REMARKS Charmm parameter set for proteins v22 b4 REMARKS FILENAME="pro_residues.par" SET ECHO=FALSE END {>>>>>>>>>> Developmental Parameter File for Proteins <<<<<<<<<< >>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>>>>>>> Jan 1993 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or bitnet: alex,tammy.harvard.edu <<<<<<<<< These files are a beta release; additional parameter development and testing may lead to alteration of the contents.} !----------------------------------------------------------------------------------------------- ! VARIOUS BOND PARAMETERS: Force Constant, Equilibrium Radius !----------------------------------------------------------------------------------------------- BOND C C 600.000 {SD= .022} 1.335 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) BOND CA CA 305.000 {SD= .031} 1.375 ! ALLOW ARO ! benzene, JES 8/25/89 BOND CP1 C 250.000 {SD= .034} 1.490 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND CP1 CC 250.000 {SD= .034} 1.490 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND CP1 CD 200.000 {SD= .038} 1.490 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND CP2 CP1 222.500 {SD= .036} 1.527 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND CP2 CP2 222.500 {SD= .036} 1.537 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND CP3 CP2 222.500 {SD= .036} 1.537 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND CPH1 CPH1 410.000 {SD= .027} 1.360 ! ALLOW ARO ! histidine, adm jr., 6/27/90 BOND CPT CA 305.000 {SD= .031} 1.368 ! ALLOW ARO ! adm jr., 12/30/91, for jwk BOND CPT CPT 360.000 {SD= .029} 1.400 ! ALLOW ARO !adm jr., 12/30/91, for jwk BOND CT1 C 250.000 {SD= .034} 1.490 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) BOND CT1 CC 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters BOND CT1 CD 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent BOND CT1 CT1 222.500 {SD= .036} 1.500 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CT2 C 250.000 {SD= .034} 1.490 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) BOND CT2 CA 230.000 {SD= .036} 1.490 ! ALLOW ALI ARO ! phe,tyr, JES 8/25/89 BOND CT2 CC 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters BOND CT2 CD 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent BOND CT2 CPH1 229.630 {SD= .036} 1.500 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals BOND CT2 CT1 222.500 {SD= .036} 1.538 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CT2 CT2 222.500 {SD= .036} 1.530 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CT3 C 250.000 {SD= .034} 1.490 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) BOND CT3 CA 230.000 {SD= .036} 1.490 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 BOND CT3 CC 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters BOND CT3 CD 200.000 {SD= .038} 1.522 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent BOND CT3 CPH1 229.630 {SD= .036} 1.500 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals BOND CT3 CS 190.000 {SD= .039} 1.531 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 BOND CT3 CT1 222.500 {SD= .036} 1.538 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CT3 CT2 222.500 {SD= .036} 1.528 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CT3 CT3 222.500 {SD= .036} 1.530 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND CY CA 350.000 {SD= .029} 1.365 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search BOND CY CPT 350.000 {SD= .029} 1.440 ! ALLOW ARO !adm jr., 12/30/91, for jwk BOND CY CT2 230.000 {SD= .036} 1.510 ! ALLOW ARO !JWK Kb from alkane freq.. b0 from TRP crystal BOND H CD 330.000 {SD= .030} 1.110 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent BOND HA C 330.000 {SD= .030} 1.100 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) BOND HA CA 340.000 {SD= .030} 1.083 ! ALLOW ARO ! trp, adm jr., 10/02/89 BOND HA CC 317.130 {SD= .031} 1.100 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations BOND HA CP2 309.000 {SD= .031} 1.111 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND HA CP3 309.000 {SD= .031} 1.111 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND HA CS 300.000 {SD= .031} 1.111 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 BOND HA CT1 309.000 {SD= .031} 1.111 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND HA CT2 309.000 {SD= .031} 1.111 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND HA CT3 322.000 {SD= .030} 1.111 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 BOND HA CY 330.000 {SD= .030} 1.080 ! ALLOW ARO ! JWK 05/14/91 new r0 from indole BOND HB CP1 330.000 {SD= .030} 1.080 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND HB CT1 330.000 {SD= .030} 1.080 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) BOND HB CT2 330.000 {SD= .030} 1.080 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) BOND HB CT3 330.000 {SD= .030} 1.080 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) BOND HP CA 340.000 {SD= .030} 1.080 ! ALLOW ARO ! phe,tyr JES 8/25/89 BOND HP CY 350.000 {SD= .029} 1.080 ! ALLOW ARO !adm jr., 12/30/91, for jwk BOND HR1 CPH1 375.000 {SD= .028} 1.083 ! ALLOW ARO ! his, adm jr., 6/27/90 BOND HR1 CPH2 340.000 {SD= .030} 1.090 ! ALLOW ARO ! his, adm jr., 6/28/29 BOND HR2 CPH2 333.000 {SD= .030} 1.070 ! ALLOW ARO ! his, adm jr., 6/27/90 BOND HR3 CPH1 365.000 {SD= .028} 1.083 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS BOND N C 260.000 {SD= .034} 1.300 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND N CP1 320.000 {SD= .030} 1.424 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND N CP3 320.000 {SD= .030} 1.447 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 BOND NC2 C 463.000 {SD= .025} 1.365 ! ALLOW PEP POL ARO ! 403.0->463.0, 1.305->1.365 guanidinium (KK) BOND NC2 CT2 261.000 {SD= .034} 1.490 ! ALLOW ALI POL ! arg, (DS) BOND NC2 CT3 261.000 {SD= .034} 1.490 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 BOND NC2 HC 455.000 {SD= .026} 1.000 ! ALLOW POL ! 