[Swift-commit] r5935 - in SwiftApps/CMTS/scaling: . conf input_files
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Thu Sep 20 10:45:33 CDT 2012
Author: davidk
Date: 2012-09-20 10:45:29 -0500 (Thu, 20 Sep 2012)
New Revision: 5935
Added:
SwiftApps/CMTS/scaling/conf/fusion.cf
SwiftApps/CMTS/scaling/conf/fusion.xml
SwiftApps/CMTS/scaling/input_files/par_all22_prot.inp
SwiftApps/CMTS/scaling/plot.sh
Modified:
SwiftApps/CMTS/scaling/conf/local.cf
SwiftApps/CMTS/scaling/input_files/h0_eq.conf
SwiftApps/CMTS/scaling/namd_wrapper.sh
SwiftApps/CMTS/scaling/runscaling.sh
SwiftApps/CMTS/scaling/scaling.swift
Log:
Various updates to scaling scripts
Added: SwiftApps/CMTS/scaling/conf/fusion.cf
===================================================================
--- SwiftApps/CMTS/scaling/conf/fusion.cf (rev 0)
+++ SwiftApps/CMTS/scaling/conf/fusion.cf 2012-09-20 15:45:29 UTC (rev 5935)
@@ -0,0 +1,11 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+
+#app namd_wrapper=$PWD/../namd_wrapper.sh
+#app plot=$PWD/../plot.sh
Added: SwiftApps/CMTS/scaling/conf/fusion.xml
===================================================================
--- SwiftApps/CMTS/scaling/conf/fusion.xml (rev 0)
+++ SwiftApps/CMTS/scaling/conf/fusion.xml 2012-09-20 15:45:29 UTC (rev 5935)
@@ -0,0 +1,18 @@
+<config>
+<pool handle="grotthuss">
+ <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxWallTime">01:00:00</profile>
+ <profile namespace="globus" key="maxTime">3600</profile>
+ <profile key="jobsPerNode" namespace="globus">8</profile>
+ <profile key="slots" namespace="globus">1</profile>
+ <profile key="maxNodes" namespace="globus">1</profile>
+ <profile key="jobThrottle" namespace="karajan">5.99</profile>
+ <profile key="initialScore" namespace="karajan">10000</profile>
+ <profile key="count" namespace="globus">1</profile>
+ <profile key="jobType" namespace="globus">single</profile>
+ <profile key="ppn" namespace="globus">8</profile>
+ <workdirectory>_WORK_</workdirectory>
+</pool>
+</config>
+
Modified: SwiftApps/CMTS/scaling/conf/local.cf
===================================================================
--- SwiftApps/CMTS/scaling/conf/local.cf 2012-09-19 04:24:57 UTC (rev 5934)
+++ SwiftApps/CMTS/scaling/conf/local.cf 2012-09-20 15:45:29 UTC (rev 5935)
@@ -7,4 +7,5 @@
provider.staging.pin.swiftfiles=false
use.wrapper.staging=false
-#app rmsd=$PWD/../rmsd.sh
+#app namd_wrapper=$PWD/../namd_wrapper.sh
+#app plot=$PWD/../plot.sh
Modified: SwiftApps/CMTS/scaling/input_files/h0_eq.conf
===================================================================
--- SwiftApps/CMTS/scaling/input_files/h0_eq.conf 2012-09-19 04:24:57 UTC (rev 5934)
+++ SwiftApps/CMTS/scaling/input_files/h0_eq.conf 2012-09-20 15:45:29 UTC (rev 5935)
@@ -5,32 +5,30 @@
# Minimization and equilibration of waters with
# protein held fixed to reduce artifacts
-set WORK _WORK_
-
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
-structure $WORK/h0_solvion.psf
-coordinates $WORK/h0_solvion.pdb
+structure h0_solvion.psf
+coordinates h0_solvion.pdb
#############################################################
# Output Names ##
#############################################################
-set basename h0_eq.JOB
-outputName $WORK/OUT/$basename
-DCDfile $WORK/OUT/$basename.dcd
-restartname $WORK/RESTART/$basename.restart
+set basename h0_eq._JOB_
+outputName $basename
+DCDfile $basename.dcd
+restartname $basename.restart
# Initial temperature
set temperature 310
# Continuing a job from the restart files
if {1} {
-set inputname h0_eq.0
-binCoordinates $WORK/RESTART/$inputname.restart.coor
-binVelocities $WORK/RESTART/$inputname.restart.vel
-extendedSystem $WORK/RESTART/$inputname.restart.xsc
+set inputname h0_eq.0
+binCoordinates $inputname.restart.coor
+binVelocities $inputname.restart.vel
+extendedSystem $inputname.restart.xsc
}
firsttimestep 0
@@ -41,7 +39,7 @@
# Input
paraTypeCharmm on
-parameters $WORK/par_all22_prot.inp
+parameters par_all22_prot.inp
# Periodic Boundary Conditions from extended system cell (.xsc)
wrapWater on
@@ -106,4 +104,4 @@
## EXECUTION SCRIPT ##
#############################################################
-run 5000
+run 500
Added: SwiftApps/CMTS/scaling/input_files/par_all22_prot.inp
