*>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<< *>>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<< *from *>>>> CHARMM22 All-Hydrogen Parameter 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 Nucleic Acid Parameter File //// * \\\\\\\\\\\\\\\\\\ Developmental //////////////////////// * Alexander D. MacKerell Jr. and Nicolas Foloppe * August 1999 * All comments to ADM jr. email: alex,mmiris.ab.umd.edu * telephone: 410-706-7442 * ! 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) ! !NUCLEIC ACIDS ! !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and !Condensed Phase Macromolecular Target Data. Journal of Computational !Chemistry, 2000, 21:86-104. ! !and ! !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA !and RNA in Solution. Journal of Computational !Chemistry, 2000, 21:105-120. ! !NAD(P)+, NAD(P)H and PPI ! !Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A !Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate !Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: !221-239. ! !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 ! BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! ! from lipids ! from CHARMm23 guessed parameters ! Rommie Jerome CC CPH1 252.000 1.483 CPH1 NC2 360.833 1.412 CN7 CTL3 262.625 1.506 CT2 CTL3 230.594 1.519 C HC 330.000 1.100 !lipids section CTL3 CL 200.0 1.522 ! methyl acetate CTL2 CL 200.0 1.522 ! methyl acetate CTL1 CL 200.0 1.522 ! methyl acetate OBL CL 750.0 1.220 ! methyl acetate OCL CL 525.0 1.260 ! acetate, protein OSL CL 150.0 1.334 ! methyl acetate OHL CL 230.0 1.40 ! methyl acetate HOL OHL 545.0 0.960 ! acetic acid CTL1 HAL1 309.00 1.111 ! alkanes, 3/92 CTL2 HAL2 309.00 1.111 ! alkanes, 4/98 CTL3 HAL3 322.00 1.111 ! alkanes, 4/98 CTL3 OSL 340.0 1.43 ! phosphate CTL2 OSL 340.0 1.43 ! phosphate CTL1 OSL 340.0 1.43 ! phosphate OSL PL 270.0 1.60 ! phosphate O2L PL 580.0 1.48 ! phosphate OHL PL 237.0 1.59 ! phosphate NH3L HCL 410.0 1.04 ! ethanolamine NH3L CTL2 261.0 1.51 ! ethanolamine NTL CTL2 215.00 1.51 ! tetramethylammonium NTL CTL5 215.00 1.51 ! tetramethylammonium CTL5 HL 300.00 1.08 ! tetramethylammonium CTL2 HL 300.00 1.08 ! tetramethylammonium CTL1 CTL1 222.500 1.500 ! alkanes, 3/92 CTL1 CTL2 222.500 1.538 ! alkanes, 3/92 CTL1 CTL3 222.500 1.538 ! alkanes, 3/92 CTL2 CTL2 222.500 1.530 ! alkanes, 3/92 CTL2 CTL3 222.500 1.528 ! alkanes, 3/92 CTL3 CTL3 222.500 1.530 ! alkanes, 3/92 OHL CTL1 428.0 1.420 ! glycerol OHL CTL2 428.0 1.420 ! glycerol OHL CTL3 428.0 1.420 ! glycerol SL O2L 540.0 1.448 ! methylsulfate SL OSL 250.0 1.575 ! methylsulfate !HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) !HT OT 450.0 0.9572 ! from TIPS3P geometry CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95 HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95 CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95 CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95 HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95 CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95 CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95 ! C C 600.000 1.3350 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) CA CA 305.000 1.3750 ! ALLOW ARO ! benzene, JES 8/25/89 CE1 CE1 440.000 1.3400 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CE2 500.000 1.3420 ! ! for propene, yin/adm jr., 12/95 CE1 CT2 365.000 1.5020 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CT3 383.000 1.5040 ! ! for butene, yin/adm jr., 12/95 CE2 CE2 510.000 1.3300 ! ! for ethene, yin/adm jr., 12/95 CP1 C 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CC 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CD 200.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 222.500 1.5270 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPB C 450.000 1.3800 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPA 299.800 1.4432 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB CPB 340.700 1.3464 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 CPH1 410.000 1.3600 ! ALLOW ARO ! histidine, adm jr., 6/27/90 CPM CPA 360.000 1.3716 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA 305.000 1.3680 ! ALLOW ARO ! adm jr., 12/30/91, for jwk CPT CPT 360.000 1.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT1 222.500 1.5000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT2 CA 230.000 1.4900 ! ALLOW ALI ARO ! phe,tyr, JES 8/25/89 CT2 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT2 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT2 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT3 CA 230.000 1.4900 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 CT3 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT3 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT3 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT3 CS 190.000 1.5310 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 222.500 1.5280 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT3 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CY CA 350.000 1.3650 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CY CPT 350.000 1.4400 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 230.000 1.5100 ! ALLOW ARO !JWK Kb from alkane freq.. b0 from TRP crystal FE CM 258.000 1.9000 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) FE CPM 0.000 3.3814 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) H CD 330.000 1.1100 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA C 330.000 1.1000 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) HA CA 340.000 1.0830 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CC 317.130 1.1000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations HA CP2 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM 367.600 1.0900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CS 300.000 1.1110 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY 330.000 1.0800 ! ALLOW ARO ! JWK 05/14/91 new r0 from indole HE1 CE1 360.500 1.1000 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 365.000 1.1000 ! ! for ethene, yin/adm jr., 12/95 HB CP1 330.000 1.0800 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HP CA 340.000 1.0800 ! ALLOW ARO ! phe,tyr JES 8/25/89 HP CY 350.000 1.0800 ! ALLOW ARO !adm jr., 12/30/91, for jwk HR1 CPH1 375.000 1.0830 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 340.000 1.0900 ! ALLOW ARO ! his, adm jr., 6/28/29 HR2 CPH2 333.000 1.0700 ! ALLOW ARO ! his, adm jr., 6/27/90 HR3 CPH1 365.000 1.0830 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HT HT 0.000 1.5139 ! ALLOW WAT ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 320.000 1.4340 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 320.000 1.4550 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO ! 