; 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 [ HISA ] ; HISD in OPLS terminology [ 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 HISA [ 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 [ HISB ] ; HISE in OPLS terminology [ 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 For software reasons, the MW particle should be called HW as well [ atoms ] OW opls_113 0.00 0 HW1 opls_114 0.52 0 HW2 opls_114 0.52 0 HW3 opls_115 -1.04 0 [ bonds ] OW HW1 OW HW2 ; Superfluous bonds are necessary to make pdb2gmx happy OW HW3 [ HO5 ] ; TIP5P. For software reasons, the lone pairs should be called HW as well [ atoms ] HW1 opls_119 0.248 0 HW2 opls_119 0.248 0 HW3 opls_120 -0.248 0 HW4 opls_120 -0.248 0 OW opls_118 0.00 0 [ bonds ] OW HW1 OW HW2 ; Superfluous bonds are necessary to make pdb2gmx happy OW HW3 OW HW4 [ 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