===================================================================
--- SwiftApps/CMTS/scaling/input_files/par_all22_prot.inp (rev 0)
+++ SwiftApps/CMTS/scaling/input_files/par_all22_prot.inp 2012-09-20 15:45:29 UTC (rev 5935)
@@ -0,0 +1,3330 @@
+*>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<
+*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
+*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
+* All comments to ADM jr. via the CHARMM web site: www.charmm.org
+* parameter set discussion forum
+*
+
+! references
+!
+!PROTEINS
+!
+!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
+!treatment of backbone energetics in protein force fields: limitations
+!of gas-phase quantum mechanics in reproducing protein conformational
+!distributions in molecular dynamics simulations, Journal of
+!Computational Chemistry, 25: 1400-1415, 2004.
+!
+!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.
+!
+!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)
+!
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+NH2 CT1 240.00 1.455 ! From LSN NH2-CT2
+!Carbon Dioxide
+CST OST 937.96 1.1600 ! JES
+!Heme to Sulfate (PSUL) link
+SS FE 250.0 2.3200 !force constant a guess
+ !equilbrium bond length optimized to reproduce
+ !CSD survey values of
+ !2.341pm0.01 (mean, standard error)
+ !adm jr., 7/01
+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 CE1 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
+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
+
+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
+!
+H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2
+NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2
+NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2
+CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1
+CT3 CT1 CD 52.000 108.00 ! Ala cter
+NH2 CT1 HB 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA
+NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C
+!Carbon Dioxide, JES
+OST CST OST 3000.00 180.0000 ! CO2, JES
+!Heme to Sulfate (PSUL) link
+CS SS FE 50.0 100.6 !force constant a guess
+ !equilibrium angle optimized to reproduce
+ !CSD survey values
+ !107.5pm0.6 (mean, standard error)
+ !adm jr., 7/01
+SS FE NPH 100.0 90.0 !force constant a guess
+ !adm jr., 7/01
+!
+CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
+ ! JES 8/25/89
+CE1 CE1 CT2 48.00 123.50 !
+ ! for 2-butene, yin/adm jr., 12/95
+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 CE1 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 CE1 CE2 70.000 121.5000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CPB CPB CE1 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
+CT3 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
+ ! 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
+HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+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
+ ! 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 HA 38.000 109.50 50.00 2.14000
+ !from NH2 CT3 HA, neutral lysine
+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 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
+ !from NH3 CT2 CT2, neutral lysine
+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
+ ! 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 CT3 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
+ ! 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
+ ! 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 CT2 58.000 112.5000 ! ALLOW ALI SUL ION
+ ! as in expt.MeEtS & DALC crystal, 5/15/92
+SM CT2 CT3 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
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+!Neutral N terminus
+NH2 CT1 C O 0.0000 1 0.00
+NH2 CT1 C NH1 0.0000 1 0.00
+H NH2 CT1 CT1 0.0000 1 0.00
+H NH2 CT1 C 0.000 1 0.00
+H NH2 CT1 HB 0.110 3 0.00 ! From LSN HC-NH2-CT2-HA
+H NH2 CT1 CT2 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2
+H NH2 CT1 CT3 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2
+!Heme to Sulfate (PSUL) link
+X FE SS X 0.0000 4 0.00 ! guess
+ !adm jr., 7/01
+X CS SS X 0.0000 3 0.20 ! guess
+ !from methanethiol, HS S CT3 HA
+ !adm jr., 7/01
+
+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 1 180.00 !