403.0->463.0, 1.305->1.365 guanidinium (KK) NC2 CT2 261.000 1.4900 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 261.000 1.4900 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NC2 HC 455.000 1.0000 ! ALLOW POL ! 405.0->455.0 GUANIDINIUM (KK) NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO ! (DS) NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide NH2 CT2 240.000 1.4550 ! from NH2 CT3, neutral glycine, adm jr. NH2 CT3 240.000 1.4550 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH2 H 480.000 1.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 HC 460.000 1.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT3 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 320.000 1.4850 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 320.000 1.5020 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP HC 460.000 1.0060 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA 377.200 1.3757 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE 270.200 1.9580 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH2 400.000 1.3600 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 H 466.000 1.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH2 400.000 1.3200 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 FE 65.000 2.2000 ! ALLOW HEM ! Heme (6-liganded): His ligand (KK 05/13/91) NR3 CPH1 380.000 1.3700 ! ALLOW ARO ! his, adm jr., 6/28/90 NR3 CPH2 380.000 1.3200 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 H 453.000 1.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA 270.000 1.3700 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT 270.000 1.3750 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY H 465.000 0.9760 ! ALLOW ARO ! indole JWK 08/28/89 O C 620.000 1.2300 ! ALLOW PEP POL ARO ! Peptide geometry, condensed phase (LK) O CC 650.000 1.2300 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide OB CC 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid vibrations and geom. OB CD 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 8/27/91, phenoxide OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid OC CT2 450.000 1.3300 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 450.000 1.3300 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA 334.300 1.4110 ! ALLOW ARO ALC ! MeOH, EMB 10/10/89, OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC ! adm jr. 5/02/91, acetic acid pure solvent OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 H 545.000 0.9600 ! ALLOW ALC ARO ! EMB 11/21/89 methanol vib fit OM CM 1115.000 1.1280 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) OM FE 250.000 1.8000 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OM OM 600.000 1.2300 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OS CD 150.000 1.3340 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent OS CT3 340.000 1.4300 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OT HT 450.000 0.9572 ! ALLOW WAT ! FROM TIPS3P GEOM ! Modified for CYG residue after 6-31G** geometry optimization Felix S CC 240.000 1.7814 ! ALLOW ALI SUL ION !S CC 240.000 1.8160 ! ALLOW ALI SUL ION ! Modified for CYG residue S CT2 198.000 1.8180 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S CT3 240.000 1.8160 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S HS 275.000 1.3250 ! ALLOW SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 SM CT2 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM CT3 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM SM 173.000 2.0290 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SS CS 205.000 1.8360 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. !nucleic acid section ! !NICH parameters to maintain back compatibility following !atom type switch from HN3 to HN6 CN3C HN6 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 CN3 HN6 350.0 1.09 !nadh, adm jr., 8/98 ! CN1 CN3 302.0 1.409 !U, adm jr. 11/97 CN1 CN3T 302.0 1.403 !T, adm jr. 11/97 CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95 CN1 CN5G 302.0 1.360 !G, adm jr. 11/97 CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN1 NN2 380.0 1.367 !C, adm jr. 11/97 CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97 CN1 NN2G 340.0 1.396 !G, adm jr. 11/97 CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97 CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97 CN1 NN3 350.0 1.335 !C, adm jr. 11/97 CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91 CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91 CN2 CN3 320.0 1.406 !C, adm jr. 11/97 CN2 CN3D 260.0 1.405 !5mc, adm jr. 9/9/93, from cn2 cn3 CN2 CN5 360.0 1.358 !A, adm jr. 11/97 CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91 CN2 NN2G 400.0 1.392 !G CN2 NN3 450.0 1.343 !C CN2 NN3A 400.0 1.342 !A, adm jr. 11/97 CN2 NN3G 320.0 1.326 !G, adm jr. 11/97 CN3 CN3 500.0 1.326 !C,U adm jr. 11/97 CN3 CN3T 560.0 1.320 !T, adm jr. 11/97 CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 560.0 1.335 !5mc, adm jr. 9/9/93, from cn3 cn3 CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN9 230.0 1.480 !5mc, adm jr. 9/9/93, from cn3 cn9 CN3T CN9 230.0 1.478 !T, adm jr. 11/97 CN3 HN3 350.0 1.09 !C,U, JWK CN3T HN3 350.0 1.09 !T, JWK CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 CN3 NN2 302.0 1.343 !C, adm jr. 11/97 CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97 CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95 CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91 CN4 NN2 320.0 1.374 !A, adm jr. 11/97 CN4 NN2B 300.0 1.378 !G, adm jr. 11/97 CN4 NN2G 350.0 1.365 !Inosine, adm jr. 2/94 CN4 NN3A 420.0 1.322 !A, adm jr. 11/97 CN4 NN3I 450.0 1.295 !Inosine, adm jr. 2/94 CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97 CN5 CN5 310.0 1.361 !A, adm jr. 11/97 CN5 CN5G 320.0 1.350 !G, adm jr. 11/97 CN5 NN2 300.0 1.375 !A, adm jr. 11/97 CN5 NN2B 302.0 1.375 !G, adm jr. 11/97 CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91 CN5 NN3G 350.0 1.315 !G, adm jr. 11/97 CN5 NN3I 350.0 1.332 !Inosine, adm jr. 9/98 CN5 NN4 310.0 1.355 !A, adm jr. 11/97 CN5G NN4 310.0 1.365 !G, adm jr. 11/97 CN8 CN8 222.50 1.528 !Alkanes, sacred CN8 CN9 222.50 1.528 !Alkanes, sacred CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR. CN8 ON5 428.0 1.42 !RIBOSE, MeOH CN9 HN9 322.0 1.111 !alkanes CN9 ON2 340.0 1.43 !DMP, ADM Jr. HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91 HN2 NN2 474.0 1.01 !C,U, JWK HN2 NN2B 474.0 1.01 !G, adm jr. 11/97 HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91 HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91 HN4 ON4 545.0 0.960 !MP_1, ADM Jr. !HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) !HT OT 450.0 0.9572 ! from TIPS3P geometry ON2 P 270.0 1.60 !DMP, ADM Jr. ON3 P 580.0 1.48 !DMP, ADM Jr. ON4 P 237.0 1.58 !MP_1, ADM Jr. ON2 P2 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95 NN5 HN1 460.0 1.01 !sugar model, adm jr. !@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@ CN7B ON6 260.0 1.420 ! From exp CN7B CN8 200.0 1.518 ! From exp CN7 ON6 240.0 1.446 ! Fom exp. CN7 CN8 222.5 1.516 ! From exp. CN7 CN7 222.5 1.529 ! From exp CN7 HN7 309.0 1.111 !Alkanes, sacred CN8 HN8 309.0 1.111 !Alkanes, sacred CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF) !@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@ !@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@ CN7B ON6B 260.0 1.420 ! From CN7B ON6 CN7 ON6B 240.0 1.480 ! From CN7 ON6 CN7B CN7B 200.0 1.450 ! CN7 CN7B 222.5 1.460 ! Specific to RNA !@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@ !@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@ ! Transfered from DNA CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8 CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8 CN7C HN7 309.0 1.111 ! From CN8 HN7 !@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@ CN7 CN8B 222.5 1.512 ! From exp. CN8B ON2 320.0 1.44 ! From exp !CN8B ON5 250.0 1.44 ! From CN8B ON2 CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 CN7 ON2 310.0 1.433 ! From exp CN7B ON2 310.0 1.433 ! From exp, for NADPH etc. !CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 ! C1'-N9 (purines)/C1'-N1 (pyrimidines) CN9 NN2 400.0 1.456 !9-M-A/C, adm jr. CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. CN7B NN2 220.0 1.456 !A/C CN7B NN2B 220.0 1.458 !G/T/U ! C5'-H in model compounds and DNA CN8B HN8 309.0 1.111 !Alkanes, sacred ON5 HN5 545.0 0.960 !RIBOSE, MeOH !@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@ !CN7B ON5 250.0 1.400 ! From CN7 ON5 CN7B ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@ !CN7C ON5 250.0 1.400 ! From CN7 ON5 CN7C ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@ !@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@ CN8 ON2 340.0 1.44 ! !@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@ ! C1'-ND1 in imidazole model compound CN7B NR1 220.000 1.4620 ! From crystal nucleosides A/G (NF) !NR1 CPH1 400.000 1.3800 ! From imidazole (NF) !NR1 CPH2 400.000 1.3600 ! From imidazole (NF) !NR2 CPH1 400.000 1.3800 ! From imidazole (NF) !NR2 CPH2 400.000 1.3200 ! From imidazole (NF) !CPH1 CPH1 410.000 1.3600 ! From imidazole (NF) !HR1 CPH2 340.000 1.0900 ! From imidazole (NF) !HR3 CPH1 365.000 1.0830 ! From imidazole (NF) ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! ! from lipids ! from CHARMm23 guessed parameters ! Rommie Jerome O CC CPH1 31.250 120.250 NH2 CC CPH1 57.500 115.500 CC CPH1 CPH1 45.800 130.000 CC CPH1 NR2 87.900 115.000 CPH1 CPH1 NC2 135.000 108.000 NR1 CPH1 NC2 62.794 120.765 CPH1 NC2 C 62.300 120.000 CN7 CN7 CTL3 60.000 100.000 ON6B CN7 CTL3 100.000 110.000 CTL3 CN7 HN7 37.265 109.050 CN7 CTL3 OSL 40.241 109.761 CN7 CTL3 HAL3 36.106 110.260 NC2 C HC 60.100 118.185 NC2 CT2 C 53.800 108.167 CT2 C CT2 70.000 121.500 C CT2 OH1 75.700 110.100 CT2 CT2 CTL3 58.070 111.520 OH1 CT2 CTL3 73.56 112.480 CTL3 CT2 HA 36.790 109.664 CT2 CTL3 OSL 40.241 109.761 CT2 CTL3 HAL3 36.106 110.260 ! END OF CHARMM-GUESSED PARAMETERS ! Modified for CYG residue after 6-31G** geometry optimization Felix CT2 S CC 34.000 100.2000 ! ALLOW ALI SUL ION CT2 CC S 34.000 114.5000 ! ALLOW ALI SUL ION O CC S 34.000 122.2000 ! ALLOW ALI SUL ION ! End of optimization Felix !lipids section OBL CL CTL3 70.0 125.0 20.0 2.442 ! methyl acetate OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate CTL2 CTL2 CL 52.0 108.00 ! alkane CTL3 CTL2 CL 52.0 108.00 ! alkane OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate OHL CL CTL3 55.0 110.50 ! acetic acid OHL CL CTL2 55.0 110.50 ! acetic acid HOL OHL CL 55.0 115.0 ! acetic acid OSL CTL1 CTL2 75.700 110.10 ! acetic acid OSL CTL1 CTL3 75.700 110.10 ! acetic acid OSL CTL2 CTL1 75.700 110.10 ! acetic acid OSL CTL2 CTL2 75.700 110.10 ! acetic acid OSL CTL2 CTL3 75.700 110.10 ! acetic acid HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92 HAL1 CTL1 OSL 60.0 109.5 ! phosphate HAL2 CTL2 OSL 60.0 109.5 ! phosphate