*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<< *>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<< *from *>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< *>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< *and * \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File /////// * \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// * Alexander D. MacKerell Jr. * August 1999 * All comments to ADM jr. email: alex,mmiris.ab.umd.edu * telephone: 410-706-7442 * 27 1 ! ! references ! !PROTEINS ! !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. ! !PHOSPHOTYROSINE ! !Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. !Structural Characterization of the Phosphotyrosine Binding Region of a !High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics !Simulation and Chemical Shift Calculations. Journal of the American !Chemical Society, 1996, 118: 11265-11277. ! !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) ! !references ! !LIPIDS ! !Feller, S. and MacKerell, Jr., A.D. manuscript in preparation ! !and ! !Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M. !Empirical Potential Energy Function for Phospholipids: Criteria for !Parameter Optimization and Applications, in "Biological Membranes: A !Molecular Perspective from Computation and Experiment," K.M. Merz and !B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81. ! !new ALKANES ! !Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach !for the Optimization of Lennard-Jones Parameters. Journal of !Computational Chemistry, 1998, 19: 334-338. ! !ALKENES ! !Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D., !Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: !Parameterization and Comparison with Diffraction Studies. Biophysical !Journal, 73:2269-2279, 1997. ! !new PHOSPHATE ! !MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics !of Dimethylphosphate and its Implications For DNA Structure, Journal !de Chimie Physique, 1997, 94: 1436-1447. ! !IONS ! !all ions from Roux and coworkers ! !Sodium ! !Beglov, D. and Roux, B., Finite Representation of an Infinite !Bulk System: Solvent Boundary Potential for Computer Simulations, !Journal of Chemical Physics, 1994, 100: 9050-9063 ! 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 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 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 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 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 2.01600 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 90 CAL 40.08000 CA ! calcium 2+ MASS 91 ZN 65.37000 ZN ! zinc (II) cation MASS 92 FE 55.84700 Fe ! heme iron 56 MASS 99 DUM 0.00000 H ! dummy atom !lipids 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 3 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 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 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 CLA 35.450000 CL ! CHLORIDE Anion MASS 191 SOD 22.989770 NA ! Sodium Ion MASS 192 MG 24.305000 MG ! Magnesium Ion MASS 193 POT 39.102000 K ! Potassium Ion MASS 194 OST 15.99900 O ! MASS 195 CST 12.01100 C ! !MASS 199 DUM 0.000000 H ! dummy atom RESI HH 0.00 ! Carbon Dioxide, John Straub GROUP ! requires AUTOgenerate ANGLes ATOM HEL HE 0.0 AUTO ANGLES DIHE PATCHING FIRS NONE LAST NONE