* \\\\\\\\\ QM/MM RTF - FOR GLYCOSIDE WORK ///////// * \\\\\\\\\\\\\\\\\\\\\\\///////////////////////// * Charged sphere modle rtf's by AJ Turner 1995 * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H, same as HN7 MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 ! aromatic H MASS 6 HB 1.00800 ! backbone H MASS 7 HR1 1.00800 ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 ! (+) his HE1 MASS 9 HN1 1.00800 ! Nucleic acid amine proton MASS 10 HN2 1.00800 ! Nucleic acid ring nitrogen proton MASS 11 HN3 1.00800 ! Nucleic acid aromatic carbon proton MASS 12 HN4 1.00800 ! Nucleic acid phosphate hydroxyl proton MASS 13 HN5 1.00800 ! Nucleic acid ribose hydroxyl proton MASS 14 HN6 1.00800 ! Nucleic acid ribose aliphatic proton MASS 15 C 12.01100 ! polar C MASS 16 CV 12.01100 ! aromatic C, CV to avoid QM/MM problems jab93 MASS 17 CT 12.01100 ! tetrahedral C, same as CN7 MASS 18 CPH1 12.01100 ! his CG and CD2 carbons MASS 19 CPH2 12.01100 ! his CE1 carbon MASS 20 CPT 12.01100 ! trp C between rings MASS 21 CY 12.01100 ! TRP C in pyrrole ring MASS 22 CP1 12.01100 ! tetrahedral C (proline CA) MASS 23 CP2 12.01100 ! tetrahedral C (proline CB/CG) MASS 24 CP3 12.01100 ! tetrahedral C (proline CD) MASS 25 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 26 CQ 12.01100 ! carbonyl C for none amides, asp,glu,cter MASS 27 CPA 12.01100 ! heme alpha-C MASS 28 CPB 12.01100 ! heme beta-C MASS 29 CPM 12.01100 ! heme meso-C MASS 30 CM 12.01100 ! heme CO carbon MASS 31 CN1 12.01100 ! Nucleic acid carbonyl carbon MASS 32 CN2 12.01100 ! Nucleic acid aromatic carbon to amide MASS 33 CN3 12.01100 ! Nucleic acid aromatic carbon MASS 34 CN4 12.01100 ! Nucleic acid purine C8 and ADE C2 MASS 35 CN5 12.01100 ! Nucleic acid purine C4 and C5 MASS 36 CN6 12.01100 ! Nucleic acid sp3 ribose ring carbon MASS 37 CN6B 12.01100 ! Nucleic acid sp3 ribose ring carbon, C1' MASS 38 N 14.00700 ! proline N MASS 39 NR1 14.00700 ! neutral his protonated ring nitrogen MASS 40 NR2 14.00700 ! neutral his unprotonated ring nitrogen MASS 41 NR3 14.00700 ! charged his ring nitrogen MASS 42 NH1 14.00700 ! peptide nitrogen MASS 43 NH2 14.00700 ! amide nitrogen MASS 44 NH3 14.00700 ! ammonium nitrogen MASS 45 NC2 14.00700 ! guanidinium nitroogen MASS 46 NY 14.00700 ! TRP N in pyrrole ring MASS 47 NP 14.00700 ! Proline ring NH2+ (N-terminal) MASS 48 NPH 14.00700 ! heme pyrrole N MASS 49 NN1 14.00700 ! Nucleic acid amide nitrogen MASS 50 NN2 14.00700 ! Nucleic acid protonated ring nitrogen MASS 51 NN2U 14.00700 ! Nucleic acid protonated ring nitrogen, ura N3 MASS 52 NN2G 14.00700 ! Nucleic acid protonated ring nitrogen, gua N1 MASS 53 NN3 14.00700 ! Nucleic acid unprotonated ring nitrogen MASS 54 NN4 14.00700 ! Nucleic acid purine N7 MASS 55 NN5 14.00700 ! Nucleic acid sp2 amine nitrogen MASS 56 NN3A 14.00700 ! Nucleic acid unprotonated ring nitrogen, ade N1 + N3 MASS 57 NTL 14.00700 ! ammonium nitrogen MASS 58 NH3L 14.00700 ! nitrogen phosphatidylethanolamine MASS 59 O 15.99900 ! carbonyl oxygen MASS 60 OB 15.99900 ! carbonyl oxygen in acetic acid MASS 61 OC 15.99900 ! carboxylate oxygen MASS 62 OH1 15.99900 ! hydroxyl oxygen MASS 63 OS 15.99940 ! ester oxygen MASS 64 OT 15.99940 ! TIPS3P WATER OXYGEN MASS 65 OM 15.99900 ! heme CO/O2 oxygen MASS 66 ON1 15.99940 ! Nucleic acid carbonyl oxygen MASS 67 ON1C 15.99940 ! Nucleic acid carbonyl oxygen, cyt O2 MASS 68 ON2 15.99940 ! Nucleic acid phosphate ester oxygen MASS 69 ON3 15.99940 ! Nucleic acid =O in phosphate MASS 70 ON4 15.99940 ! Nucleic acid phosphate hydroxyl oxygen MASS 71 ON5 15.99940 ! Nucleic acid ribose hydroxyl oxygen MASS 72 ON6 15.99940 ! Nucleic acid ribose ring oxygen MASS 73 