HAL3 CTL3 OSL 60.0 109.5 ! phosphate CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate OSL PL OSL 80.0 104.3 ! phosphate OSL PL O2L 98.9 111.6 ! phosphate OSL PL OHL 48.1 108.0 ! phosphate O2L PL O2L 120.0 120.0 ! phosphate O2L PL OHL 98.9 108.23 ! phosphate NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98 NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine HCL NH3L HCL 41.0 109.50 ! ethanolamine NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92 CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92 HOL OHL CTL1 57.500 106.00 ! glycerol HOL OHL CTL2 57.500 106.00 ! glycerol HOL OHL CTL3 57.500 106.00 ! glycerol OHL CTL1 CTL2 75.700 110.10 ! glycerol OHL CTL2 CTL1 75.700 110.10 ! glycerol OHL CTL2 CTL2 75.700 110.10 ! glycerol OHL CTL2 CTL3 75.700 110.10 ! glycerol OHL CTL1 HAL1 45.900 108.89 ! glycerol OHL CTL2 HAL2 45.900 108.89 ! glycerol OHL CTL3 HAL3 45.900 108.89 ! glycerol O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate O2L SL OSL 85.0 98.0 ! methylsulfate CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate !HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95 CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95 CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95 HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95 HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95 HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95 HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95 HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95 CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95 ! CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO ! JES 8/25/89 CE1 CE1 CT3 48.00 123.50 ! ! for 2-butene, yin/adm jr., 12/95 CE1 CT2 CT3 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT2 48.00 126.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT3 47.00 125.20 ! ! for propene, yin/adm jr., 12/95 CP1 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 C 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 100.000 114.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 100.000 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPA CPB C 70.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPA CPM CPA 94.200 125.1200 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPA NPH CPA 139.300 103.9000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB C C 70.000 121.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB C 70.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB CPA 30.800 106.5100 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPM CPA CPB 61.600 124.0700 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA CA 60.000 118.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CPT CA 60.000 122.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT NY CA 110.000 108.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! from CT2 CT1 C, for lactams, adm jr. CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CY CA 45.800 129.4000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 CY CPT 45.800 124.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! 107.5->120.0 to make planar Arg (KK) CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! ethylbenzene, adm jr., 3/7/92 CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! methylguanidinium, adm jr., 3/26/92 CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION ! Modified for CYG residue !CT2 S CC 34.000 95.0000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 CT1 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK CY CT2 CT3 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK FE NPH CPA 96.150 128.0500 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO ! his, adm jr. 8/13/90 acetamide geometry and vibrations H NH2 H 23.000 120.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NY CA 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO ! JES 8/25/89 phenol H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 HA C C 50.000 120.5000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA C CPB 50.000 120.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CA CPT 41.000 122.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM CPA 12.700 117.4400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CPM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd ! based on HA CT2 HA HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT2 CE1 45.00 111.50 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HA CT2 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CY 33.430 109.5000 ! ALLOW ARO ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT3 CE1 42.00 111.50 ! ! for 2-butene, yin/adm jr., 12/95 HA CT3 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HE1 CE1 CE1 52.00 119.50 ! ! for 2-butene, yin/adm jr., 12/95 HE1 CE1 CE2 42.00 118.00 ! ! for propene, yin/adm jr., 12/95 HE1 CE1 CT2 40.00 116.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HE1 CE1 CT3 22.00 117.00 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE1 45.00 120.50 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE2 55.50 120.50 ! ! for ethene, yin/adm jr., 12/95 HE2 CE2 HE2 19.00 119.00 ! ! for propene, yin/adm jr., 12/95 HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT1 CT1 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT2 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT2 HB 36.000 115.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO ! 35.3->49.0 GUANIDINIUM (KK) HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI ! 107.5->120.0 to make planar Arg (KK) HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI ! methylguanidinium, adm jr., 3/26/92 HC NC2 HC 25.000 120.0000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH2 CT2 50.000 111.0000 ! ALLOW POL ! from HC NH2 CT3, neutral glycine, adm jr. HC NH2 CT3 50.000 111.