+ ! 1-butene, adm jr., 2/00 update
+CE2 CE1 CT2 CT3 1.3000 3 180.00 !
+ ! 1-butene, adm jr., 2/00 update
+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
+ ! 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
+ ! 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 CE1 HE1 1.0000 2 180.00 !
+ ! 2-butene, adm jr., 8/98 update
+CT3 CE1 CE1 HE1 1.0000 2 180.00 !
+ ! 2-butene, adm jr., 8/98 update
+HE1 CE1 CE2 HE2 5.2000 2 180.00 !
+ ! for propene, yin/adm jr., 12/95
+HE1 CE1 CT2 HA 0.0000 3 0.00
+ ! butene, adm jr., 2/00 update
+HE1 CE1 CT2 CT3 0.1200 3 0.00 !
+ ! for butene, yin/adm jr., 12/95
+HE1 CE1 CT3 HA 0.0000 3 0.00
+ ! butene, adm jr., 2/00 update
+HE2 CE2 CE1 CT2 5.2000 2 180.00 !
+ ! for butene, yin/adm jr., 12/95
+HE2 CE2 CE1 CPB 5.2000 2 180.00 !
+ ! for vinyl, from 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 CT2 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral lysine
+HC NH2 CT2 HA 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral lysine
+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 4/23/93
+N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! from NH1 C CT1 CT2, for lactams, adm jr.
+NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! adm jr. 3/24/92, for PRES GLYP
+NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK
+NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! Backbone parameter set made complete RLD 8/8/90
+O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP
+ ! from O C CT1 CT2, for lactams, adm jr.
+O C CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! Backbone parameter set made complete RLD 8/8/90
+O C CT3 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP3 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP3 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 H 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! adm jr. 4/10/91, acetamide update
+OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! adm jr. 8/27/91, phenoxide
+OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO
+ ! adm jr. 8/27/91, phenoxide
+OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
+ ! adm jr. 4/17/94, zwitterionic glycine
+OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
+ ! adm jr. 4/17/94, zwitterionic glycine
+OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 phenol
+OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 phenol
+S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
+SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
+SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+!X C C X 4.0000 2 180.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO
+ ! 9.0->2.25 GUANIDINIUM (KK)
+X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC
+ ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
+X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CE1 CE1 X 0.1500 1 0.00
+ ! 2-butene, adm jr., 2/00 update
+X CE1 CE1 X 8.5000 2 180.00
+ ! 2-butene, adm jr., 2/00 update
+X CE2 CE2 X 4.9000 2 180.00 !
+ ! for ethene, yin/adm jr., 12/95
+X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! changed to 0.0 RLD 5/19/92
+X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
+X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
+ ! toluene, adm jr., 3/7/92
+X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI
+ ! rotation barrier in Ethane (SF)
+X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
+X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
+ ! toluene, adm jr., 3/7/92
+X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL
+ ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92
+X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X FE CM X 0.0500 4 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): ligands (KK 05/13/91)
+X FE NPH X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
+X FE NR2 X 0.0500 4 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): from param19.inp
+X FE OM X 0.0000 4 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): ligands (KK 05/13/91)
+X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK, from propene (JCS))
+HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK, from propene (JCS))
+HE2 HE2 CE2 CE2 3.0 0 0.00 !
+ ! for ethene, yin/adm jr., 12/95
+HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! 5.75->40.0 GUANIDINIUM (KK)
+NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! NMA Vibrational Modes (LK)
+NH2 X X H 4.0000 0 0.0000 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO
+ !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf.
+O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! NMA Vibrational Modes (LK)
+OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL
+ ! adm jr., 10/17/90, acetic acid vibrations
+OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+
+CMAP
+! 2D grid correction data. The following surfaces are the correction
+! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces.
