper_O_C_X_Y
[ GLUH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_267 0.520 4
OE1 opls_269 -0.440 4
OE2 opls_268 -0.530 5
HE2 opls_270 0.450 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
CG CD OE2 HE2 dih_sidechain_COOH_C_C_O_H
OE1 CD OE2 HE2 dih_sidechain_COOH_O_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG OE1 CD OE2 improper_O_C_X_Y
[ GLY ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_223B 0.080 1
HA1 opls_140 0.060 1
HA2 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ HISD ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.297 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_508 -0.261 3
ND1 opls_503 -0.291 4
HD1 opls_504 0.326 4
CD2 opls_507 0.504 5
HD2 opls_146 0.183 5
CE1 opls_506 0.182 6
HE1 opls_146 0.098 6
NE2 opls_511 -0.564 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIS_chi1_N_C_C_C
CG CB CA C dih_HIS_chi1_C_C_C_CO
CA CB CG ND1 dih_HIS_chi2_C_C_C_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
CG CE1 ND1 HD1 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
[ HIS1 ] ; Identical to HISD
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.297 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_508 -0.261 3
ND1 opls_503 -0.291 4
HD1 opls_504 0.326 4
CD2 opls_507 0.504 5
HD2 opls_146 0.183 5
CE1 opls_506 0.182 6
HE1 opls_146 0.098 6
NE2 opls_511 -0.564 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIS_chi1_N_C_C_C
CG CB CA C dih_HIS_chi1_C_C_C_CO
CA CB CG ND1 dih_HIS_chi2_C_C_C_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
CG CE1 ND1 HD1 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
[ HISE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.297 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_507 0.504 3
ND1 opls_511 -0.564 3
CD2 opls_508 -0.261 4
HD2 opls_146 0.183 4
CE1 opls_506 0.182 5
HE1 opls_146 0.098 5
NE2 opls_503 -0.291 6
HE2 opls_504 0.326 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIS_chi1_N_C_C_C
CG CB CA C dih_HIS_chi1_C_C_C_CO
CA CB CG ND1 dih_HIS_chi2_C_C_C_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CE1 CD2 NE2 HE2 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
[ HISH ] ; also known as HISP (or HIS+)
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_510 0.215 3
ND1 opls_512 -0.540 4
HD1 opls_513 0.460 4
CD2 opls_510 0.215 5
HD2 opls_146 0.115 5
CE1 opls_509 0.385 6
HE1 opls_146 0.115 6
NE2 opls_512 -0.540 7
HE2 opls_513 0.460 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIP_chi1_N_C_C_C
CG CB CA C dih_HIP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE1 ND1 HD1 improper_Z_N_X_Y
CE1 CD2 NE2 HE2 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
[ HOH ]
; We believe SPC has slightly better properties than TIP3P...
[ atoms ]
OW opls_116 -0.82 0
HW1 opls_117 0.41 0
HW2 opls_117 0.41 0
[ bonds ]
OW HW1
OW HW2
[ HO4 ]
; TIP4P
[ atoms ]
OW opls_113 0.00 0
HW1 opls_114 0.52 0
HW2 opls_114 0.52 0
MW opls_115 -1.04 0
[ bonds ]
OW HW1
OW HW2
[ HO5 ]
; TIP5P
[ atoms ]
OW opls_118 0.00 0
HW1 opls_119 0.248 0
HW2 opls_119 0.248 0
LP1 opls_120 -0.248 0
LP2 opls_120 -0.248 0
[ bonds ]
OW HW1
OW HW2
[ ILE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_137 -0.060 2
HB opls_140 0.060 2
CG1 opls_136 -0.120 3
HG11 opls_140 0.060 3
HG12 opls_140 0.060 3
CG2 opls_135 -0.180 4
HG21 opls_140 0.060 4
HG22 opls_140 0.060 4
HG23 opls_140 0.060 4
CD opls_135 -0.180 5
HD1 opls_140 0.060 5
HD2 opls_140 0.060 5
HD3 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 CD
CG2 HG21
CG2 HG22
CG2 HG23
CD HD1
CD HD2
CD HD3
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG1 dih_ILE_chi1_N_C_C_C
N CA CB CG2 dih_ILE_chi1_N_C_C_C
CG1 CB CA C dih_ILE_chi1_C_C_C_CO
CG2 CB CA C dih_ILE_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LEU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.060 3