405.0->455.0 GUANIDINIUM (KK) BOND NH1 C 370.000 {SD= .028} 1.345 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) BOND NH1 CT1 320.000 {SD= .030} 1.430 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) BOND NH1 CT2 320.000 {SD= .030} 1.430 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) BOND NH1 CT3 320.000 {SD= .030} 1.430 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) BOND NH1 H 440.000 {SD= .026} .997 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) BOND NH1 HC 405.000 {SD= .027} .980 ! ALLOW PEP POL ARO ! (DS) BOND NH2 CC 430.000 {SD= .026} 1.360 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide BOND NH2 CT3 240.000 {SD= .035} 1.455 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 BOND NH2 H 480.000 {SD= .025} 1.000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations BOND NH2 HC 460.000 {SD= .025} 1.000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 BOND NH3 CT1 200.000 {SD= .038} 1.480 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) BOND NH3 CT2 200.000 {SD= .038} 1.480 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) BOND NH3 CT3 200.000 {SD= .038} 1.480 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) BOND NH3 HC 403.000 {SD= .027} 1.040 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) BOND NP CP1 320.000 {SD= .030} 1.485 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND NP CP3 320.000 {SD= .030} 1.502 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND NP HC 460.000 {SD= .025} 1.006 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 BOND NR1 CPH1 400.000 {SD= .027} 1.380 ! ALLOW ARO ! his, ADM JR., 7/20/89 BOND NR1 CPH2 400.000 {SD= .027} 1.360 ! ALLOW ARO ! his, ADM JR., 7/20/89 BOND NR1 H 466.000 {SD= .025} 1.000 ! ALLOW ARO ! his, ADM JR., 7/20/89 BOND NR2 CPH1 400.000 {SD= .027} 1.380 ! ALLOW ARO ! his, ADM JR., 7/20/89 BOND NR2 CPH2 400.000 {SD= .027} 1.320 ! ALLOW ARO ! his, ADM JR., 7/20/89 BOND NR3 CPH1 380.000 {SD= .028} 1.370 ! ALLOW ARO ! his, adm jr., 6/28/90 BOND NR3 CPH2 380.000 {SD= .028} 1.320 ! ALLOW ARO ! his, adm jr., 6/27/90 BOND NR3 H 453.000 {SD= .026} 1.000 ! ALLOW ARO ! his, adm jr., 6/27/90 BOND NY CA 270.000 {SD= .033} 1.370 ! ALLOW ARO !adm jr., 12/30/91, for jwk BOND NY CPT 270.000 {SD= .033} 1.375 ! ALLOW ARO !adm jr., 12/30/91, for jwk BOND NY H 465.000 {SD= .025} .976 ! ALLOW ARO ! indole JWK 08/28/89 BOND O C 620.000 {SD= .022} 1.230 ! ALLOW PEP POL ARO ! Peptide geometry, condensed phase (LK) BOND O CC 650.000 {SD= .021} 1.230 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide BOND OB CC 750.000 {SD= .020} 1.220 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid vibrations and geom. BOND OB CD 750.000 {SD= .020} 1.220 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent BOND OC CA 525.000 {SD= .024} 1.260 ! ALLOW PEP POL ARO ION ! adm jr. 8/27/91, phenoxide BOND OC CC 525.000 {SD= .024} 1.260 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid BOND OC CT2 450.000 {SD= .026} 1.330 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 BOND OC CT3 450.000 {SD= .026} 1.330 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 BOND OH1 CA 334.300 {SD= .030} 1.411 ! ALLOW ARO ALC ! MeOH, EMB 10/10/89, BOND OH1 CD 230.000 {SD= .036} 1.400 ! ALLOW PEP POL ARO ALC ! adm jr. 5/02/91, acetic acid pure solvent BOND OH1 CT1 428.000 {SD= .026} 1.420 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 BOND OH1 CT2 428.000 {SD= .026} 1.420 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 BOND OH1 CT3 428.000 {SD= .026} 1.420 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 BOND OH1 H 545.000 {SD= .023} .960 ! ALLOW ALC ARO ! EMB 11/21/89 methanol vib fit BOND OS CD 150.000 {SD= .044} 1.334 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent BOND OS CT3 340.000 {SD= .030} 1.430 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate BOND S CT2 198.000 {SD= .039} 1.818 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) BOND S CT3 240.000 {SD= .035} 1.816 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) BOND S HS 275.000 {SD= .033} 1.325 ! ALLOW SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 BOND SM CT2 214.000 {SD= .037} 1.816 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) BOND SM CT3 214.000 {SD= .037} 1.816 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) BOND SM SM 173.000 {SD= .041} 2.029 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) BOND SS CS 205.000 {SD= .038} 1.836 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 !------------------------------------------------------------------------------------------------------ ! VARIOUS ANGLE PARAMETERS: Force Constant, Equilibrium Angle, Urie-Bradley Force Const., ! U.-B. equilibrium (if any) !------------------------------------------------------------------------------------------------------ ANGLE CA CA CA 40.00 {SD= .086} 120.0000 UB 35.000 2.416 ! ALLOW ARO ! JES 8/25/89 ANGLE CP1 N C 60.00 {SD= .070} 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP2 CP1 C 52.00 {SD= .075} 114.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP2 CP1 CC 52.00 {SD= .075} 114.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP2 CP1 CD 50.00 {SD= .077} 114.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP2 CP2 CP1 70.00 {SD= .065} 109.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP3 CP2 CP2 70.00 {SD= .065} 109.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP3 N C 60.00 {SD= .070} 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP3 N CP1 100.00 {SD= .054} 115.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CP3 NP CP1 100.00 {SD= .054} 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE CPH2 NR1 CPH1 130.00 {SD= .048} 107.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE CPH2 NR2 CPH1 130.00 {SD= .048} 104.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE CPH2 NR3 CPH1 145.00 {SD= .045} 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 ANGLE CPT CA CA 60.00 {SD= .070} 118.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CPT CPT CA 60.00 {SD= .070} 122.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CPT CY CA 120.00 {SD= .050} 107.4000 UB 25.000 2.261 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CPT NY CA 110.00 {SD= .052} 108.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CT1 CT1 C 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE CT1 CT1 CC 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE CT1 CT1 CT1 53.35 {SD= .074} 111.