+! Use of CMAP requires generation with the topology file containing the
+! CMAP specifications along with version 31 or later of CHARMM. Note that
+! use of "skip CMAP" yields the charmm22 energy surfaces.
+!
+! references
+!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of
+!Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted
+!for publication.
+
+!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the
+!Protein Backbone in Empirical Force Fields, Journal of the American Chemical
+!Society, In Press.
+
+
+! alanine map
+C NH1 CT1 C NH1 CT1 C NH1 24
+
+!-180
+0.126790 0.768700 0.971260 1.250970 2.121010
+2.695430 2.064440 1.764790 0.755870 -0.713470
+0.976130 -2.475520 -5.455650 -5.096450 -5.305850
+-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
+-2.335350 -2.010440 -1.608040 -0.482250
+
+!-165
+-0.802290 1.377090 1.577020 1.872290 2.398990
+2.461630 2.333840 1.904070 1.061460 0.518400
+-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
+-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
+-1.008810 -0.637100 -1.603360 -1.776870
+
+!-150
+-0.634810 1.156210 1.624350 2.047200 2.653910
+2.691410 2.296420 1.960450 1.324930 2.038290
+-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
+-1.039340 -1.618060 -1.725460 -1.376360
+
+!-135
+0.214000 1.521370 1.977440 2.377950 2.929470
+2.893410 2.435810 2.162970 1.761500 1.190090
+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
+
+!-120
+0.873950 1.959160 2.508990 2.841100 3.698960
+3.309330 2.614300 2.481720 2.694660 1.082440
+-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
+-0.855480 -0.087320 0.439040 0.691880 -0.586330
+-1.027210 -0.976640 -0.467580 0.104020
+
+!-105
+1.767380 2.286650 2.818030 3.065500 3.370620
+3.397440 2.730310 2.878790 2.542010 1.545240
+-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
+-0.306240 -0.122440 0.444680 0.810150 -0.058630
+-0.270290 -0.178830 0.202360 0.493810
+
+!-90
+1.456010 2.743180 2.589450 3.046230 3.451510
+3.319160 3.052900 3.873720 2.420650 0.949100
+0.008370 -1.382980 -2.138930 -2.087380 -1.268300
+-0.494370 0.267580 0.908250 0.537520 0.306260
+0.069540 0.097460 0.263060 0.603220
+
+!-75
+1.396790 3.349090 2.180920 2.942960 3.814070
+3.675800 3.555310 3.887290 2.101260 -0.190940
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+-0.339050 -0.563330 -0.794980 -0.710760
+
+!-135
+-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
+-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
+-1.062570 0.338010 -4.372310 -2.435890 -2.220710
+-1.718060 -0.758950 -0.207560 0.100910 -0.055650
+-0.288370 -0.880610 -1.267450 -1.465530
+
+!-120
+-2.348270 -2.593790 -2.596140 -2.364070 -1.970070
+-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
+-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
+-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
+-0.661220 -1.068330 -1.601800 -1.914850
+
+!-105
+-2.788800 -3.079570 -3.178150 -3.013710 -2.626630
+-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
+-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
+-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
+-0.950190 -1.401500 -1.959970 -2.412680
+
+!-90
+-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
+-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
+-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
+-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
+-1.141350 -1.794480 -2.420970 -2.939990
+
+!-75
+-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
+-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
+-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
+-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
+-1.892510 -2.659400 -3.347950 -3.970600
+
+!-60
+-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
+-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
+-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
+-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
+-2.948140 -4.008100 -4.821040 -5.565810
+
+!-45
+-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
+-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
+-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
+-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
+-4.094860 -5.207530 -6.128530 -6.613030
+
+!-30
+-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
+-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
+-3.181640 -3.594720 -1.231370 -0.603790 0.128810
+-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
+-4.731110 -5.844860 -6.428460 -6.424880
+
+!-15
+-3.991110 -2.046000 0.082550 -2.676110 -2.828500
+-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
+-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
+-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
+-5.330320 -5.992270 -5.588080 -5.408360
+
+!0
+-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
+-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
+-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
+-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
+-4.537100 -4.619970 -4.310890 -3.318290
+
+!15
+-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
+-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
+-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
+-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
+-2.828500 -2.676110 0.082550 -2.046000
+
+!30
+-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
+-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
+0.128810 -0.603790 -1.231370 -3.594720 -3.181640
+-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
