H 1.00800 ; polar H HC 1.00800 ; N-ter H HA 1.00800 ; nonpolar H HT 1.00800 ; TIPS3P WATER HYDROGEN HP 1.00800 ; aromatic H HB 1.00800 ; backbone H HR1 1.00800 ; his he1, (+) his HG,HD2 HR2 1.00800 ; (+) his HE1 HR3 1.00800 ; neutral his HG, HD2 HS 1.00800 ; thiol hydrogen HE1 1.00800 ; for alkene; RHC=CR HE2 1.00800 ; for alkene; H2C=CR HA1 1.00800 ; alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) HA2 1.00800 ; alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) HA3 1.00800 ; alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) HF1 1.00800 ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) HF2 1.00800 ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) C 12.01100 ; carbonyl C, peptide backbone CA 12.01100 ; aromatic C CT1 12.01100 ; aliphatic sp3 C for CH CT2 12.01100 ; aliphatic sp3 C for CH2 CT3 12.01100 ; aliphatic sp3 C for CH3 CPH1 12.01100 ; his CG and CD2 carbons CPH2 12.01100 ; his CE1 carbon CPT 12.01100 ; trp C between rings CY 12.01100 ; TRP C in pyrrole ring CP1 12.01100 ; tetrahedral C (proline CA) CP2 12.01100 ; tetrahedral C (proline CB/CG) CP3 12.01100 ; tetrahedral C (proline CD) CC 12.01100 ; carbonyl C, asn,asp,gln,glu,cter,ct2 CD 12.01100 ; carbonyl C, pres aspp,glup,ct1 CPA 12.01100 ; heme alpha-C CPB 12.01100 ; heme beta-C CPM 12.01100 ; heme meso-C CM 12.01100 ; heme CO carbon CS 12.01100 ; thiolate carbon CE1 12.01100 ; for alkene; RHC=CR CE2 12.01100 ; for alkene; H2C=CR CST 12.01100 ; CO2 carbon CT 12.01100 ; aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) CT1x 12.01100 ; aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) CT2x 12.01100 ; aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) CT3x 12.01100 ; aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) CN 12.01100 ; C for cyano group (see toppar_all22_prot_pyridines.str) CAP 12.01100 ; aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) COA 12.01100 ; carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) C3 12.01100 ; cyclopropyl carbon N 14.00700 ; proline N NR1 14.00700 ; neutral his protonated ring nitrogen NR2 14.00700 ; neutral his unprotonated ring nitrogen NR3 14.00700 ; charged his ring nitrogen NH1 14.00700 ; peptide nitrogen NH2 14.00700 ; amide nitrogen NH3 14.00700 ; ammonium nitrogen NC2 14.00700 ; guanidinium nitroogen NY 14.00700 ; TRP N in pyrrole ring NP 14.00700 ; Proline ring NH2+ (N-terminal) NPH 14.00700 ; heme pyrrole N NC 14.00700 ; N for cyano group (see toppar_all22_prot_pyridines.str) O 15.99900 ; carbonyl oxygen OB 15.99900 ; carbonyl oxygen in acetic acid OC 15.99900 ; carboxylate oxygen OH1 15.99900 ; hydroxyl oxygen OS 15.99940 ; ester oxygen OT 15.99940 ; TIPS3P WATER OXYGEN OM 15.99900 ; heme CO/O2 oxygen OST 15.99900 ; CO2 oxygen OCA 15.99900 ; carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str) S 32.06000 ; sulphur SM 32.06000 ; sulfur C-S-S-C type SS 32.06000 ; thiolate sulfur HE 4.00260 ; helium NE 20.17970 ; neon CF1 12.01100 ; monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) CF2 12.01100 ; difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) CF3 12.01100 ; trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) FE 55.84700 ; heme iron 56 CLAL 35.45300 ; Chlorine Atom (see toppar_all22_prot_aldehydes.str) FA 18.99800 ; aromatic flourine (see toppar_all22_prot_pyridines.str) F1 18.99800 ; Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str) F2 18.99800 ; Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str) F3 18.99800 ; Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str) DUM 0.00000 ; dummy atom HL 1.008000 ; polar H (equivalent to protein H) HCL 1.008000 ; charged H for PE (equivalent to protein HC) HOL 1.008000 ; Nucleic acid phosphate hydroxyl proton HAL1 1.008000 ; alphatic proton HAL2 1.008000 ; alphatic proton HAL3 1.008000 ; alphatic proton HEL1 1.008000 ; for alkene; RHC=CR HEL2 1.008000 ; for alkene; H2C=CR CL 12.011000 ; carbonyl C (acetic acid/methyl acetate) CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-) CTL2 12.011000 ; carbon of methylene group (-CH2-) CTL3 12.011000 ; carbon of methyl group (-CH3) CTL5 12.011000 ; carbon of methyl group (-CH3) for tetramethylammonium CEL1 12.011000 ; for alkene; RHC=CR CEL2 12.011000 ; for alkene; H2C=CR NTL 14.007000 ; ammonium nitrogen NH3L 14.007000 ; nitrogen phosphatidylethanolamine OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; Nucleic acid phosphate ester oxygen O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen PL 30.974000 ; phosphorus SL 32.060000 ; Sulfate sulfur SOD 22.989770 ; Sodium Ion MG 24.305000 ; Magnesium Ion POT 39.102000 ; Potassium Ion! check masses CES 132.900000 ; Cesium Ion CAL 40.080000 ; Calcium Ion CLA 35.450000 ; Chloride Ion ZN 65.370000 ; zinc (II) cation CC1A 12.01100 ; alkene conjugation CC1B 12.01100 ; alkene conjugation CC2 12.01100 ; alkene conjugation NS1 14.00700 ; N for deprotonated Schiff's base NS2 14.00700 ; N for protonated Schiff's base ; extra atomtypes not part of the CHARMM distribution OWT4 15.9994 ; TIP4P O HWT4 1.0080 ; TIP4P H MWT4 0.0000 ; TIP4P vsite OW 15.9994 ; SPC O HW 1.0080 ; SPC H MNH3 0.0000 ; vsite MNH2 0.0000 ; vsite MCH3 0.0000 ; vsite Cu2+ 63.5460 ; Copper Ar 39.9480 ; Argon SI 28.0800 ; Silicon, copied from GROMACS