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT1 CT2 CA 51.80 {SD= .076} 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) ANGLE CT1 CT2 CC 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE CT1 CT2 CD 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE CT1 CT2 CPH1 58.35 {SD= .071} 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted ANGLE CT1 CT2 CT1 58.35 {SD= .071} 113.5000 UB 11.160 2.561 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE CT1 NH1 C 50.00 {SD= .077} 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE CT2 CA CA 45.80 {SD= .080} 122.3000 ! ALLOW ALI ARO ! PARALLH19 (JES) ANGLE CT2 CPH1 CPH1 45.80 {SD= .080} 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS ANGLE CT2 CT1 C 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE CT2 CT1 CC 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE CT2 CT1 CD 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE CT2 CT1 CT1 53.35 {SD= .074} 111.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT2 CT2 CC 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE CT2 CT2 CD 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE CT2 CT2 CT1 58.35 {SD= .071} 113.5000 UB 11.160 2.561 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE CT2 CT2 CT2 58.35 {SD= .071} 113.6000 UB 11.160 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT2 CT3 CT1 58.35 {SD= .071} 113.5000 UB 11.160 2.561 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE CT2 CY CA 45.80 {SD= .080} 129.4000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search ANGLE CT2 CY CPT 45.80 {SD= .080} 124.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search ANGLE CT2 NC2 C 62.30 {SD= .069} 120.0000 ! ALLOW ALI POL PEP ARO ! 107.5->120.0 to make planar Arg (KK) ANGLE CT2 NH1 C 50.00 {SD= .077} 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE CT2 OS CD 40.00 {SD= .086} 109.6000 UB 30.000 2.265 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent ANGLE CT3 CA CA 45.80 {SD= .080} 122.3000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 ANGLE CT3 CPH1 CPH1 45.80 {SD= .080} 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS ANGLE CT3 CT1 C 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE CT3 CT1 CC 52.00 {SD= .075} 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter ANGLE CT3 CT1 CT1 53.35 {SD= .074} 108.5000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT3 CT1 CT2 53.35 {SD= .074} 114.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT3 CT1 CT3 53.35 {SD= .074} 114.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT3 CT2 CA 51.80 {SD= .076} 107.5000 ! ALLOW ALI ARO ! ethylbenzene, adm jr., 3/7/92 ANGLE CT3 CT2 CPH1 58.35 {SD= .071} 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted ANGLE CT3 CT2 CT1 58.35 {SD= .071} 113.5000 UB 11.160 2.561 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE CT3 CT2 CT2 58.00 {SD= .071} 115.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT3 CT2 CT3 53.35 {SD= .074} 114.0000 UB 8.000 2.561 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE CT3 NC2 C 62.30 {SD= .069} 120.0000 ! ALLOW ALI POL PEP ARO ! methylguanidinium, adm jr., 3/26/92 ANGLE CT3 NH1 C 50.00 {SD= .077} 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE CT3 OS CD 40.00 {SD= .086} 109.6000 UB 30.000 2.265 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent ANGLE CT3 S CT2 34.00 {SD= .093} 95.0000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) ANGLE CY CPT CA 160.00 {SD= .043} 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CY CPT CPT 110.00 {SD= .052} 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE CY CT2 CT1 58.35 {SD= .071} 114.0000 ! ALLOW ARO ! from TRP crystal, JWK ANGLE CY CT2 CT3 58.35 {SD= .071} 114.0000 ! ALLOW ARO ! from TRP crystal, JWK ANGLE H NH1 C 34.00 {SD= .093} 123.0000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) ANGLE H NH1 CT1 35.00 {SD= .092} 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) ANGLE H NH1 CT2 35.00 {SD= .092} 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) ANGLE H NH1 CT3 35.00 {SD= .092} 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) ANGLE H NH2 CC 50.00 {SD= .077} 120.0000 ! ALLOW POL PEP ARO ! his, adm jr. 8/13/90 acetamide geometry and vibrations ANGLE H NH2 H 23.00 {SD= .113} 120.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations ANGLE H NR1 CPH1 30.00 {SD= .099} 125.5000 UB 20.000 2.150 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE H NR1 CPH2 30.00 {SD= .099} 127.0000 UB 20.000 2.140 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE H NR3 CPH1 25.00 {SD= .109} 126.0000 UB 15.000 2.130 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE H NR3 CPH2 25.00 {SD= .109} 126.0000 UB 15.000 2.090 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE H NY CA 28.00 {SD= .103} 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE H NY CPT 28.00 {SD= .103} 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE H OH1 CA 65.00 {SD= .067} 108.0000 ! ALLOW ALC ARO ! JES 8/25/89 phenol ANGLE H OH1 CD 55.00 {SD= .073} 115.0000 ! ALLOW ALC ARO PEP POL ! adm jr. 5/02/91, acetic acid pure solvent ANGLE H OH1 CT1 57.50 {SD= .072} 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 ANGLE H OH1 CT2 57.50 {SD= .072} 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 ANGLE H OH1 CT3 57.50 {SD= .072} 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 ANGLE HA C C 50.00 {SD= .077} 120.5000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) ANGLE HA C HA 50.00 {SD= .077} 118.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) ANGLE HA CA CA 29.00 {SD= .101} 120.0000 UB 25.000 2.152 ! ALLOW ARO ! trp, adm jr., 10/02/89 ANGLE HA CA CPT 41.00 {SD= .085} 122.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search ANGLE HA CA CY 32.00 {SD= .096} 125.0000 UB 25.000 2.173 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE HA CP2 CP1 33.43 {SD= .094} 110.1000 UB 22.530 2.179 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CP2 CP2 26.50 {SD= .106} 110.1000 UB 22.530 2.179 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CP2 CP3 26.50 {SD= .106} 110.1000 UB 22.530 2.179 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CP2 HA 35.50 {SD= .091} 109.0000 UB 5.400 1.802 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CP3 CP2 26.50 {SD= .106} 110.1000 UB 22.530 2.179 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CP3 HA 35.50 {SD= .091} 109.0000 UB 5.400 1.802 ! ALLOW ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HA CS CT3 34.60 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE HA CS HA 35.50 {SD= .091} 108.4000 UB 14.000 1.775 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE HA CT1 C 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 ANGLE HA CT1 CD 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE HA CT1 CT1 34.50 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT1 CT2 34.50 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT1 CT3 34.50 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT1 HA 35.50 {SD= .091} 109.0000 UB 5.400 1.802 !for model cpd, untested ANGLE HA CT2 C 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 ANGLE HA CT2 CA 49.30 {SD= .077} 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) ANGLE HA CT2 CC 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE HA CT2 CD 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE HA CT2 CPH1 33.43 {SD= .094} 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED ANGLE HA CT2 CT1 33.43 {SD= .094} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE HA CT2 CT2 26.50 {SD= .106} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT2 CT3 34.60 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT2 CY 33.43 {SD= .094} 109.5000 ! ALLOW ARO ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA ANGLE HA CT2 HA 35.50 {SD= .091} 109.0000 UB 5.400 1.802 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT3 C 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 ANGLE HA CT3 CA 49.30 {SD= .077} 107.5000 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 ANGLE HA CT3 CC 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE HA CT3 CD 33.00 {SD= .095} 109.5000 UB 30.000 2.163 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE HA CT3 CPH1 33.43 {SD= .094} 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED ANGLE HA CT3 CS 34.60 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE HA CT3 CT1 33.43 {SD= .094} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) ANGLE HA CT3 CT2 34.60 {SD= .093} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT3 CT3 37.50 {SD= .089} 110.1000 UB 22.530 2.179 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CT3 HA 35.50 {SD= .091} 108.4000 UB 5.400 1.802 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 ANGLE HA CY CA 20.00 {SD= .122} 126.4000 UB 25.000 2.186 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE HA CY CPT 32.00 {SD= .096} 126.4000 UB 25.000 2.255 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE HB CP1 C 50.00 {SD= .077} 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE HB CP1 CC 50.00 {SD= .077} 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE HB CP1 CD 50.00 {SD= .077} 112.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE HB CP1 CP2 35.00 {SD= .092} 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE HB CT1 C 50.00 {SD= .077} 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT1 CC 50.00 {SD= .077} 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE HB CT1 CD 50.00 {SD= .077} 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent ANGLE HB CT1 CT1 35.00 {SD= .092} 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT1 CT2 35.00 {SD= .092} 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT1 CT3 35.00 {SD= .092} 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT2 C 50.00 {SD= .077} 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT2 CC 50.00 {SD= .077} 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE HB CT2 CD 50.00 {SD= .077} 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent ANGLE HB CT2 HB 36.00 {SD= .091} 115.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HB CT3 C 50.00 {SD= .077} 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE HC NC2 C 49.00 {SD= .078} 120.0000 ! ALLOW POL PEP ARO ! 35.3->49.0 GUANIDINIUM (KK) ANGLE HC NC2 CT2 40.40 {SD= .086} 120.0000 ! ALLOW POL ALI ! 107.5->120.0 to make planar Arg (KK) ANGLE HC NC2 CT3 40.40 {SD= .086} 120.0000 ! ALLOW POL ALI ! methylguanidinium, adm jr., 3/26/92 ANGLE HC NC2 HC 25.00 {SD= .109} 120.0000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) ANGLE HC NH2 CT3 50.00 {SD= .077} 111.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 ANGLE HC NH2 HC 39.00 {SD= .087} 106.5000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) ANGLE HC NH3 CT1 30.00 {SD= .099} 109.5000 UB 20.000 2.074 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE HC NH3 CT2 30.00 {SD= .099} 109.5000 UB 20.000 2.074 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE HC NH3 CT3 30.00 {SD= .099} 109.5000 UB 20.000 2.074 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE HC NH3 HC 44.00 {SD= .082} 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE HC NP CP1 33.00 {SD= .095} 109.5000 UB 4.000 2.056 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HC NP CP3 33.00 {SD= .095} 109.5000 UB 4.000 2.056 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HC NP HC 51.00 {SD= .076} 107.5000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE HP CA CA 30.00 {SD= .099} 120.0000 UB 22.000 2.152 ! ALLOW ARO ! JES 8/25/89 benzene ANGLE HP CA CPT 30.00 {SD= .099} 122.0000 UB 22.000 2.146 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE HP CA CY 32.00 {SD= .096} 125.0000 UB 25.000 2.173 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE HP CY CA 32.00 {SD= .096} 126.4000 UB 25.000 2.186 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE HP CY CPT 32.00 {SD= .096} 126.4000 UB 25.000 2.255 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE HR1 CPH1 CPH1 22.00 {SD= .116} 130.0000 UB 15.000 2.215 ! ALLOW ARO ! adm jr., 6/27/90, his ANGLE HR3 CPH1 CPH1 25.00 {SD= .109} 130.0000 UB 20.000 2.200 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS ANGLE HS S CT2 38.80 {SD= .087} 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 ANGLE HS S CT3 43.00 {SD= .083} 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 ANGLE N C CP1 20.00 {SD= .122} 112.5000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE N C CT1 20.00 {SD= .122} 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE N C CT2 20.00 {SD= .122} 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE N C CT3 20.00 {SD= .122} 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE N CP1 C 50.00 {SD= .077} 104.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP1 CC 50.00 {SD= .077} 104.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP1 CD 50.00 {SD= .077} 104.