HG opls_140 0.060 3
CD1 opls_135 -0.180 4
HD11 opls_140 0.060 4
HD12 opls_140 0.060 4
HD13 opls_140 0.060 4
CD2 opls_135 -0.180 5
HD21 opls_140 0.060 5
HD22 opls_140 0.060 5
HD23 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ 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 ] ; override some with residue-specific ones
N CA CB CG dih_LEU_chi1_N_C_C_C
CG CB CA C dih_LEU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LYS ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_136 -0.120 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
CE opls_906 0.060 5
HE1 opls_911 0.060 5
HE2 opls_911 0.060 5
NZ opls_900 -0.900 6
HZ1 opls_909 0.360 6
HZ2 opls_909 0.360 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_LYS_chi1_N_C_C_C
CG CB CA C dih_LYS_chi1_C_C_C_CO
CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LYSH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_136 -0.120 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
CE opls_292 0.190 5
HE1 opls_140 0.060 5
HE2 opls_140 0.060 5
NZ opls_287 -0.300 6
HZ1 opls_290 0.330 6
HZ2 opls_290 0.330 6
HZ3 opls_290 0.330 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_LYS_chi1_N_C_C_C
CG CB CA C dih_LYS_chi1_C_C_C_CO
CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ3 dih_LYS_chi5_C_C_N_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ MET ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_210 0.048 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
SD opls_202 -0.335 4
CE opls_209 -0.013 5
HE1 opls_140 0.060 5
HE2 opls_140 0.060 5
HE3 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_MET_chi1_N_C_C_C
CG CB CA C dih_MET_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ NAC ] ; metylamide, a.k.a NMA.
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CH3 opls_242 0.020 2
HH31 opls_140 0.060 2
HH32 opls_140 0.060 2
HH33 opls_140 0.060 2
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ impropers ]
-C CH3 N H improper_Z_N_X_Y
[ NH2 ]
[ atoms ]
N opls_237 -0.760 1
H1 opls_240 0.380 1
H2 opls_240 0.380 1
[ bonds ]
-C N
N H1
N H2
[ impropers ]
-C H1 N H2 improper_Z_N_X_Y
[ NHE ]
; same as NH2
[ atoms ]
N opls_237 -0.760 1
H1 opls_240 0.380 1
H2 opls_240 0.380 1
[ bonds ]
-C N
N H1
N H2
[ impropers ]
-C H1 N H2 improper_Z_N_X_Y
[ PHE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 2
CD1 opls_145 -0.115 3
HD1 opls_146 0.115 3
CD2 opls_145 -0.115 4
HD2 opls_146 0.115 4
CE1 opls_145 -0.115 5
HE1 opls_146 0.115 5
CE2 opls_145 -0.115 6
HE2 opls_146 0.115 6
CZ opls_145 -0.115 7
HZ opls_146 0.115 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ 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
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ HZ
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE2 CD2 HD2 improper_Z_CA_X_Y
CD2 CZ CE2 HE2 improper_Z_CA_X_Y
CE1 CE2 CZ HZ improper_Z_CA_X_Y
CD1 CZ CE1 HE1 improper_Z_CA_X_Y
CG CE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
[ PRO ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
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 N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ SER ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_157 0.145 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
OG opls_154 -0.683 3
HG opls_155 0.418 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB OG dih_SER_THR_chi1_N_C_C_O
C CA CB OG dih_SER_THR_chi1_CO_C_C_O
CA CB OG HG dih_SER_THR_chi2_C_C_OH_HO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ THR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_158 0.205 2
HB opls_140 0.060 2
OG1 opls_154 -0.683 2
HG1 opls_155 0.418 2
CG2 opls_135 -0.180 3
HG21 opls_140 0.060 3
HG22 opls_140 0.060 3
HG23 opls_140 0.060 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB OG1
CB CG2
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB OG1 dih_SER_THR_chi1_N_C_C_O