+-0.729200 -0.974400 -2.788600 -4.434060
+
+!45
+-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
+-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
+-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
+-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
+-1.708710 -2.714090 -4.362190 -5.850030
+
+!60
+-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
+-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
+-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
+-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
+-2.683230 -4.000820 -4.878940 -5.456080
+
+!75
+-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
+-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
+-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
+-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
+-3.228630 -3.892550 -4.485310 -4.995210
+
+!90
+-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
+-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
+-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
+-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
+-3.040850 -3.611370 -3.902110 -3.713610
+
+!105
+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
+-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
+-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
+-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
+-2.626630 -3.013710 -3.178150 -3.079570
+
+!120
+-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
+-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
+-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
+-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
+-1.970070 -2.364070 -2.596140 -2.593790
+
+!135
+-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
+-0.055650 0.100910 -0.207560 -0.758950 -1.718060
+-2.220710 -2.435890 -4.372310 0.338010 -1.062570
+-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
+-1.567160 -1.803720 -2.143020 -2.117750
+
+!150
+-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
+-0.092820 0.033160 0.000490 -0.628990 -1.664160
+-2.225630 -2.949180 0.753400 -1.546500 -2.165440
+-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
+-1.119780 -1.656770 -1.665900 -1.482430
+
+!165
+-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
+-0.000430 0.196710 0.180860 -0.410680 -1.810120
+-2.675640 1.822690 -1.636020 -3.153350 -2.780320
+-1.715700 -0.534910 0.258100 0.329180 -0.126160
+-0.940260 -1.319240 -0.990850 -0.896700
+
+NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+ !adm jr., 5/08/91, suggested cutoff scheme
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
+!
+!carbons
+C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
+ ! NMA pure solvent, adm jr., 3/3/93
+CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
+ ! benzene (JES)
+CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
+ ! adm jr. 3/3/92, acetic acid heat of solvation
+CD 0.000000 -0.070000 2.000000 ! ALLOW POL
+ ! adm jr. 3/19/92, acetate a.i. and dH of solvation
+CE1 0.000000 -0.068000 2.090000 !
+ ! for propene, yin/adm jr., 12/95
+CE2 0.000000 -0.064000 2.080000 !
+ ! for ethene, yin/adm jr., 12/95
+CM 0.000000 -0.110000 2.100000 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
+CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
+CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
+CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO
+ ! benzene (JES)
+CS 0.000000 -0.110000 2.200000 ! ALLOW SUL
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+CST 0.000000 -0.058000 1.563000 !
+ ! carbon dioxide, JES
+CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! isobutane pure solvent properties, adm jr, 2/3/92
+CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! propane pure solvent properties, adm jr, 2/3/92
+CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+CY 0.000000 -0.070000 1.992400 ! ALLOW ARO
+ ! TRP, JWK 08/29/89
+!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
+CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! from CT1x: needs work
+CT1x 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92: needs work
+CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+! hydrogens
+H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
+ ! same as TIP3P hydrogen, adm jr., 7/20/89
+HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HE1 0.000000 -0.031000 1.250000 !
+ ! for propene, yin/adm jr., 12/95
+HE2 0.000000 -0.026000 1.260000 !
+ ! for ethene, yin/adm jr., 12/95
+HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HC 0.000000 -0.046000 0.224500 ! ALLOW POL
+ ! new, small polar Hydrogen, see also adm jr. JG 8/27/89
+HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO
+ ! JES 8/25/89 values from Jorgensen fit to hydration energy
+HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO
+ ! adm jr., 6/27/90, his
+HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO
+ ! adm jr., 6/27/90, his
+HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS 0.000000 -0.100000 0.450000 ! ALLOW SUL
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
+ !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
+!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
+HA1 0.0 -0.022 1.3200 ! alkane, 3/92
+HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
+HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
+!nitrogens
+N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
+NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+NH2 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! adm jr.
+NH3 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! adm jr.