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP1 CP2 70.00 {SD= .065} 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP1 HB 48.00 {SD= .079} 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP3 CP2 70.00 {SD= .065} 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE N CP3 HA 48.00 {SD= .079} 108.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE NC2 C NC2 52.00 {SD= .075} 120.0000 UB 90.000 2.364 ! ALLOW POL PEP ARO ! changed from 60.0/120.3 for guanidinium (KK) ANGLE NC2 CT2 CT2 67.70 {SD= .066} 107.5000 ! ALLOW ALI POL ! arg, (DS) ANGLE NC2 CT2 HA 51.50 {SD= .076} 107.5000 ! ALLOW ALI POL ! arg, (DS) ANGLE NC2 CT3 HA 51.50 {SD= .076} 107.5000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 ANGLE NH1 C CP1 80.00 {SD= .061} 116.5000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NH1 C CT1 80.00 {SD= .061} 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE NH1 C CT2 80.00 {SD= .061} 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE NH1 C CT3 80.00 {SD= .061} 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) ANGLE NH1 CT1 C 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT1 CC 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE NH1 CT1 CD 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent ANGLE NH1 CT1 CT1 70.00 {SD= .065} 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT1 CT2 70.00 {SD= .065} 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT1 CT3 70.00 {SD= .065} 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT1 HB 48.00 {SD= .079} 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT2 C 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT2 CC 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/20/92, for asn,asp,gln,glu and cters ANGLE NH1 CT2 CD 50.00 {SD= .077} 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent ANGLE NH1 CT2 HB 48.00 {SD= .079} 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) ANGLE NH1 CT3 HA 51.50 {SD= .076} 109.5000 ! ALLOW ALI PEP POL ARO ! NMA crystal (JCS) ANGLE NH2 CC CP1 80.00 {SD= .061} 113.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NH2 CC CT1 50.00 {SD= .077} 116.5000 UB 50.000 2.450 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations ANGLE NH2 CC CT2 50.00 {SD= .077} 116.5000 UB 50.000 2.450 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations ANGLE NH2 CC CT3 50.00 {SD= .077} 116.5000 UB 50.000 2.450 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations ANGLE NH2 CC HA 44.00 {SD= .082} 111.0000 UB 50.000 1.980 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations ANGLE NH2 CT3 HA 38.00 {SD= .088} 109.5000 UB 50.000 2.140 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 ANGLE NH3 CT1 C 43.70 {SD= .082} 110.0000 ! ALLOW PEP POL ARO ALI ! new aliphatics, adm jr., 2/3/92 ANGLE NH3 CT1 CC 43.70 {SD= .082} 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE NH3 CT1 CT1 67.70 {SD= .066} 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 ANGLE NH3 CT1 CT2 67.70 {SD= .066} 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 ANGLE NH3 CT1 CT3 67.70 {SD= .066} 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 ANGLE NH3 CT1 HB 51.50 {SD= .076} 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 ANGLE NH3 CT2 C 43.70 {SD= .082} 110.0000 ! ALLOW PEP POL ARO ALI ! alanine (JCS) ANGLE NH3 CT2 CC 43.70 {SD= .082} 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters ANGLE NH3 CT2 CD 43.70 {SD= .082} 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent ANGLE NH3 CT2 CT2 67.70 {SD= .066} 110.0000 ! ALLOW ALI POL ! alanine (JCS) ANGLE NH3 CT2 HA 45.00 {SD= .081} 107.5000 UB 35.000 2.101 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE NH3 CT2 HB 51.50 {SD= .076} 107.5000 ! ALLOW ALI POL PEP ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) ANGLE NH3 CT3 HA 45.00 {SD= .081} 107.5000 UB 35.000 2.101 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) ANGLE NP CP1 C 50.00 {SD= .077} 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NP CP1 CC 50.00 {SD= .077} 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NP CP1 CD 50.00 {SD= .077} 106.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NP CP1 CP2 70.00 {SD= .065} 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NP CP1 HB 51.50 {SD= .076} 107.5000 ! ALLOW ALI POL PEP PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE NP CP3 CP2 70.00 {SD= .065} 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE NP CP3 HA 51.50 {SD= .076} 109.1500 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE NR1 CPH1 CPH1 130.00 {SD= .048} 106.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 ANGLE NR1 CPH1 CT2 45.80 {SD= .080} 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT ANGLE NR1 CPH1 CT3 45.80 {SD= .080} 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT ANGLE NR1 CPH1 HR3 25.00 {SD= .109} 124.0000 UB 20.000 2.140 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS ANGLE NR1 CPH2 HR1 25.00 {SD= .109} 122.5000 UB 20.000 2.140 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE NR2 CPH1 CPH1 130.00 {SD= .048} 110.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 ANGLE NR2 CPH1 CT2 45.80 {SD= .080} 120.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT ANGLE NR2 CPH1 HR3 25.00 {SD= .109} 120.0000 UB 20.000 2.140 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS ANGLE NR2 CPH2 HR1 25.00 {SD= .109} 125.0000 UB 20.000 2.120 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE NR2 CPH2 NR1 130.00 {SD= .048} 112.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE NR3 CPH1 CPH1 145.00 {SD= .045} 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 ANGLE NR3 CPH1 CT2 45.80 {SD= .080} 122.