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 HC NH2 HC 39.000 106.5000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP HC 51.000 107.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HT OT HT 55.000 104.5200 ! ALLOW WAT ! TIP3P GEOMETRY, ADM JR. N C CP1 20.000 112.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 C 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CC 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CP2 70.000 110.8000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 CP2 70.000 110.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO ! changed from 60.0/120.3 for guanidinium (KK) NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/20/92, for asn,asp,gln,glu and cters NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT1 CT2, for lactams, adm jr. NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT3 HA, for lactams, adm jr. NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! NMA crystal (JCS) NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! Modified for CYG residue !S CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations NH2 CT2 HB 38.000 109.50 50.00 2.14000 !from NH2 CT3 HA, neutral glycine, adm jr. NH2 CT2 CD 52.000 108.0000 !from CT2 CT2 CD, neutral glycine, adm jr. NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! Modified for CYG residue NH3 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! alanine (JCS) NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL ! alanine (JCS) NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 C 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CC 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA CPB 122.000 111.5400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPM 88.000 124.3900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE CM 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NPH FE CPM 0.000 45.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) NPH FE NPH 14.390 90.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 FE CM 50.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR2 FE NPH 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk O C CP1 80.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C H 50.000 121.7000 ! ALLOW PEP POL ARO ! acetaldehyde (JCS) O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC HA 44.000 122.0000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO ! Modified for CYG residue !O CC S 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO ! adm jr. 4/10/91, acetamide update OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA CA 40.000 120.0000 ! ALLOW POL ARO ! adm jr. 8/27/91, phenoxide OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) OC CT2 CT3 65.000 122.0000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT2 HA 65.000 118.3000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 HA 65.000 118.3000 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC ! PARALLH19 WITH [122.3] (JES) OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! Modified for CYG residue OH1 CD CT1 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OM CM FE 35.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM FE NPH 5.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM OM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SS CS CT3 55.000 118.0000 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 SS CS HA 40.000 112.3000 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. !nucleic acid section !NICH parameters to maintain back compatibility following !atom type switch from HN3 to HN6 NN2 CN3C HN6 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 HN6 CN3C CN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 HN6 CN3 CN8 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3C CN3 HN6 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 ! pyrmidines !@@@@@@@@ Adenine ! ade 6-mem ring CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97 NN3A CN4 NN3A 60.0 133.0 !6R) CN4 NN3A CN5 90.0 110.1 !6R) CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4 CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5 CN5 CN2 NN3A 60.0 110.7 !6R) CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4 CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5 CN4 NN4 CN5 120.0 104.6 !5R) NN2 CN4 NN4 100.0 113.4 !5R) CN4 NN2 CN5 100.0 106.3 !5R) NN2 CN5 NN3A 100.0 126.9 !bridgeC4 CN2 CN5 NN4 100.0 129.0 !bridgeC5 HN3 CN4 NN3A 38.0 113.5 !h2 NN3A CN2 NN1 50.0 130.7 !n6 CN5 CN2 NN1 50.0 118.6 ! CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G HN1 NN1 HN1 31.0 117.0 !C,A,G NN4 CN4 HN3 39.0 124.8 !h8, G,A NN2 CN4 HN3 39.0 121.8 ! CN5 NN2 HN2 30.0 129.4 !h9 CN4 NN2 HN2 30.0 125.0 ! !@@@@@@@@ Guanine ! gua 6-mem ring CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97 NN2G CN2 NN3G 70.0 122.2 !6R) CN2 NN3G CN5 90.0 109.4 !6R) CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4 CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5 CN5G CN1 NN2G 70.0 107.8 !6R) CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4 CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5 CN4 NN4 CN5G 120.0 103.8 !5R) NN2B CN4 NN4 100.0 113.0 !5R) CN4 NN2B CN5 100.0 107.2 !5R) NN2B CN5 NN3G 140.0 125.5 ! bridgeC4 CN1 CN5G NN4 125.0 129.0 ! bridgeC5 CN1 NN2G HN2 45.0 113.3 ! h1 CN2 NN2G HN2 45.0 115.6 ! NN1 CN2 NN2G 95.0 115.4 ! n2 NN1 CN2 NN3G 95.0 122.4 ! NN2G CN1 ON1 50.0 127.5 ! o6 CN5G CN1 ON1 50.0 124.7 ! HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8) CN4 NN2B HN2 30.0 124.6 ! h9 CN5 NN2B HN2 30.0 129.3 ! !@@@@@@@@ Cytosine ! cyt 6-mem ring CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97 NN2 CN1 NN3 50.0 116.8 !C CN1 NN3 CN2 85.0 119.1 !C CN3 CN2 NN3 85.0 119.3 !C CN2 CN3 CN3 85.0 117.8 !C CN3 CN3 NN2 85.0 122.9 !C CN1 NN2 HN2 37.0 121.2 !C, h1 CN3 NN2 HN2 37.0 114.7 !C NN2 CN1 ON1C 130.0 119.4 !C, o2 NN3 CN1 ON1C 130.0 123.8 !C NN3 CN2 NN1 81.0 122.3 !C, n4 CN3 CN2 NN1 81.0 118.4 !C CN2 CN3 HN3 38.0 120.1 !C h5 CN3 CN3 HN3 38.0 122.1 !C,U HN3 CN3 NN2 44.0 115.0 !C, h6 !