+NP 0.000000 -0.200000 1.850000 ! ALLOW PRO
+ ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90
+NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NY 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! trp, JWK
+! oxygens
+O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO
+ ! adm jr., 10/17/90, acetic acid carbonyl O
+OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
+ ! JG 8/27/89
+OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
+ ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
+OM 0.000000 -0.120000 1.700000 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
+OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
+ ! adm jr. 9/17/90, avoid O* wildcard
+OST 0.000000 -0.165000 1.692000 !
+ ! carbon dioxide, JES
+OT 0.000000 -0.152100 1.768200 ! ALLOW WAT
+ !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
+! sulfurs
+S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION
+ ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
+SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION
+ ! adm jr., 3/3/92, dimethyldisulphide pure solvent
+SS 0.000000 -0.470000 2.200000 ! ALLOW SUL
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+! ions and miscellaneous types
+SOD 0.0 -0.0469 1.36375 ! sodium
+ ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
+POT 0.0 -0.0870 1.76375 ! potassium
+ ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
+CLA 0.0 -0.150 2.27 ! chloride
+ ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
+CAL 0.0 -0.120 1.367 ! Calcium
+ ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
+!CAL 0.000000 -0.120000 1.710000 ! Calcium (BP) in proteins prior
+ ! to 2003; not recommended due to need for NBFIX terms
+MG 0.0 -0.0150 1.18500 ! Magnesium
+ ! B. Roux dA = -441.65
+CES 0.0 -0.1900 2.100
+ ! Cesium, so far untested.
+ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
+ ! RHS March 18, 1990
+FE 0.010000 0.000000 0.650000 ! ALLOW HEM
+ ! Heme (6-liganded): Iron atom (KK 05/13/91)
+HE 0.000000 -0.021270 1.4800 !
+ ! helium, experimental pot. energy surface, adm jr., 12/95
+NE 0.000000 -0.086000 1.5300
+ ! neon, semiempirical pot. energy surface, adm jr., 12/95
+CLAL 0.000000 -0.030000 1.908200 ! chlorine from Jorgensen/BOSS
+ ! for choroacetaldehyde
+DUM 0.000000 -0.000000 0.000000 !
+ ! dummy atom
+!pyridine series LJ parametes (see toppar_pyridines.str)
+CAP 0.000000 -0.070000 1.992400 !
+FA 0.000000 -0.12000 1.700000
+ ! from 1,3-difluorobenzene pure solvent
+CN 0.000000 -0.200000 1.750000 ! cyanopyridine
+NC 0.000000 -0.600000 1.850000 ! cyanopyridine
+OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp
+COA 0.000000 -0.110000 2.000000 ! 3acp
+!fluorinated alkanes LJ parameters (see toppar_fluoro_alkanes.str)
+CF1 0.000000 -0.060000 1.900000
+CF2 0.000000 -0.042000 2.050000
+CF3 0.000000 -0.020000 2.300000
+HF1 0.000000 -0.028000 1.3200
+HF2 0.000000 -0.030000 1.3000
+F1 0.0 -0.135 1.63
+F2 0.0 -0.105 1.63
+F3 0.0 -0.097 1.60
+!protein model compounds (see toppar_all22_prot_model.str)
+C3 0.000000 -0.020000 2.275000 ! cyclopropane, JMW and CBP 4/04
+!retinol model compounds
+CC1A 0.0 -0.0680 2.0900 !
+CC1B 0.0 -0.0680 2.0900 !
+CC2 0.0 -0.0640 2.0800 !