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT ANGLE NR3 CPH1 HR1 22.00 {SD= .116} 122.0000 UB 15.000 2.180 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE NR3 CPH2 HR2 32.00 {SD= .096} 126.0000 UB 25.000 2.140 ! ALLOW ARO ! his, adm jr., 6/27/90 ANGLE NR3 CPH2 NR3 145.00 {SD= .045} 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 ANGLE NY CA CY 120.00 {SD= .050} 110.0000 UB 25.000 2.240 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE NY CA HA 32.00 {SD= .096} 125.0000 UB 25.000 2.177 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE NY CA HP 32.00 {SD= .096} 125.0000 UB 25.000 2.177 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole ANGLE NY CPT CA 160.00 {SD= .043} 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE NY CPT CPT 110.00 {SD= .052} 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk ANGLE O C CP1 80.00 {SD= .061} 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE O C CT1 80.00 {SD= .061} 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE O C CT2 80.00 {SD= .061} 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE O C CT3 80.00 {SD= .061} 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) ANGLE O C H 50.00 {SD= .077} 121.7000 ! ALLOW PEP POL ARO ! acetaldehyde (JCS), untested ANGLE O C N 80.00 {SD= .061} 122.5000 ! ALLOW PRO PEP POL ARO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE O C NH1 80.00 {SD= .061} 122.5000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) ANGLE O CC CP1 80.00 {SD= .061} 118.0000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 ANGLE O CC CT1 15.00 {SD= .140} 121.0000 UB 50.000 2.440 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update ANGLE O CC CT2 15.00 {SD= .140} 121.0000 UB 50.000 2.440 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update ANGLE O CC CT3 15.00 {SD= .140} 121.0000 UB 50.000 2.440 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update ANGLE O CC HA 44.00 {SD= .082} 122.0000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations ANGLE O CC NH2 75.00 {SD= .063} 122.5000 UB 50.000 2.370 ! ALLOW POL PEP ARO ! adm jr. 4/10/91, acetamide update ANGLE OB CD CP1 70.00 {SD= .065} 125.0000 UB 20.000 2.442 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE OB CD CT1 70.00 {SD= .065} 125.0000 UB 20.000 2.442 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE OB CD CT2 70.00 {SD= .065} 125.0000 UB 20.000 2.442 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE OB CD CT3 70.00 {SD= .065} 125.0000 UB 20.000 2.442 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent ANGLE OC CA CA 40.00 {SD= .086} 120.0000 ! ALLOW POL ARO ! adm jr. 8/27/91, phenoxide ANGLE OC CC CP1 40.00 {SD= .086} 118.0000 UB 50.000 2.388 ! ALLOW ALI PEP POL ARO ION PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE OC CC CT1 40.00 {SD= .086} 118.0000 UB 50.000 2.388 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) ANGLE OC CC CT2 40.00 {SD= .086} 118.0000 UB 50.000 2.388 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) ANGLE OC CC CT3 40.00 {SD= .086} 118.0000 UB 50.000 2.388 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) ANGLE OC CC OC 100.00 {SD= .054} 124.0000 UB 70.000 2.225 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) ANGLE OC CT2 CT3 65.00 {SD= .067} 122.0000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE OC CT2 HA 65.00 {SD= .067} 118.3000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE OC CT3 HA 65.00 {SD= .067} 118.3000 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE OH1 CA CA 45.20 {SD= .081} 120.0000 ! ALLOW ARO ALC ! PARALLH19 WITH [122.3] (JES) ANGLE OH1 CD CT2 55.00 {SD= .073} 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations ANGLE OH1 CD CT3 55.00 {SD= .073} 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations ANGLE OH1 CD OB 50.00 {SD= .077} 123.0000 UB 210.000 2.262 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations ANGLE OH1 CT1 CT1 75.70 {SD= .063} 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT1 CT3 75.70 {SD= .063} 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT1 HA 45.90 {SD= .080} 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT2 CT1 75.70 {SD= .063} 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT2 CT3 75.70 {SD= .063} 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT2 HA 45.90 {SD= .080} 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OH1 CT3 HA 45.90 {SD= .080} 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 ANGLE OS CD CP1 55.00 {SD= .073} 109.0000 UB 20.000 2.326 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 ANGLE OS CD CT1 55.00 {SD= .073} 109.0000 UB 20.000 2.326 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate ANGLE OS CD CT2 55.00 {SD= .073} 109.0000 UB 20.000 2.326 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate ANGLE OS CD CT3 55.00 {SD= .073} 109.0000 UB 20.000 2.326 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate ANGLE OS CD OB 90.00 {SD= .057} 125.9000 UB 160.000 2.258 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate ANGLE OS CT2 HA 60.00 {SD= .070} 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate ANGLE OS CT3 HA 60.00 {SD= .070} 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate ANGLE S CT2 CT1 58.00 {SD= .071} 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 ANGLE S CT2 CT2 58.00 {SD= .071} 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) ANGLE S CT2 CT3 58.00 {SD= .071} 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) ANGLE S CT2 HA 46.10 {SD= .080} 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 ANGLE S CT3 HA 46.10 {SD= .080} 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 ANGLE SM CT2 CT1 58.00 {SD= .071} 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 ANGLE SM CT2 HA 38.00 {SD= .088} 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 ANGLE SM CT3 HA 38.00 {SD= .088} 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 ANGLE SM SM CT2 72.50 {SD= .064} 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) ANGLE SM SM CT3 72.50 {SD= .064} 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) ANGLE SS CS CT3 55.00 {SD= .073} 118.0000 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 ANGLE SS CS HA 40.00 {SD= .086} 112.3000 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 !