*> CHARMM22 All-Hydrogen Topology File for Paracetamol<< *>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<< *>>>>>>>>>>>>>>>>>>>>>> Feb 2009 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * 31 1 ! references ! !PROTEINS ! !MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the !treatment of backbone energetics in protein force fields: limitations !of gas-phase quantum mechanics in reproducing protein conformational !distributions in molecular dynamics simulations, Journal of !Computational Chemistry, 25: 1400-1415, 2004. ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. ! !IONS (see lipid and nucleic acid topology and parameter files for !additional ions ! !ZINC ! !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: !Structure, Function, and Genetics 23:12-31 (1995) ! MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HE1 1.00800 H ! for alkene; RHC=CR MASS 12 HE2 1.00800 H ! for alkene; H2C=CR MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) MASS 20 C 12.01100 C ! carbonyl C, peptide backbone MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR MASS 41 CST 12.01100 C ! CO2 carbon MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str) MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 49 C3 12.01100 C ! cyclopropyl carbon MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str) MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 77 OST 15.99900 O ! CO2 oxygen MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 90 FE 55.84700 Fe ! heme iron 56 MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str) MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str) MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 99 DUM 0.00000 H ! dummy atom !lipid section MASS 101 HL 1.008000 H ! polar H (equivalent to protein H) MASS 102 HCL 1.008000 H ! charged H for PE (equivalent to protein HC) !MASS 103 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 104 HOL 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 105 HAL1 1.008000 H ! alphatic proton MASS 106 HAL2 1.008000 H ! alphatic proton MASS 107 HAL3 1.008000 H ! alphatic proton MASS 108 HEL1 1.008000 H ! for alkene; RHC=CR MASS 109 HEL2 1.008000 H ! for alkene; H2C=CR MASS 110 HBL 1.008000 H ! POPS SER backbone H MASS 120 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate) MASS 121 CTL1 12.011000 C ! sp3 carbon with 1 H (-CH1-) MASS 122 CTL2 12.011000 C ! carbon of methylene group (-CH2-) MASS 123 CTL3 12.011000 C ! carbon of methyl group (-CH3) MASS 124 CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium MASS 125 CEL1 12.011000 C ! for alkene; RHC=CR MASS 126 CEL2 12.011000 C ! for alkene; H2C=CR MASS 127 CCL 12.011000 C ! for POPS MASS 140 NTL 14.007000 N ! ammonium nitrogen MASS 141 NH3L 14.007000 N ! nitrogen phosphatidylethanolamine MASS 160 OBL 15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB) MASS 161 OCL 15.999400 O ! acetate oxygen !MASS 162 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 163 OSL 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 164 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate MASS 165 OHL 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 180 PL 30.974000 P ! phosphorus MASS 185 SL 32.060000 S ! Sulfate sulfur MASS 190 SOD 22.989770 NA ! Sodium Ion MASS 191 MG 24.305000 MG ! Magnesium Ion MASS 192 POT 39.102000 K ! Potassium Ion! check masses MASS 193 CES 132.900000 CS ! Cesium Ion MASS 194 CAL 40.080000 CA ! Calcium Ion MASS 195 CLA 35.450000 CL ! Chloride Ion MASS 196 ZN 65.370000 ZN ! zinc (II) cation !the following masses must be added to the parent RTF for retinol/al MASS 212 CC1A 12.01100 C ! alkene conjugation MASS 213 CC1B 12.01100 C ! alkene conjugation MASS 214 CC2 12.01100 C ! alkene conjugation MASS 220 NS1 14.00700 N ! N for deprotonated Schiff's base MASS 221 NS2 14.00700 N ! N for protonated Schiff's base DEFA FIRS NONE LAST NONE AUTO ANGLES DIHE RESI PAR 0.00 GROUP ATOM CA CT3 -0.27 ! HA1 HD1 HE1 ATOM HA1 HA 0.09 ! | | | ATOM HA2 HA 0.09 ! HA3-CA-HA2 CD1--CE1 ATOM HA3 HA 0.09 ! | // \\ GROUP ! C --N--CG CZ--OH ATOM C C 0.51 ! || | \ __ / \ ATOM O O -0.51 ! O HN CD2--CE2 HH GROUP ! | | ATOM N NH1 -0.65 ! HD2 HE2 ATOM HN H 0.65 GROUP ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 BOND CD2 CG CE1 CD1 BOND CZ CE2 OH CZ BOND N CG N C C CA BOND CA HA1 CA HA2 CA HA3 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH N HN DOUBLE O C CD1 CG CE1 CZ CE2 CD2 IMPR CMAP DONOR HN N DONOR HH OH ACCEPTOR OH ACCEPTOR O C ACCEPTOR N IC END