C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O
CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ TRP ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_500 0.075 3
CD1 opls_514 -0.115 4
HD1 opls_146 0.115 4
CD2 opls_501 -0.055 5
NE1 opls_503 -0.570 6
HE1 opls_504 0.420 6
CE2 opls_502 0.130 6
CE3 opls_145 -0.115 7
HE3 opls_146 0.115 7
CZ2 opls_145 -0.115 8
HZ2 opls_146 0.115 8
CZ3 opls_145 -0.115 9
HZ3 opls_146 0.115 9
CH2 opls_145 -0.115 10
HH2 opls_146 0.115 10
C opls_235 0.500 11
O opls_236 -0.500 11
[ 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
CD2 CE2
CD2 CE3
NE1 HE1
NE1 CE2
CE2 CZ2
CE3 HE3
CE3 CZ3
CZ2 HZ2
CZ2 CH2
CZ3 HZ3
CZ3 CH2
CH2 HH2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_TRP_chi1_N_C_C_C
CG CB CA C dih_TRP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD1 CE2 NE1 HE1 improper_Z_N_X_Y
CE2 CH2 CZ2 HZ2 improper_Z_CA_X_Y
CZ2 CZ3 CH2 HH2 improper_Z_CA_X_Y
CH2 CE3 CZ3 HZ3 improper_Z_CA_X_Y
CZ3 CD2 CE3 HE3 improper_Z_CA_X_Y
CG NE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
[ TYR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 2
CD1 opls_145 -0.115 4
HD1 opls_146 0.115 4
CD2 opls_145 -0.115 5
HD2 opls_146 0.115 5
CE1 opls_145 -0.115 6
HE1 opls_146 0.115 6
CE2 opls_145 -0.115 7
HE2 opls_146 0.115 7
CZ opls_166 0.150 8
OH opls_167 -0.585 8
HH opls_168 0.435 8
C opls_235 0.500 9
O opls_236 -0.500 9
[ 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
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ OH
OH HH
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE2 CD2 HD2 improper_Z_CA_X_Y
CD2 CZ CE2 HE2 improper_Z_CA_X_Y
CD1 CZ CE1 HE1 improper_Z_CA_X_Y
CG CE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
CE1 CE2 CZ OH improper_Z_CA_X_Y
[ VAL ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_137 -0.060 2
HB opls_140 0.060 2
CG1 opls_135 -0.180 3
HG11 opls_140 0.060 3
HG12 opls_140 0.060 3
HG13 opls_140 0.060 3
CG2 opls_135 -0.180 4
HG21 opls_140 0.060 4
HG22 opls_140 0.060 4
HG23 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ 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
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG1 dih_VAL_chi1_N_C_C_C
N CA CB CG2 dih_VAL_chi1_N_C_C_C
CG1 CB CA C dih_VAL_chi1_C_C_C_CO
CG2 CB CA C dih_VAL_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ F ]
[ atoms ]
F opls_400 -1.000 0
[ CL ]
[ atoms ]
CL opls_401 -1.000 0
[ BR ]
[ atoms ]
BR opls_402 -1.000 0
; Aqvists cation parameters
[ LI ]
[ atoms ]
LI opls_406 1.000 0 ; Jorgensen ion type would be opls_404
[ NA ]
[ atoms ]
NA opls_407 1.000 0 ; Jorgensen ion type would be opls_405
[ K ]
[ atoms ]
K opls_408 1.000 0
[ RB ]
[ atoms ]
RB opls_409 1.000 0
[ CS ]
[ atoms ]
CS opls_410 1.000 0
[ MG ]
[ atoms ]
MG opls_411 2.000 0
[ CA ]
[ atoms ]
CA opls_412 2.000 0
[ SR ]
[ atoms ]
SR opls_413 2.000 0
[ BA ]
[ atoms ]
BA opls_414 2.000 0
; Metal ions
[ CU ]
[ atoms ]
CU Cu2+ 2.000 0
[ FE ]
[ atoms ]
FE Fe2+ 2.000 0
[ ZN ]
[ atoms ]
ZN Zn2+ 2.000 0
; And argon...
[ Ar ]
[ atoms ]
Ar Ar 0.000 0
; Ethanol - CA is the carbon bound to the OH group
[ EtOH ]
[ atoms ]
CB opls_135 -0.180 1
HB1 opls_140 0.060 1
HB2 opls_140 0.060 1
HB3 opls_140 0.060 1
CA opls_157 0.145 2
HA1 opls_140 0.060 2
HA2 opls_140 0.060 2
OH opls_154 -0.683 2
HO opls_155 0.418 2
[ bonds ]
CB HB1
CB HB2
CB HB3
CB CA
CA HA1
CA HA2
CA OH
OH HO
; New All atom DMSO model, DvdS, 17/06/2006
; Use at your own risk!
[ DMSO ]
[ atoms ]
OD opls_125 -0.459 1
SD opls_124 0.139 1
CD1 opls_139 -0.020 1
HD11 opls_140 0.060 1
HD12 opls_140 0.060 1
HD13 opls_140 0.060 1
CD2 opls_139 -0.020 1
HD21 opls_140 0.060 1
HD22 opls_140 0.060 1
HD23 opls_140 0.060 1
[ bonds ]
OD SD
SD CD1
SD CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
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