------------------------------------------------------------------------------------------------------ ! VARIOUS DIHEDRAL PARAMETERS: Energy Constant, Periodicity, Phase Shift ! (energy minima correspond to dihedral angles k*delta, 02.25 GUANIDINIUM (KK) DIHEDRAL X CD OH1 X 2.05 {SD= .380} 2 180.0000 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier DIHEDRAL X CD OS X 2.05 {SD= .380} 2 180.0000 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CP1 CC X .00 {SD=999999.000} 6 180.0000 ! ALLOW POL PEP ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 DIHEDRAL X CP1 CD X .00 {SD=999999.000} 6 180.0000 ! ALLOW POL PEP ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 DIHEDRAL X CP1 CP2 X .14 {SD= 1.454} 3 .0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 DIHEDRAL X CP2 CP2 X .16 {SD= 1.360} 3 .0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 DIHEDRAL X CP3 CP2 X .14 {SD= 1.454} 3 .0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2, changed RLD 12/11/92 DIHEDRAL X CPT CPT X .00 {SD=999999.000} 2 180.0000 ! ALLOW ARO ! JWK indole 05/14/91 DIHEDRAL X CT1 CC X .05 {SD= 2.433} 6 180.0000 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) DIHEDRAL X CT1 CD X .00 {SD=999999.000} 6 180.0000 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CT1 CT1 X .20 {SD= 1.217} 3 .0000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 DIHEDRAL X CT1 CT2 X .20 {SD= 1.217} 3 .0000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 DIHEDRAL X CT1 CT3 X .20 {SD= 1.217} 3 .0000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 DIHEDRAL X CT1 NH3 X .10 {SD= 1.721} 3 .0000 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) DIHEDRAL X CT1 OH1 X .14 {SD= 1.454} 3 .0000 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit DIHEDRAL X CT1 OS X -.10 {SD=999999.000} 3 .0000 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CT2 CA X .00 {SD=999999.000} 6 .0000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 DIHEDRAL X CT2 CC X .05 {SD= 2.433} 6 180.0000 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) DIHEDRAL X CT2 CD X .00 {SD=999999.000} 6 180.0000 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CT2 CT2 X .20 {SD= 1.232} 3 .0000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 DIHEDRAL X CT2 CT3 X .16 {SD= 1.360} 3 .0000 ! ALLOW ALI ! rotation barrier in Ethane (SF) DIHEDRAL X CT2 NC2 X .00 {SD=999999.000} 6 180.0000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 DIHEDRAL X CT2 NH3 X .10 {SD= 1.721} 3 .0000 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) DIHEDRAL X CT2 OH1 X .14 {SD= 1.454} 3 .0000 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit DIHEDRAL X CT2 OS X -.10 {SD=999999.000} 3 .0000 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CT3 CA X .00 {SD=999999.000} 6 .0000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 DIHEDRAL X CT3 CC X .05 {SD= 2.433} 6 180.0000 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) DIHEDRAL X CT3 CD X .00 {SD=999999.000} 6 180.0000 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate DIHEDRAL X CT3 CT3 X .15 {SD= 1.382} 3 .0000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 DIHEDRAL X CT3 NC2 X .00 {SD=999999.000} 6 180.0000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 DIHEDRAL X CT3 NH2 X .11 {SD= 1.641} 3 .0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 DIHEDRAL X CT3 NH3 X .09 {SD= 1.814} 3 .0000 ! ALLOW ALI POL ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 DIHEDRAL X CT3 OH1 X .14 {SD= 1.454} 3 .0000 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit DIHEDRAL X CT3 OS X -.10 {SD=999999.000} 3 .0000 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate !------------------------------------------------------------------------------------------------------------------ ! VARIOUS IMPROPER PARAMETERS: Energy Constant, Periodicity(0), Phase Shift(0) ! Improper angles are almost the same as dihedrals but they are introduced for PLANARITY maintaining, ! that's why they all have zero periodicity and phase shift (the only energy minima is 0) and no multiplicity. !------------------------------------------------------------------------------------------------------------------ IMPROPER HA C C HA 20.00 {SD= .122} 0 .0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) IMPROPER HA HA C C 20.00 {SD= .122} 0 180.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) IMPROPER HR1 NR1 NR2 CPH2 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! his, adm jr., 7/05/90 IMPROPER HR1 NR2 NR1 CPH2 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! his, adm jr., 7/05/90 IMPROPER HR3 CPH1 NR1 CPH1 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS IMPROPER HR3 CPH1 NR2 CPH1 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS IMPROPER HR3 CPH1 NR3 CPH1 1.00 {SD= .544} 0 .0000 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS IMPROPER HR3 NR1 CPH1 CPH1 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS IMPROPER HR3 NR2 CPH1 CPH1 .50 {SD= .770} 0 .0000 ! ALLOW ARO ! adm jr., 3/24/92, old aliphatic H VDW params for HIS IMPROPER N C CP1 CP3 .00 {SD=999999.000} 0 .0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 IMPROPER NC2 X X C 40.00 {SD= .086} 0 .0000 ! ALLOW PEP POL ARO ! 5.75->40.0 GUANIDINIUM (KK) IMPROPER NH1 X X H 20.00 {SD= .122} 0 .0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) IMPROPER NH2 X X H 4.00 {SD= .272} 0 .0000 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER NR1 CPH1 CPH2 H .45 {SD= .811} 0 .0000 ! ALLOW ARO ! his, adm jr., 7/05/90 IMPROPER NR1 CPH2 CPH1 H .45 {SD= .811} 0 .0000 ! ALLOW ARO ! his, adm jr., 7/05/90 IMPROPER NR3 CPH1 CPH2 H 1.20 {SD= .497} 0 .0000 ! ALLOW ARO ! his, adm jr., 6/27/90 IMPROPER NR3 CPH2 CPH1 H 1.20 {SD= .497} 0 .0000 ! ALLOW ARO ! his, adm jr., 6/27/90 IMPROPER NY CA CY CPT 100.00 {SD= .054} 0 .0000 ! ALLOW ARO !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. IMPROPER O CP1 NH2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 IMPROPER O CT1 NH2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O CT2 NH2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O CT3 NH2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O HA NH2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL PRO ! adm jr., 5/13/91, formamide geometry and vibrations IMPROPER O N CT2 CC 120.00 {SD= .050} 0 .0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 IMPROPER O NH2 CP1 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 IMPROPER O NH2 CT1 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O NH2 CT2 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O NH2 CT3 CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations IMPROPER O NH2 HA CC 45.00 {SD= .081} 0 .0000 ! ALLOW PEP POL ! adm jr., 5/13/91, formamide geometry and vibrations IMPROPER O X X C 120.00 {SD= .050} 0 .0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) IMPROPER OB X X CD 100.00 {SD= .054} 0 .0000 ! ALLOW ALC ARO POL ! adm jr., 10/17/90, acetic acid vibrations IMPROPER OC X X CC 96.00 {SD= .056} 0 .0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) !--------------------------------------------------------------------------------------------------- ! Here are supplied DEFAULT ENERGY PARAMETERS for nonbonded atom interactions. !