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| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 03:38:13 -0400 |
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*>>>>>>>>> Combined Residue Topology File for Proteins <<<<<<<<< *>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<< *>>>>>>>>>>>>>>>>>>>>> January 1996 <<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< * These files are a beta release; additional parameter development * and testing may lead to alteration of the contents. * * $Id: //depot/dev/client3/rdock/2013.1/data/cnx.rtf#2 $ * * 30 Apr 1999 (D Morley, RiboTargets) * Modified for RiboDock: * Added hybridisation state tags to comment field * Removed all but the MASS records (added element name) * 22 1 !MASS 1 H 1.00800 H ! polar H (RBT::SP3) !MASS 2 HC 1.00800 H ! N-ter H (RBT::SP3) !MASS 3 HA 1.00800 H ! nonpolar H (RBT::SP3) MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN (RBT::SP3) MASS 5 HP 1.00800 H ! aromatic H (RBT::SP3) MASS 6 HB 1.00800 H ! backbone H (RBT::SP3) MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 (RBT::SP3) MASS 8 HR2 1.00800 H ! (+) his HE1 (RBT::SP3) MASS 9 HR3 1.00800 H ! neutral his HG, HD2 (RBT::SP3) MASS 10 HS 1.00800 H ! thiol hydrogen (RBT::SP3) MASS 11 HA1 1.00800 H ! for alkene; RHC=CR (RBT::SP3) MASS 12 HA2 1.00800 H ! for alkene; H2C=CR (RBT::SP3) !MASS 20 C 12.01100 C ! polar C (RBT::SP3) MASS 21 CA 12.01100 C ! aromatic C (RBT::SP2) MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH (RBT::SP3) MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 (RBT::SP3) MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 (RBT::SP3) MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons (RBT::SP2) MASS 26 CPH2 12.01100 C ! his CE1 carbon (RBT::SP2) MASS 27 CPT 12.01100 C ! trp C between rings (RBT::SP2) !MASS 28 CY 12.01100 C ! TRP C in pyrrole ring (RBT::SP2) MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) (RBT::SP3) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) (RBT::SP3) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) (RBT::SP3) MASS 32 CC 12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu (RBT::SP2) MASS 33 CD 12.01100 C ! carbonyl C for none amides, asp,glu,cter (RBT::SP2) 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 (RBT::SP2) 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 (RBT::SP3) MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen (RBT::TRI) MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen (RBT::SP2) MASS 53 NR3 14.00700 N ! charged his ring nitrogen (RBT::TRI) !MASS 54 NH1 14.00700 N ! peptide nitrogen (RBT::TRI) !MASS 55 NH2 14.00700 N ! amide nitrogen (RBT::TRI) !MASS 56 NH3 14.00700 N ! ammonium nitrogen (RBT::SP3) !MASS 57 NC2 14.00700 N ! guanidinium nitroogen (RBT::TRI) MASS 58 NY 14.00700 N ! TRP N in pyrrole ring (RBT::TRI) MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) (RBT::SP3) MASS 60 NPH 14.00700 N ! heme pyrrole N (RBT::TRI) !MASS 70 O 15.99900 O ! carbonyl oxygen (RBT::SP2) MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid (RBT::SP2) !MASS 72 OC 15.99900 O ! carboxylate oxygen (RBT::SP2) !MASS 73 OH1 15.99900 O ! hydroxyl oxygen (RBT::SP3) MASS 74 OS 15.99940 O ! ester oxygen (RBT::SP3) MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN (RBT::SP3) MASS 76 OM 15.99900 O ! heme CO/O2 oxygen (RBT::SP2) MASS 81 S 32.06000 S ! sulphur (RBT::SP3) !MASS 82 SM 32.06000 S ! sulfur C-S-S-C type (RBT::SP3) MASS 83 SS 32.06000 S ! thiolate sulfur ! ! nucleic acid section !MASS 104 HT 1.008000 ! TIPS3P WATER HYDROGEN MASS 106 HN1 1.008000 H ! Nucleic acid amine proton (RBT::SP3) MASS 107 HN2 1.008000 H ! Nucleic acid ring nitrogen proton (RBT::SP3) MASS 108 HN3 1.008000 H ! Nucleic acid aromatic carbon proton (RBT::SP3) MASS 109 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton (RBT::SP3) MASS 110 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton (RBT::SP3) MASS 111 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton (RBT::SP3) MASS 112 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) (RBT::SP3) MASS 113 HN3B 1.008000 H ! NAD+ aromatic hydrogen (RBT::SP3) MASS 128 CN1 12.011000 C ! Nucleic acid carbonyl carbon (RBT::SP2) MASS 129 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide (RBT::SP2) MASS 130 CN3 