S 32.06000 ! sulphur MASS 74 SM 32.06000 ! sulfur C-S-S-C type MASS 75 CAL 40.08000 ! calcium 2+ MASS 76 ZN 65.37000 ! zinc (II) cation MASS 77 FE 55.84700 ! heme iron 56 MASS 78 P 30.97400 ! phosphorus MASS 79 SOD 22.98977 ! Sodium Ion MASS 80 MG 24.30500 ! Magnesium Ion MASS 81 CLA 34.00000 ! CHLORIDE Anion MASS 100 QQ 1.008 ! Quantum Chemical link atom DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA DECL +P DECL +O1P DECL +O2P DECL +O5' DECL -O3' DEFA FIRS NTER LAST CTER RESI AGLY 0.00000 ! Alpha methyl glycoside - Charge ESP CHELP Gaussian 94 GROUP ! Charged sphere model - no bonding information! ATOM C1 CN6 0.866310 ! Ring Carbon C6-OH ATOM C2 CN6 -0.019778 ! Ring Carbon / \ ATOM C3 CN6 0.999603 ! Ring Carbon HO-C1 C5-(CH3) ATOM O4 ON6 -0.865133 ! Ring Oxygen | | ATOM C5 CN6 0.525168 ! Ring Carbon HO-C2 O4 ATOM C6 CN6 -0.266488 ! Ring Carbon \ / ATOM O7 CN6 -0.602262 ! Ring Carbon C3-O7-(CH3) ATOM C8 CT 0.247046 ! Methyl Carbon ATOM H9 HA 0.022219 ! Methyl Hydrogen ATOM H10 HA 0.028288 ! Methyl Hydrogen ATOM H11 HA 0.003857 ! Methyl Hydrogen ATOM H12 HN6 -0.087810 ! Ring attatched Hydrogen ATOM O13 ON5 -0.726502 ! Hydroxyl Oxygen ATOM O14 ON5 -0.822045 ! Hydroxyl Oxygen ATOM O15 ON5 -0.743705 ! Hydroxyl Oxygen ATOM C16 CT 0.606790 ! Methyl Carbon ATOM O17 ON5 -0.863239 ! Hydrogyl Oxgygen ATOM H18 HN5 0.473744 ! Hydroxyl Hydrogen ATOM H19 HA -0.046764 ! Methyl Hydrogen ATOM H20 HA -0.078857 ! Methyl Hydrogen ATOM H21 HN6 -0.026893 ! Ring attatched Hydrogen ATOM H22 HN5 0.489299 ! Hydroxyl Hydrogen ATOM H23 HN6 0.114930 ! Ring attatched Hydrogen ATOM H24 HN5 0.452162 ! Hydroxyl Hydrogen ATOM H25 HN6 -0.117517 ! Ring attached Hydrogen ATOM H26 HN5 0.384383 ! Hydroxyl Hydrogen ATOM H27 HN6 0.053194 ! Ring attached Hydrogen PATCHING FIRS NONE LAST NONE RESI MTHO 0.00000 ! Metnanol - not bond form - QM only !!!!!!!!!!!!! ATOM H1 HN5 0.489299 ATOM O2 ON5 -0.726502 ATOM C3 CT 0.247046 ATOM H4 HA -0.003281 ! " ATOM H5 HA -0.003281 ! " ATOM H6 HA -0.003281 ! hydroxyly hydrongen PATCHING FIRS NONE LAST NONE RESI MTHE 0.00000 ! Methanol - bullshit test MM force fieied!!!!!!!!!!!!! ATOM H1 HN5 0.489299 ATOM O2 ON5 -0.726502 ATOM C3 CT 0.247046 ATOM H4 HA -0.003281 ! " ATOM H5 HA -0.003281 ! " ATOM H6 HA -0.003281 ! hydroxyly hydrongen BOND H1 O2 BOND O2 C3 BOND C3 H4 BOND C3 H5 BOND C3 H6 PATCHING FIRS NONE LAST NONE RESI TIP3 0.00000 ! tips3p water model, generate using noangle nodihedral GROUP ATOM OH2 OT -0.83400 ! ALLOW WAT ATOM H1 HT 0.41700 ! ALLOW WAT ATOM H2 HT 0.41700 ! ALLOW WAT BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI GION 1.00000 ! methyl glycoside ion - Charges ignored GROUP ! Charged sphere model - no bonding information! ATOM C1 CN6 0.138646 ! Ring Carbon C6-OH ATOM C2 CN6 0.007592 ! Ring Carbon / \ ATOM C3 CN6 0.333086 ! Ring Carbon HO-C1 C5-(CH3) ATOM O4 ON6 -0.191344 ! Ring Oxygen | | ATOM C5 CN6 -0.200855 ! Ring Carbon HO-C2 O4 ATOM C6 CN6 0.006455 ! Ring Carbon \ / ATOM H7 HN6 0.265770 ! Ring attatched Hydrogen C6 ATOM O8 ON5 -0.511777 ! Hydroxyl Oxygen ATOM O9 ON5 -0.592359 ! Hydroxyl Oxygen ATOM O10 ON5 -0.557738 ! Hydroxyl Oxygen ATOM C11 CT 0.099662 ! Methyl Carbon ATOM O12 ON5 -0.538330 ! Hydrogyl Oxgygen ATOM H13 HN5 0.393089 ! Hydroxyl Hydrogen ATOM H14 HA 0.146379 ! Methyl Hydrogen ATOM H15 HA 0.135448 ! Methyl Hydrogen ATOM H16 HN6 0.215937 ! Ring attatched Hydrogen ATOM H17 HN5 0.416024 ! Hydroxyl Hydrogen ATOM H18 HN6 0.160829 ! Ring attatched Hydrogen ATOM H19 HN5 0.418964 ! Hydroxyl Hydrogen ATOM H20 HN6 0.204305 ! Ring attached Hydrogen ATOM H21 HN5 0.426250 ! Hydroxyl Hydrogen ATOM H22 HN6 0.223965 ! Ring attached Hydrogen PATCHING FIRS NONE LAST NONE