@@@@@@@@ Uracil ! ura 6-mem ring CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97 NN2B CN1T NN2U 50.0 114.0 !U CN1T NN2U CN1 50.0 130.2 !U NN2U CN1 CN3 70.0 112.6 !U CN1 CN3 CN3 100.0 117.6 !U CN3 CN3 NN2B 100.0 123.6 !U CN1T NN2B HN2 40.5 122.0 !U, h1 CN3 NN2B HN2 32.0 116.0 !U NN2B CN1T ON1 100.0 121.6 !U, o2 NN2U CN1T ON1 100.0 124.4 !U CN1T NN2U HN2 40.5 114.4 !U, h3 CN1 NN2U HN2 40.5 115.4 !U NN2U CN1 ON1 100.0 121.9 !U, o4 CN3 CN1 ON1 100.0 125.5 !U, CN1 CN3 HN3 30.0 120.3 !U, h5 HN3 CN3 NN2B 30.0 114.3 !U, h6 ! thymine 6-mem ring (unique from ura) CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97 CN1 CN3T CN3 120.0 116.7 !T CN3T CN3 NN2B 120.0 123.6 !125.3 !T CN3T CN1 ON1 100.0 124.6 !T, o4 CN1 CN3T CN9 38.0 118.7 !T, c5 methyl CN3 CN3T CN9 38.0 124.6 !T CN3T CN3 HN3 30.0 122.1 !T, h6 ! Inosine, adm jr., 9/98 update HN3 CN4 NN3I 35.0 116.75 !c2 HN3 CN4 NN2G 35.0 115.75 !c2 NN3I CN4 NN2G 80.0 127.5 !c2 CN5G CN5 NN3I 100.0 127.0 !c4, r6 NN2B CN5 NN3I 140.0 128.4 !c4, r5 CN1 NN2G CN4 125.0 129.7 !n1 CN4 NN2G HN2 40.5 117.0 !n1 CN4 NN3I CN5 90.0 108.4 !n3 ! base to methyl connection CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr. CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91 CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr. CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91 CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr. CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr. CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr. CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr. CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr. CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr. NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr. !===== For glycosydic linkage, base to c1' CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A CN3 NN2B CN7B 45.0 119.6 !U/T CN1 NN2 CN7B 45.0 120.0 !C, FC from A CN3 NN2 CN7B 45.0 115.9 !C CN5 NN2 CN7B 45.0 126.1 !A CN4 NN2 CN7B 45.0 127.6 !A CN5 NN2B CN7B 45.0 126.5 !G CN4 NN2B CN7B 45.0 126.3 !G ON6 CN7B NN2 110.0 108.0 !C/A DNA ON6B CN7B NN2 110.0 112.0 !C/A RNA CN8 CN7B NN2 110.0 113.7 !C/A CN7B CN7B NN2 110.0 111.0 !C/A, RNA CN7C CN7B NN2 110.0 111.0 !C/A, Arabinose (NF) ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A CN8 CN7B NN2B 110.0 113.7 !T/U/G CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA CN7C CN7B NN2B 110.0 111.0 !T/U/G, Arabinose (NF) HN7 CN7B NN2 43.0 111.0 ! HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2 !===== End of glycosydic linkage ! remaining terms ordered based on central atom CN3 CN1A NN1 85.0 113.0 80.0 2.46 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A ON1 85.0 118.5 20.0 2.43 !nad/ppi, jjp1/adm jr. 7/95 NN1 CN1A ON1 85.0 128.5 20.0 2.17 !nad/ppi, jjp1/adm jr. 7/95 CN3D CN2 NN1 110.0 116.4 !5mc, adm jr. 9/9/93 CN3D CN2 NN3 30.0 121.3 !5mc, adm jr. 9/9/93 CN1A CN3 CN3C 5.0 107.8 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN8 125.0 124.2 !nadh/ppi, jjp1/adm jr. 7/95 CN2 CN3D CN3 100.0 117.8 !5mc, adm jr. 9/9/93 CN2 CN3D CN9 40.0 118.0 !5mc, adm jr. 9/9/93 CN3A CN3 CN1A 40.0 110.2 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A 10.0 131.8 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 50.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN3B 40.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3 CN8 53.5 108.5 !nadh/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN8 53.5 108.5 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 CN8 43.5 128.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3D CN9 40.0 124.2 !5mc, adm jr. 9/9/93 CN3D CN3 HN3 30.0 122.0 !5mc, adm jr. 9/9/93 CN3B CN3 HN3B 30.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 HN3B 30.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C HN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3C CN3 HN3 42.0 116.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A HN3B 80.0 121.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3B HN3B 80.0 120.5 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3B NN2 120.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C NN2 60.0 122.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 NN2 100.0 124.2 !5mc, adm jr. 9/9/93 CN8 CN3 HN3 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 HN3B CN3B NN2 80.0 117.5 !nad/ppi, jjp1/adm jr. 7/95 HN3 CN3C NN2 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN8 CN3 125.0 108.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3 CN8 HN8 55.0 110.10 !nadh/ppi, jjp1/adm jr. 7/95 CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN3D CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr. HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr. HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr. HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr. CN1A NN1 HN1 35.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN3B 30.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN3C 20.0 114.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 HN2 32.0 117.4 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 HN2 39.0 123.0 !nad/ppi, jjp1/adm jr. 7/95 HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr. CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr. CN9 ON2 P2 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH ON2 P ON2 80.0 104.3 !DMP, ADM Jr. ON2 P ON4 48.1 108.0 !MP_1, ADM Jr. ON3 P ON4 98.9 108.23 !MP_1, ADM Jr. ON4 P ON4 98.9 104.0 !MP_0, ADM Jr. ON2 P2 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95 ON2 P2 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92 !