1H 1.00800 ; polar H 2HC 1.00800 ; N-ter H 3HA 1.00800 ; nonpolar H 4HT 1.00800 ; TIPS3P WATER HYDROGEN 5HP 1.00800 ; aromatic H 6HB 1.00800 ; backbone H 7HR1 1.00800 ; his he1, (+) his HG,HD2 8HR2 1.00800 ; (+) his HE1 9HR3 1.00800 ; neutral his HG, HD2 10HS 1.00800 ; thiol hydrogen 11HE1 1.00800 ; for alkene; RHC=CR 12HE2 1.00800 ; for alkene; H2C=CR 13HA1 1.00800 ; alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 14HA2 1.00800 ; alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 15HA3 1.00800 ; alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 16HF1 1.00800 ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) 17HF2 1.00800 ; Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) 18C 12.01100 ; carbonyl C, peptide backbone 19CA 12.01100 ; aromatic C 20CT1 12.01100 ; aliphatic sp3 C for CH 21CT2 12.01100 ; aliphatic sp3 C for CH2 22CT3 12.01100 ; aliphatic sp3 C for CH3 23CPH1 12.01100 ; his CG and CD2 carbons 24CPH2 12.01100 ; his CE1 carbon 25CPT 12.01100 ; trp C between rings 26CY 12.01100 ; TRP C in pyrrole ring 27CP1 12.01100 ; tetrahedral C (proline CA) 28CP2 12.01100 ; tetrahedral C (proline CB/CG) 29CP3 12.01100 ; tetrahedral C (proline CD) 30CC 12.01100 ; carbonyl C, asn,asp,gln,glu,cter,ct2 31CD 12.01100 ; carbonyl C, pres aspp,glup,ct1 32CPA 12.01100 ; heme alpha-C 33CPB 12.01100 ; heme beta-C 34CPM 12.01100 ; heme meso-C 35CM 12.01100 ; heme CO carbon 36CS 12.01100 ; thiolate carbon 37CE1 12.01100 ; for alkene; RHC=CR 38CE2 12.01100 ; for alkene; H2C=CR 39CST 12.01100 ; CO2 carbon 40CT 12.01100 ; aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) 41CT1x 12.01100 ; aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 42CT2x 12.01100 ; aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 43CT3x 12.01100 ; aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 44CN 12.01100 ; C for cyano group (see toppar_all22_prot_pyridines.str) 45CAP 12.01100 ; aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) 46COA 12.01100 ; carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) 47C3 12.01100 ; cyclopropyl carbon 48N 14.00700 ; proline N 49NR1 14.00700 ; neutral his protonated ring nitrogen 50NR2 14.00700 ; neutral his unprotonated ring nitrogen 51NR3 14.00700 ; charged his ring nitrogen 52NH1 14.00700 ; peptide nitrogen 53NH2 14.00700 ; amide nitrogen 54NH3 14.00700 ; ammonium nitrogen 55NC2 14.00700 ; guanidinium nitroogen 56NY 14.00700 ; TRP N in pyrrole ring 57NP 14.00700 ; Proline ring NH2+ (N-terminal) 58NPH 14.00700 ; heme pyrrole N 59NC 14.00700 ; N for cyano group (see toppar_all22_prot_pyridines.str) 60O 15.99900 ; carbonyl oxygen 61OB 15.99900 ; carbonyl oxygen in acetic acid 62OC 15.99900 ; carboxylate oxygen 63OH1 15.99900 ; hydroxyl oxygen 64OS 15.99940 ; ester oxygen 65OT 15.99940 ; TIPS3P WATER OXYGEN 66OM 15.99900 ; heme CO/O2 oxygen 67OST 15.99900 ; CO2 oxygen 68OCA 15.99900 ; carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str) 69S 32.06000 ; sulphur 70SM 32.06000 ; sulfur C-S-S-C type 71SS 32.06000 ; thiolate sulfur 72HE 4.00260 ; helium 73NE 20.17970 ; neon 74CF1 12.01100 ; monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) 75CF2 12.01100 ; difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) 76CF3 12.01100 ; trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) 77FE 55.84700 ; heme iron 56 78CLAL 35.45300 ; Chlorine Atom (see toppar_all22_prot_aldehydes.str) 79FA 18.99800 ; aromatic flourine (see toppar_all22_prot_pyridines.str) 80F1 18.99800 ; Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str) 81F2 18.99800 ; Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str) 82F3 18.99800 ; Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str) 83DUM 0.00000 ; dummy atom 84HL 1.008000 ; polar H (equivalent to protein H) 85HCL 1.008000 ; charged H for PE (equivalent to protein HC) 86HOL 1.008000 ; Nucleic acid phosphate hydroxyl proton 87HAL1 1.008000 ; alphatic proton 88HAL2 1.008000 ; alphatic proton 89HAL3 1.008000 ; alphatic proton 90HEL1 1.008000 ; for alkene; RHC=CR 91HEL2 1.008000 ; for alkene; H2C=CR 92CL 12.011000 ; carbonyl C (acetic acid/methyl acetate) 93CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-) 94CTL2 12.011000 ; carbon of methylene group (-CH2-) 95CTL3 12.011000 ; carbon of methyl group (-CH3) 96CTL5 12.011000 ; carbon of methyl group (-CH3) for tetramethylammonium 97CEL1 12.011000 ; for alkene; RHC=CR 98CEL2 12.011000 ; for alkene; H2C=CR 99NTL 14.007000 ; ammonium nitrogen 100NH3L 14.007000 ; nitrogen phosphatidylethanolamine 101OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) 102OCL 15.999400 ; acetate oxygen 103OSL 15.999400 ; Nucleic acid phosphate ester oxygen 104O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate 105OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen 106PL 30.974000 ; phosphorus 107SL 32.060000 ; Sulfate sulfur 108SOD 22.989770 ; Sodium Ion 109MG 24.305000 ; Magnesium Ion 110POT 39.102000 ; Potassium Ion! check masses 111CES 132.900000 ; Cesium Ion 112CAL 40.080000 ; Calcium Ion 113CLA 35.450000 ; Chloride Ion 114ZN 65.370000 ; zinc (II) cation 115CC1A 12.01100 ; alkene conjugation 116CC1B 12.01100 ; alkene conjugation 117CC2 12.01100 ; alkene conjugation 118NS1 14.00700 ; N for deprotonated Schiff's base 119NS2 14.00700 ; N for protonated Schiff's base 120OWT3 15.9994 ; TIP3P 121HWT3 1.0080 ; TIP3P 122OWT4 15.9994 ; TIP4P 123HWT4 1.0080 ; TIP4P 124MWT4 0.0000 ; TIP4P 125OWT5 15.9994 ; TIP5P 126HWT5 1.0080 ; TIP5P 127MWT5 0.0000 ; TIP5P 128MNH3 0.0000 ; vsite (rigid tetrahedrical NH3 group) 129MNH2 0.0000 ; vsite 130MCH3 0.0000 ; vsite (rigid CH3 group connected to carbons) 131MCH3S 0.0000 ; vsite (rigid CH3 group connected to S) 132MW 0.0 ; Dummy mass in rigid tyrosine rings 133; DNA and RNA section 134P 30.974 ; Phosphorus ### For DNA 135P2 30.974000 ; pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) ### For DNA 136P3 30.974000 ; protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) ### For DNA 137HN1 1.008000 ; Nucleic acid amine proton ### For DNA 138HN2 1.008000 ; Nucleic acid ring nitrogen proton ### For DNA 139HN3 1.008000 ; Nucleic acid aromatic carbon proton ### For DNA 140HN3B 1.008000 ; NAD+ aromatic hydrogen ### For DNA 141HN3C 1.008000 ; Standard aromatic hydrogen (as in benzene) ### For DNA 142HNP 1.008000 ; pure aromatic H ### For DNA 143HN4 1.008000 ; Nucleic acid phosphate hydroxyl proton ### For DNA 144HN5 1.008000 ; Nucleic acid ribose hydroxyl proton ### For DNA 145HN6 1.008000 ; Nucleic acid ribose aliphatic proton ### For DNA 146HN7 1.008000 ; Nucleic acid proton (equivalent to protein HA) ### For DNA 147HN8 1.008000 ; Bound to CN8 in nucleic acids/model compounds ### For DNA 148HN9 1.008000 ; Bound to CN9 in nucleic acids/model compounds ### For DNA 149HNE1 1.008000 ; for alkene; RHC=CR (modified thy patch Sasha) ### For DNA 150HNE2 1.008000 ; for alkene; H2C=CR (modified thy patch Sasha) ### For DNA 151CN1 12.011000 ; Nucleic acid carbonyl carbon ### For DNA 152CN1A 12.011000 ; NAD+/NADH amide carbonyl carbon ### For DNA 153CN1T 12.011000 ; Nucleic acid carbonyl carbon (T/U C2) ### For DNA 154CN2 12.011000 ; Nucleic acid aromatic carbon to amide ### For DNA 155CN3 12.011000 ; Nucleic acid aromatic carbon ### For DNA 156CN3A 12.011000 ; NAD+ aromatic carbon ### For DNA 157CN3B 12.011000 ; NAD+ aromatic carbon ### For DNA 158CN3C 12.011000 ; NADH aromatic carbon ### For DNA 159CN3D 12.011000 ; Nucleic acid aromatic carbon for 5MC ### For DNA 160CN3T 12.011000 ; Nucleic acid aromatic carbon, Thy C5 ### For DNA 161CN4 12.011000 ; Nucleic acid purine C8 and ADE C2 ### For DNA 162CN5 12.011000 ; Nucleic acid purine C4 and C5 ### For DNA 163CN5G 12.011000 ; Nucleic acid guanine C5 ### For DNA 164CN7 12.011000 ; Nucleic acid carbon (equivalent to protein CT1) ### For DNA 165CN7B 12.011000 ; Nucleic acid aliphatic carbon for C1' ### For DNA 166CN7C 12.011000 ; C2' in arabinose ### For DNA 167CN7D 12.011000 ; C2' in nucleic acids fluorine derivatives ### For DNA 168CN8 12.011000 ; Nucleic acid carbon (equivalent to protein CT2) ### For DNA 169CN8B 12.011000 ; Nucleic acid carbon (equivalent to protein CT2) ### For DNA 170CN9 12.011000 ; Nucleic acid carbon (equivalent to protein CT3) ### For DNA 171CNE1 12.011000 ; for alkene; RHC=CR (modified thy patch Sasha) ### For DNA 172CNE2 12.011000 ; for alkene; H2C=CR (modified thy patch Sasha) ### For DNA 173CNA 12.011000 ; pure aromatic carbon ### For DNA 174CNA2 12.011000 ; pure aromatic carbon bound to F ### For DNA 175CN6 12.011000 ; carbocyclic sugar (see toppar_all27_na_carbocyclic.str) ### For DNA 176CN7E 12.011000 ; carbocyclic sugar (see toppar_all27_na_carbocyclic.str) ### For DNA 177NN1 14.007000 ; Nucleic acid amide nitrogen ### For DNA 178NN1C 14.007000 ; Nucleic acid imino nitrogen (cyt taut Sasha) ### For DNA 179NN2 14.007000 ; Nucleic acid protonated ring nitrogen ### For DNA 180NN2B 14.007000 ; From NN2, for N9 in GUA different from ADE ### For DNA 181NN2C 14.007000 ; Nucleic acid protonated ring nitrogen (cyt taut Sasha) ### For DNA 182NN2U 14.007000 ; Nucleic acid protonated ring nitrogen, ura N3 ### For DNA 183NN2G 14.007000 ; Nucleic acid protonated ring nitrogen, gua N1 ### For DNA 184NN3 14.007000 ; Nucleic acid unprotonated ring nitrogen ### For DNA 185NN3A 14.007000 ; Nucleic acid unprotonated ring nitrogen, ade N1 and N3 ### For DNA 186NN3I 14.007000 ; Nucleic acid unprotonated ring nitrogen, inosine N3 ### For DNA 187NN3G 14.007000 ; Nucleic acid unprotonated ring nitrogen, gua N3 ### For DNA 188NN4 14.007000 ; Nucleic acid purine N7 ### For DNA 189NN5 14.007000 ; Nucleic acid sp2 amine nitrogen ### For DNA 190NN6 14.007000 ; Nucleic acid sp3 amine nitrogen (equiv to protein nh3) ### For DNA 191ON1 15.999400 ; Nucleic acid carbonyl oxygen ### For DNA 192ON1C 15.999400 ; Nucleic acid carbonyl oxygen, cyt O2 ### For DNA 193ON2 15.999400 ; Nucleic acid phosphate ester oxygen ### For DNA 194ON3 15.999400 ; Nucleic acid =O in phosphate ### For DNA 195ON4 15.999400 ; Nucleic acid phosphate hydroxyl oxygen ### For DNA 196ON5 15.999400 ; Nucleic acid ribose hydroxyl oxygen ### For DNA 197ON6 15.999400 ; Nucleic acid deoxyribose ring oxygen ### For DNA 198ON6B 15.999400 ; Nucleic acid ribose ring oxygen ### For DNA 199ON2B 15.999400 ; Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) ### For DNA 200FN1 18.998400 ; Fluorine for sugar derivatives (NF) ### For DNA 201FNA 18.998400 ; Aromatic fluorine ### For DNA 202CC1A 12.011000 ; alkene conjugation ### For DNA 203CC1B 12.011000 ; alkene conjugation ### For DNA 204CC2 12.011000 ; alkene conjugation ### For DNA 205NS1 14.007000 ; N for deprotonated Schiff's base ### For DNA 206NS2 14.007000 ; N for protonated Schiff's base ### For DNA 207SP 32.060000 ; positive Sulphur, S-adenosylmethionine (SAM) ### For DNA 208CPH1 12.011000 ; For imidazole model compound (NF) 209CPH2 12.011000 ; For imidazole model compound (NF) 210HR3 1.008000 ; For imidazole model compound (NF) 211HR1 1.008000 ; For imidazole model compound (NF) 212NR1 14.007000 ; For nitrogen in imidazol (NF) 213NR2 14.007000 ; For nitrogen in imidazol (NF) 214