+NS1 0.000000 -0.200000 1.850000 !N for deprotonated Schiff's base
+NS2 0.000000 -0.200000 1.850000 !N for protonated Schiff's base
+
+HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
+ ! READ PARAM APPEND CARD
+ ! to append hbond parameters from the file: par_hbond.inp
+
+END
Modified: SwiftApps/CMTS/scaling/namd_wrapper.sh
===================================================================
--- SwiftApps/CMTS/scaling/namd_wrapper.sh 2012-09-19 04:24:57 UTC (rev 5934)
+++ SwiftApps/CMTS/scaling/namd_wrapper.sh 2012-09-20 15:45:29 UTC (rev 5935)
@@ -1,10 +1,8 @@
-#!/bin/bash
+#!/bin/bash -x
-echo Args are: $@
-echo Node file is: $PBS_NODEFILE
-echo Contents of nodefile: $( cat $PBS_NODEFILE )
+numNodes=$1
+namdConf=h0_eq.$numNodes.conf
-sed -ei 's/_WORK_/$PWD/g' h0_eq.conf
-
-mpiexec namd2 h0_eq.conf
-
+echo Arguments are: $@
+sed -e "s/_JOB_/$numNodes/g" h0_eq.conf > $namdConf
+mpiexec namd2 $namdConf
Added: SwiftApps/CMTS/scaling/plot.sh
===================================================================
--- SwiftApps/CMTS/scaling/plot.sh (rev 0)
+++ SwiftApps/CMTS/scaling/plot.sh 2012-09-20 15:45:29 UTC (rev 5935)
@@ -0,0 +1,3 @@
+# Get scaling results and plot them
+# CPUS vs days per ns
+grep -m 1 "Bench" logs/*.out | gawk -F" " '{print $4,$8}' > scale.dat
Modified: SwiftApps/CMTS/scaling/runscaling.sh
===================================================================
--- SwiftApps/CMTS/scaling/runscaling.sh 2012-09-19 04:24:57 UTC (rev 5934)
+++ SwiftApps/CMTS/scaling/runscaling.sh 2012-09-20 15:45:29 UTC (rev 5935)
@@ -66,6 +66,9 @@
export WORK=$PWD/swiftwork
mkdir -p $PWD/swiftwork/workers
+# Create CDM config
+# echo "rule .* DIRECT $PWD" >> fs.data
+
# Use start-coaster-service if the site uses a .conf file
if [ "$USE_SCS" == "1" ]; then
cp ../conf/$execsite.conf coaster-service.conf
Modified: SwiftApps/CMTS/scaling/scaling.swift
===================================================================
--- SwiftApps/CMTS/scaling/scaling.swift 2012-09-19 04:24:57 UTC (rev 5934)
+++ SwiftApps/CMTS/scaling/scaling.swift 2012-09-20 15:45:29 UTC (rev 5935)
@@ -1,15 +1,23 @@
type file;
-app (file out, file err) namd_wrapper (int numnodes, file psf_file, file pdb_file, file coord_restart_file,
- file velocity_restart_file, file system_restart_file)
+// Namd wrapper
+app (file out, file err) namd_wrapper (int numnodes, file psf_file, file pdb_file,
+ file coord_restart_file, file velocity_restart_file,
+ file system_restart_file, file namd_conf, file charmm_params)
{
profile "count" = numnodes;
- namd_wrapper @psf_file @pdb_file @coord_restart_file @velocity_restart_file @system_restart_file stdout=@out stderr=@err;
+ namd_wrapper numnodes @namd_conf stdout=@out stderr=@err;
}
+// Plotting script
+app (file png) plot (file[] namdlogs)
+{
+ plot @png @namdlogs;
+}
+
# Range of nodes to test on
int minNodes=1;
-int maxNodes=2;
+int maxNodes=4;
int delta=1;
# Files
@@ -18,10 +26,20 @@
file coord_restart <"h0_eq.0.restart.coor">;
file velocity_restart <"h0_eq.0.restart.vel">;
file system_restart <"h0_eq.0.restart.xsc">;
+file namd_config <"h0_eq.conf">;
+file charmm_parameters <"par_all22_prot.inp">;
+file logs[];
+// Run scaling tests
foreach nodes in [minNodes:maxNodes:delta] {
- file output <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".out")>;
- file error <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".err")>;
- (output, error) = namd_wrapper(nodes, psf, pdb, coord_restart, velocity_restart, system_restart);
+ file namd_output <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".out")>;
+ file namd_error <single_file_mapper; file=@strcat("logs/h0scale.", nodes, ".err")>;
+ (namd_output, namd_error) = namd_wrapper(nodes, psf, pdb, coord_restart, velocity_restart,
+ system_restart, namd_config, charmm_parameters);
+ logs[nodes] = namd_output;
}
+// Plot output
+file plot_output <"scale.dat">;
+plot_output = plot(logs);
+
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