@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@ CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1' ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1' CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4' CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4' HN7 CN7 ON6 45.2 107.24 ! HN7 CN7B ON6 45.2 107.24 ! HN7 CN7 CN7 40.0 108.00 ! CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes HN7 CN7 CN8 34.5 110.1 22.53 2.179 ! HN8 CN8 CN7 34.53 110.10 22.53 2.179 ! HN8 CN8 CN8 34.53 110.10 22.53 2.179 ! HN8 CN8 HN8 35.5 109.00 5.40 1.802 ! HN7 CN7 HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@ !@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@ CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6 ON6B CN7B CN7B 90.0 106.0 ! 030998 CN7B CN7B CN7 110.0 96.0 ! CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4' HN7 CN7 ON6B 45.2 107.24 ! HN7 CN7B ON6B 45.2 107.24 ! CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly HN7 CN7B HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@ !@@@@@@@@@ Beginning of endocyclic valence angles for arabinose @@@@@@@ ON6 CN7B CN7C 90.0 102.0 ! NF, 11/97, C4'O4'C1' CN7B CN7C CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' CN7C CN7 CN7 60.00 102.0 8.00 2.561 !NF, 11/97, C2'C3'C4' CN7B CN7C HN7 33.4 110.10 22.53 2.179 ! following terms directly CN7C CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes HN7 CN7 CN7C 34.5 110.1 22.53 2.179 ! HN7 CN7C CN7 34.53 110.10 22.53 2.179 ! HN7 CN7C HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@ ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5' CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5' CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5' CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH CN7 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH ! sugar HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8 HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2 HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8 HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2 HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH !===== For 5ter patch: CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5 HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5 !===== For 3ter patch: ON5 CN7 CN8 75.7 110.0 ! from CHARMM22 ON5 CN7 CN7 75.7 110.1 ! HN7 CN7 ON5 60.0 109.5 ! HN5 ON5 CN7 57.5 109.0 ! !@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@ !@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@ !O4'-C4'-C5' ON6B CN7 CN8B 90.0 108.2 ! !O3'-C3'-C2' ON2 CN7 CN7B 90.0 110.0 ! ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8 !O2'-C2'-C1' ON5 CN7B CN7B 80.0 108.4 ! !O2'-C2'-C3' ON5 CN7B CN7 90.0 108.0 ! HN7 CN7B ON5 60.0 109.5 ! HN5 ON5 CN7B 57.5 109.0 ! HN7 CN7B CN7 34.53 110.10 22.53 2.179 HN7 CN7 CN7B 34.53 110.10 22.53 2.179 !@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@ CN7C CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' !===== For 3ter patch: !From DNA: ON5 CN7 CN7C 75.7 110.0 ! from CHARMM22 !From RNA: ON5 CN7C CN7B 80.0 108.4 ! From ON5 CN7B CN7B !O2'-C2'-C3' ON5 CN7C CN7 90.0 108.0 ! From ON5 CN7B CN7 HN7 CN7C ON5 60.0 109.5 ! HN5 ON5 CN7C 57.5 109.0 ! 032598 !@@@@@@@@@ Beginning of exocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ End of exocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@ CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr. !@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@ ON2 P ON3 98.9 111.6 !DMP, adm jr. ON3 P ON3 120.0 120.0 !DMP, adm jr. HN8 CN8 ON2 60.0 109.5 !DMP, adm jr. ON5 P ON3 98.9 111.6 ! From ON2 P ON3 !-- For imidazole, from imidazole alone: !-- and for link between sugar and imidazole ON6 CN7B NR1 140.0 108.00 ! k guessed, theta from ribo./desox. xtal (NF) ON6B CN7B NR1 140.0 108.00 ! RNUS CN8 CN7B NR1 140.0 113.70 ! k guessed, theta from ribo./desox. xtal (NF) CN7B CN7B NR1 140.0 113.70 ! RNUS CN7B NR1 CPH2 130.0 127.00 ! k guessed, theta from A/G xtal (NF) CN7B NR1 CPH1 130.0 126.00 ! k guessed, theta from A/G xtal (NF) HN7 CN7B NR1 30.0 106.3 ! k guessed, theta from ai (NF) !CPH2 NR1 CPH1 130.0 107.0000 ! From imidazole (NF), modified for 360 deg. condition !CPH2 NR2 CPH1 130.0 104.0000 ! From imidazole (NF) !NR1 CPH1 CPH1 130.0 106.0000 ! From imidazole (NF) !NR1 CPH2 NR2 130.0 112.5000 ! From imidazole !NR2 CPH1 CPH1 130.0 110.0000 ! From imidazole (NF) !NR1 CPH2 HR1 25.0 122.50 20.00 2.14000 ! From imidazole (NF) !NR2 CPH2 HR1 25.0 125.00 20.00 2.12000 ! From imidazole (NF) !HR3 CPH1 CPH1 25.0 130.00 20.00 2.20000 ! From imidazole (NF) !NR1 CPH1 HR3 25.0 124.00 20.00 2.14000 ! From imidazole (NF) !NR2 CPH1 HR3 25.0 120.00 20.00 2.14000 ! From imidazole (NF) !------------------------ For water ------------------- !HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY !------------------------ added for arao ----------------------- !------------------------ added for araim ---------------------- ON6 CN7B CN7 120.0 106.25 ! CN7B CN7 CN8 58.35 113.6 11.16 2.561 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! ! from lipids ! FROM CHARMM23 Guessed parameters ! Rommie Jerome ! C6-C7 O CC CPH1 CPH1 .550 1 180.0 ! param O CC CPH1 NR2 .550 1 0.0 ! param NH2 CC CPH1 CPH1 .550 1 0.0 ! param NH2 CC CPH1 NR2 .550 1 180.0 ! param O CC CPH1 CPH1 1.7 2 180.0 ! param ! CC CPH1 CPH1 NR1 5.200 2 0.0 !cycle CC CPH1 CPH1 NC2 5.200 2 0.0 !cycle NR2 CPH1 CPH1 NC2 5.200 2 0.0 !cycle CC CPH1 NR2 CPH2 5.200 2 0.0 !cycle CPH1 CC NH2 H 0.200 2 0.0 ! cis or trans terminal NH2 ! C8-N4 CPH1 CPH1 NC2 C 1.300 2 180.0 ! param NR1 CPH1 NC2 C 1.300 2 180.0 ! param ! CPH2 NR1 CPH1 NC2 0.200 3 0.0 ! cycle CN7B NR1 CPH1 NC2 0.200 3 0.0 ! cycle ! CN7B ON6B CN7 CTL3 0.200 3 0.0 !cycle cycle CN7B CN7 CN7 CTL3 0.200 3 0.!cycle 0 !C4-C9 * CN7 CTL3 * 0.200 3 0.0 ON6B CN7 CTL3 OSL 4.00 1 180.0 CN7 CN7 CTL3 OSL 0.200 3 0.0 CN7 CN7 CTL3 HAL3 0.200 3 0.0 ON6B CN7 CTL3 HAL3 0.200 3 0.0 ON5 CN7 CN7 CTL3 0.200 3 0.0 !cycle CTL3 CN7 CN7 HN7 0.200 3 0.0 !cycle OSL CTL3 CN7 HN7 0.000 3 0.0 HN7 CTL3 CN7 HAL3 0.000 3 0.0 HN7 CN7 CTL3 HAL3 0.200 3 0.0 !C11-C12 NC2 