--------------------------------------------------------------------------------------------------- NBONDS ! -----NONBONDED-LIST-OPTIONS------------------------------- CUTNB= 13.000 TOLERANCE= .500 WMIN= 1.500 ATOM INHIBIT= .250 ! -----ELECTROSTATIC OPTIONS-------------------------------- EPS= 1.000 E14FAC= 1.000 CDIELECTRIC SHIFT ! -----VAN DER WAALS OPTIONS-------------------------------- VSWITCH ! -----SWITCHING /SHIFTING PARAMETERS----------------------- CTONNB= 10.000 CTOFNB= 12.000 ! -----EXCLUSION LIST OPTIONS------------------------------- NBXMOD= 5 ! ---------------------------------------------------------- END !------------------------------------------------------------------------------------------------- ! VAN-DER-VAALS PARAMETERS: Energy Well Depth, Distance of Minimum(div. by 2**1/6) ! for "atoms itself", i.e. for X-X interactions; for X-Y interactions the parameters ! values are taken as arithmetic mean of appropriate "atomic" parameters. ! "(1:4)" values refer to special intramolecular interactions between atoms connected through ! three bonds. These interactions are taken into consideration only when NBXMOD switch is set ! to 5 in NBONDS...END statement, which is taken for default (see 10 lines above). !------------------------------------------------------------------------------------------------- ! EPS SIGMA EPS(1:4) SIGMA(1:4) NONBONDED C .1100 4.0090 .1100 4.0090 ! ALLOW PEP POL ARO ! NMA nonbond and solvent properties, adm jr., 2/3/92 NONBONDED CA .0700 3.5501 .0700 3.5501 ! ALLOW ARO ! benzene (JES) NONBONDED CC .0700 3.5636 .0700 3.5636 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation NONBONDED CD .0700 3.5636 .0700 3.5636 ! ALLOW POL ! adm jr. 3/19/92, acetate a.i. and dH of solvation NONBONDED CP1 .0200 4.0536 .0100 3.3854 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 NONBONDED CP2 .0550 3.8754 .0100 3.3854 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 NONBONDED CP3 .0550 3.8754 .0100 3.3854 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 NONBONDED CPH1 .0500 3.2072 .0500 3.2072 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation NONBONDED CPH2 .0500 3.2072 .0500 3.2072 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation NONBONDED CPT .0900 3.2072 .0900 3.3854 ! ALLOW ARO ! benzene (JES) NONBONDED CS .1100 3.9200 .1100 3.9200 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 NONBONDED CT1 .0200 4.0536 .0100 3.3854 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 NONBONDED CT2 .0550 3.8754 .0100 3.3854 ! ALLOW ALI ! propane pure solvent properties, adm jr, 2/3/92 NONBONDED CT3 .0800 3.6705 .0100 3.3854 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 NONBONDED CY .0700 3.5501 .0700 3.5501 ! ALLOW ARO ! TRP, JWK 08/29/89 NONBONDED H .0460 .4000 .0460 .4000 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 NONBONDED HA .0220 2.3520 .0220 2.3520 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 NONBONDED HB .0220 2.3520 .0220 2.3520 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 NONBONDED HC .0460 .4000 .0460 .4000 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NONBONDED HP .0300 2.4200 .0300 2.4200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy NONBONDED HR1 .0460 1.6036 .0460 1.6036 ! ALLOW ARO ! adm jr., 6/27/90, his NONBONDED HR2 .0460 1.2473 .0460 1.2473 ! ALLOW ARO ! adm jr., 6/27/90, his NONBONDED HR3 .0078 2.6157 .0078 2.6157 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NONBONDED HS .1000 .8018 .1000 .8018 ! ALLOW SUL ! methanethiol pure solvent, adm jr., 6/22/92 NONBONDED N .2000 3.2963 .2000 3.2963 ! ALLOW PRO ! ALL NITROGENS NOW IDENTICAL, ADM JR., 10/3/89 NONBONDED NC2 .2000 3.2963 .2000 3.2963 ! ALLOW POL ! JG 8/27/89; note: NH1 in ARG was changed to NC2. NONBONDED NH1 .2000 3.2963 .2000 2.7618 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NONBONDED NH2 .2000 3.2963 .2000 3.2963 ! ALLOW POL ! adm jr. NONBONDED NH3 .2000 3.2963 .2000 3.2963 ! ALLOW POL ! adm jr. NONBONDED NP .2000 3.2963 .2000 3.2963 ! ALLOW PRO ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 NONBONDED NR1 .2000 3.2963 .2000 3.2963 ! ALLOW ARO ! His, adm jr., 9/4/89 NONBONDED NR2 .2000 3.2963 .2000 3.2963 ! ALLOW ARO ! His, adm jr., 9/4/89 NONBONDED NR3 .2000 3.2963 .2000 3.2963 ! ALLOW ARO ! His, adm jr., 9/4/89 NONBONDED NY .2000 3.2963 .2000 3.2963 ! ALLOW ARO ! trp, JWK NONBONDED O .1200 3.0291 .1200 2.4945 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NONBONDED OB .1200 3.0291 .1200 2.4945 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid carbonyl O NONBONDED OC .1200 3.0291 .1200 3.0291 ! ALLOW POL ION ! JG 8/27/89 NONBONDED OH1 .1521 3.1538 .1521 3.1538 ! ALLOW ALC ARO ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) NONBONDED OS .1521 3.1538 .1521 3.1538 ! ALLOW ALC ARO ! adm jr. 9/17/90, avoid O* wildcard ! NONBONDED S .4500 3.5636 .4500 3.5636 ! ALLOW SUL ION ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent NONBONDED SM .3800 3.5190 .3800 3.5190 ! ALLOW SUL ION ! adm jr., 3/3/92, dimethyldisulphide pure solvent NONBONDED SS .4700 3.9200 .4700 3.9200 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 !------------------------------------------------------------------------------------------------------------- ! H-BOND GLOBAL DEFAULTS and PARTICULAR PAIR's PARAMETERS: Energy Well Depth, Equilibrium Distance ! intended for explicit hydrogen bond description. Since it's exotics then EMIN is set to zero and defaults ! are "commented off"; it practically exludes this energy term. To use it it is necessary to create globals ! anew and substitute desired EMIN values. !------------------------------------------------------------------------------------------------------------- ! HBOND for analysis only ! HBONDS ! -----HYDROGEN-BOND-LIST-OPTIONS--------------------------- ! TOLERANCE= .500 ! DCUTOFF= 7.50 DOFF= 6.50 DON= 5.50 ! ACUTOFF=100.00 AOFF= 80.00 AON= 60.00 ! ACCEPTOR= TRUE ! REXP= 6 AEXP= 4 HAEX= 0 AAEX= 0 ! ---------------------------------------------------------- ! END ! HBOND EMIN RMIN HBOND N*+* N% .0000 3.0000 HBOND N*+* O* .0000 2.8500 ! SUREADD HBOND O* N*+* .0000 2.9000 HBOND OH* N% .0000 2.8500 HBOND OH* O* .0000 2.7500 HBOND S N% .0000 3.0000 HBOND S O* .0000 2.9000 !--------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------- SET ECHO=TRUE END