12.011000 C ! Nucleic acid aromatic carbon (RBT::SP2) MASS 131 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 (RBT::SP2) MASS 132 CN5 12.011000 C ! Nucleic acid purine C4 and C5 (RBT::SP2) MASS 133 CN6 12.011000 C ! Nucleic acid sp3 ribose ring carbon (RBT::SP3) MASS 134 CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1' (RBT::SP3) MASS 135 CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2' (RBT::SP3) MASS 136 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) (RBT::SP3) MASS 137 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) (RBT::SP3) MASS 138 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) (RBT::SP3) MASS 139 CN3A 12.011000 C ! NAD+ aromatic carbon (RBT::SP2) MASS 140 CN3B 12.011000 C ! NAD+ aromatic carbon (RBT::SP2) MASS 141 CN3C 12.011000 C ! NADH aromatic carbon (RBT::SP2) MASS 142 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC (RBT::SP2) MASS 143 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon (RBT::SP2) MASS 150 NN1 14.007000 N ! Nucleic acid amide nitrogen (RBT::TRI) MASS 151 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen (RBT::TRI) MASS 152 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 (RBT::TRI) MASS 153 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 (RBT::TRI) MASS 154 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen (RBT::SP2) MASS 155 NN4 14.007000 N ! Nucleic acid purine N7 (RBT::SP2) MASS 156 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen (RBT::TRI) MASS 157 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 (RBT::SP2) MASS 158 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 (RBT::SP2) !MASS 164 OT 15.999400 ! TIPS3P WATER OXYGEN MASS 165 ON1 15.999400 O ! Nucleic acid carbonyl oxygen (RBT::SP2) MASS 166 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 (RBT::SP2) MASS 167 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen (RBT::SP3) MASS 168 ON3 15.999400 O ! Nucleic acid =O in phosphate (RBT::SP2) MASS 169 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen (RBT::SP3) MASS 170 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen (RBT::SP3) MASS 171 ON6 15.999400 O ! Nucleic acid ribose ring oxygen (RBT::SP3) MASS 172 ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate (RBT::SP3) MASS 182 P 30.974000 P ! phosphorus (RBT::SP2) MASS 183 P2 30.974000 P ! pyrophosphate phosphorus MASS 192 SOD 22.989770 Na ! Sodium Ion MASS 193 MG 24.305000 Mg ! Magnesium Ion * 1 Nov 2002 (DM) Dummy atom type MASS 666 DUM 0.00000 DU ! Dummy atom !MASS 199 DUM 0.001 ! dummy atom * 9 Dec 2002 (SJ) CNX atom types * types with the same name but not necessarily with the same functionality MASS 701 H 1.00800 H ! polar H (RBT::SP3) MASS 702 HC 1.00800 H ! charged polar H ie in ARG,LYS (RBT::SP3) MASS 703 HA 1.00800 H ! apolar H (RBT::SP3) MASS 704 C 12.01100 C ! amide C (RBT::SP2) MASS 705 CH1E 12.01100 C ! Alpha-carbons with one hydrogen (RBT::SP3) MASS 706 CH2E 12.01100 C ! Carbon with two hydrogens (RBT::SP3) MASS 707 CH3E 12.01100 C ! Carbon with three hydrogens (RBT::SP3) MASS 708 CH2G 12.01100 C ! GLY alpha carbon (RBT::SP3) MASS 709 CH2P 12.01100 C ! Gamma and delta carbons in prolin (RBT::SP3) MASS 710 C5W 12.01100 C ! TRP gamma carbon in pyrrole ring (RBT::SP2) MASS 711 CW 12.01100 C ! TRP CD2 and CE2 at the fuse of the rings (RBT::SP2) MASS 712 CR1E 12.01100 C ! PHE aromatic deltas epss and zeta (RBT::SP2) MASS 713 C5 12.01100 C ! HIS gamma carbon (RBT::SP2) MASS 714 CRH 12.01100 C ! HIS doubly protonated CE1 (RBT::SP2) MASS 715 CR1H 12.01100 C ! HIS delta CD2 (RBT::SP2) MASS 716 CRHH 12.01100 C ! HIS epsilon CE1 (RBT::SP2) MASS 717 CF 12.01100 C ! PHE gamma carbon (RBT::SP2) MASS 718 CY 12.01100 C ! TYR CG (RBT::SP2) MASS 719 CY2 12.01100 C ! TYR CZ (RBT::SP2) MASS 720 N 14.00700 N ! PRO N (RBT::TRI) MASS 721 NR 14.00700 N ! HIS non-protonated ND1 (RBT::SP2) MASS 722 NH1 14.00700 N ! amide N (RBT::TRI) MASS 723 NH2 14.00700 N ! ammonium N (RBT::SP3) MASS 724 NH3 14.00700 N ! charged N (RBT::SP3) MASS 725 NC2 14.00700 N ! guanidinium charged N (RBT::TRI) MASS 726 O 15.99900 O ! carbonyl oxygen (RBT::SP2) MASS 727 OC 15.99900 O ! carboxylate oxygen (RBT::SP2) MASS 728 OH1 15.99900 O ! hydroxyl oxygen (RBT::SP3) MASS 729 SH1E 32.06000 S ! CYS SG (RBT::SP3) MASS 730 SM 32.06000 S ! MET SD (RBT::SP3)