CT2 C CT2 1.500 1 0.0 NC2 CT2 C CT2 2.000 2 0.0 NC2 CT2 C O 0.000 3 0.0 CT2 C CT2 HA 0.000 3 0.0 !C12-C13 CT2 C CT2 CT2 1.000 3 0.0 CT2 C CT2 OH1 0.000 3 0.0 O C CT2 OH1 0.000 3 0.0 !C14-C15 CT2 CT2 CTL3 OSL 0.200 3 0.0 CT2 CT2 CTL3 HAL3 0.200 3 0.0 OH1 CT2 CTL3 OSL 0.200 3 0.0 OH1 CT2 CTL3 HAL3 0.200 3 0.0 OSL CTL3 CT2 HA 0.200 3 0.0 HA CT2 CTL3 HAL3 0.200 3 0.0 ! END OF CHARMM-GUESSED PARAMETERS !lipids section X CTL1 OHL X 0.14 3 0.00 ! glycerol X CTL2 OHL X 0.14 3 0.00 ! glycerol X CTL3 OHL X 0.14 3 0.00 ! glycerol OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate X CL OSL X 2.05 2 180.00 ! methyl acetate X CTL2 CL X 0.05 6 180.00 ! methyl acetate X CTL3 CL X 0.05 6 180.00 ! methyl acetate X CL OHL X 2.05 2 180.00 ! acetic acid HAL2 CTL2 CL OHL 0.00 6 180.00 HAL3 CTL3 CL OHL 0.00 6 180.00 OSL PL OSL CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate X OHL PL X 0.30 3 0.00 ! terminal phosphate X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. CTL3 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL2 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL3 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL2 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 CTL2 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL2 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 CTL3 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL3 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine NH3L CTL2 CTL2 OSL 0.7 1 180.00 ! ethanolamine NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92 NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92 NTL CTL2 CTL2 OSL 3.3 1 180.00 ! choline, 12/92 NTL CTL2 CTL2 OSL -0.4 3 180.00 ! choline, 12/92 X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92 X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92 X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell CTL3 CTL2 CTL2 CTL3 0.10 2 180.00 ! alkane, 4/98, adm jr., lower butane gauche conformer CTL3 CTL2 CTL2 CTL3 0.15 4 0.00 ! alkane, 4/98, adm jr. CTL3 CTL2 CTL2 CTL3 0.10 6 180.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL3 0.10 2 180.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL3 0.15 4 0.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL3 0.10 6 180.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL2 0.10 2 180.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL2 0.15 4 0.00 ! alkane, 4/98, adm jr. CTL2 CTL2 CTL2 CTL2 0.10 6 180.00 ! alkane, 4/98, adm jr. HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update X CEL1 CEL1 X 0.1300 1 180.00 ! 2-butene, adm jr., 8/98 update X CEL1 CEL1 X 24.0000 2 180.00 ! 2-butene, adm jr., 8/98 update X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95 CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 CEL1 CEL1 CTL2 HAL2 0.0300 3 0.00 ! butene, yin,adm jr., 12/95 CEL1 CEL1 CTL3 HAL3 0.0300 3 0.00 ! butene, yin,adm jr., 12/95 CEL1 CEL1 CTL2 CTL2 0.4000 3 0.00 ! 1-butene, adm jr., 8/98 update CEL2 CEL1 CTL2 CTL2 0.4000 3 0.00 ! 1-butene, adm jr., 8/98 update CEL2 CEL1 CTL2 CTL3 0.4000 3 0.00 ! 1-butene, adm jr., 8/98 update CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 CEL2 CEL1 CTL3 HAL3 0.050 3 180.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 HAL2 0.8700 3 0.00 ! butene, yin,adm jr., 12/95 HEL1 CEL1 CTL3 HAL3 0.3400 3 0.00 ! butene, yin,adm jr., 12/95 ! C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c CE1 CE1 CT3 HA 0.0300 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 CT3 0.5000 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 HA 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT3 HA 0.0500 3 180.00 ! ! for propene, yin/adm jr., 12/95 CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP ! from CT2 C NH1 CT2, adm jr. 10/21/96 CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! from CT2 C NH1 CT2, adm jr. 10/21/96 CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! from CT2 CT1 NH1 C, for lactams, adm jr. CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO !JWK CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 CT3 CE1 CE2 HE2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION ! DTN 8/24/90 CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION ! Modified for CYG residue CC S CT2 CT1 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CC S CT2 CT1 0.3700 3 0.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) !!!!! ! expt. MeEtS, 3/26/92 (FL) CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP ! from H NH1 CT2 CT3, for lactams, adm jr. H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/20/89 H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NY CA CY 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO ! adm jr., 10/02/89 HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO ! ADM JR., 10/02/89 HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! TRP (JES) HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA NY H 1.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ! adm jr. 4/10/91, acetamide update HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION ! Modified for CYG residue HA CT2 S CC 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HE1 CE1 CE2 HE2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 HE1 CE1 CT2 HA 0.8700 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CT2 CT3 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CT3 HA 0.3400 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE2 CE2 CE1 CT2 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NH2 CT2 HB 0.1100 3 0.00 !from X CT3 NH2 X, neutral glycine, adm jr. HC NH2 CT2 CD 0.1100 3 0.00 !from X CT3 NH2 X, neutral glycine, adm jr. HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA NY H 0.4000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, his HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, YES, 0.0 HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD