CHARMM> banner 1 Chemistry at HARvard Macromolecular Mechanics (CHARMm) - Version 42.2 Copyright(c) 1984-2014 President and Fellows of Harvard College All Rights Reserved Current operating system: Microsoft Windows [Version 10.0.22000.856] Created on 9/24/22 at 10:40:22 by user: ABDUSEMIABDU Maximum number of ATOMS: 60000, and RESidues: 20000 CHARMM> UPPER CHARMM> BOMBLEVEL -2 CHARMM> WRNLEV 0 CHARMM> PRNLEV 5 CHARMM> CHARMM> CHARMM> CHARMM> STREAM "ModelBuild.stream" VOPEN> Attempting to open::ModelBuild.stream:: OPNLGU> Unit 98 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\ModelBuild.stream INPUT STREAM SWITCHING TO UNIT 98 RDTITL> ** RDTITL> * Parameter: IN1 <- "" CHARMM> OPEN READ UNIT 21 CARD NAME "forcefield.rtf" VOPEN> Attempting to open::forcefield.rtf:: OPNLGU> Unit 21 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\forcefield.rtf CHARMM> READ RTF UNIT 21 CARD MAINIO> Residue topology file being read from unit 21. TITLE> * ... TITLE> * TOPOLOGY FILE FOR CHARMM VERSION 22 (ALL HYDROGENS) TITLE> * ... TITLE> * ... TITLE> * COPYRIGHT (C) 1986, 1987, 1988, 1989, 1990, 1991, 1992 TITLE> * ACCELRYS INC. TITLE> * CONFIDENTIAL AND PROPRIETARY: ALL RIGHTS RESERVED TITLE> * ... TITLE> * THIS FILE INCORPORATES AMINOH.RTF, AMINO2H.RTF, TITLE> * AND PATCHAH.RTF. IT INCLUDES: TITLE> * 1) FROM AMINOH.RTF- TOPOLOGY DEFINITIONS FOR THE TWENTY NATURALLY TITLE> * OCCURRING AMINO ACIDS AND WATER. TITLE> * 2) FROM AMINO2H.RTF- "abnormal" AMINO ACIDS AS WELL AS OTHER TITLE> * AMINO ACID-LIKE STRUCTURES. TITLE> * 3) FROM PATCHAH.RTF- PATCH RESIDUES FOR THE C AND N TERMINAL ENDS TITLE> * OF POLYPEPTIDE CHAINS. TITLE> * ... TITLE> * HYDROGENS ARE SPECIFIED FOR ALL ATOMS, NEW CHARGES FOR NONPOLAR C AND H'S. TITLE> * ... TITLE> * LATEST MODIFICATION: $DATE: 2009/10/28 21:45:43 $ TITLE> * ... TITLE> * RESI NO3 -1.0 PRES 5TER 0.00 PRES 5PHO -0.54 PRES PYR 0.00 PRES CTER -0.90 CHARMM> CLOSE UNIT 21 VCLOSE: Closing unit 21 with status "KEEP" CHARMM> CHARMM> OPEN READ UNIT 21 CARD NAME "molecule_missing.rtf" VOPEN> Attempting to open::molecule_missing.rtf:: OPNLGU> Unit 21 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\molecule_missing.rtf CHARMM> READ RTF UNIT 21 CARD APPEND MAINIO> Residue topology file being read from unit 21. TITLE> * RTF FILE TITLE> * ... TITLE> * CHARMM> CLOSE UNIT 21 VCLOSE: Closing unit 21 with status "KEEP" CHARMM> CHARMM> stream "readcustomrtf.stream" VOPEN> Attempting to open::readcustomrtf.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\readcustomrtf.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** RDTITL> * Parameter: IN1 <- "" CHARMM> open unit 20 read card name molecule_specific.rtf VOPEN> Attempting to open::MOLECULE_SPECIFIC.RTF:: OPNLGU> Unit 20 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\MOLECULE_SPECIFIC.RTF CHARMM> read rtf card unit 20 append MAINIO> Residue topology file being read from unit 20. TITLE> * RTF FILE TITLE> * ... TITLE> * CHARMM> close unit 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> open unit 21 read card name molecule_patch.rtf VOPEN> Attempting to open::MOLECULE_PATCH.RTF:: OPNLGU> Unit 21 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\MOLECULE_PATCH.RTF CHARMM> read rtf card unit 21 append MAINIO> Residue topology file being read from unit 21. TITLE> * RTF FILE TITLE> * ... TITLE> * CHARMM> close unit 21 VCLOSE: Closing unit 21 with status "KEEP" VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> CHARMM> OPEN READ UNIT 20 CARD NAME "molecule.prm" VOPEN> Attempting to open::molecule.prm:: OPNLGU> Unit 20 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\molecule.prm CHARMM> READ PARA UNIT 20 CARD PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * ACCELRYS GENERATED PARAMETER FILE FOR THE CHARMM FORCEFIELD. TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CLOSE UNIT 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> OPEN READ UNIT 20 CARD NAME "molecule_custom.prm" VOPEN> Attempting to open::molecule_custom.prm:: OPNLGU> Unit 20 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\molecule_custom.prm CHARMM> READ PARA UNIT 20 CARD APPEND PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * ACCELRYS GENERATED PARAMETER FILE FOR THE CHARMM FORCEFIELD. TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CLOSE UNIT 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> CHARMM> stream "readseq.stream" VOPEN> Attempting to open::readseq.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\readseq.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** RDTITL> * Parameter: IN1 <- "" CHARMM> open unit 20 read form name 1.crd VOPEN> Attempting to open::1.CRD:: OPNLGU> Unit 20 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\1.CRD CHARMM> read sequ coor unit 20 MAINIO> Sequence information being read from unit 20. TITLE> * CRD FILE GENERATED BY ACCELRYS DISCOVERY STUDIO USING THE CHARMM FORCEFIELD TITLE> * RESIDUE SEQUENCE -- 1 RESIDUES R01 CHARMM> close unit 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> generate 1 first none last none NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is 1. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 50 Number of groups = 1 Number of bonds = 54 Number of angles = 93 Number of dihedrals = 143 Number of impropers = 20 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> stream "readdeoxy.stream" VOPEN> Attempting to open::readdeoxy.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\readdeoxy.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** RDTITL> * Parameter: IN1 <- "" VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> stream "disulnk.stream" VOPEN> Attempting to open::disulnk.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\disulnk.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** STREAM FILE TO BUILD DISULFIDE BOND RDTITL> * Parameter: IN1 <- "" VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> stream "patchlnk.stream" VOPEN> Attempting to open::patchlnk.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\patchlnk.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** RDTITL> * Parameter: IN1 <- "" VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> autogen angles dihedrals AUTOGEN: All angles are removed and regenerated. AUTOGEN: All dihedrals are removed and regenerated. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 1 Number of atoms = 50 Number of groups = 1 Number of bonds = 54 Number of angles = 93 Number of dihedrals = 143 Number of impropers = 20 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> stream "readcrd.stream" VOPEN> Attempting to open::readcrd.stream:: OPNLGU> Unit 97 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\readcrd.stream INPUT STREAM SWITCHING TO UNIT 97 RDTITL> ** RDTITL> * Parameter: IN1 <- "" CHARMM> open unit 20 read card name 1.crd VOPEN> Attempting to open::1.CRD:: OPNLGU> Unit 20 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\1.CRD CHARMM> read coor card unit 20 SPATIAL COORDINATES BEING READ FROM UNIT 20 TITLE> * CRD FILE GENERATED BY ACCELRYS DISCOVERY STUDIO USING THE CHARMM FORCEFIELD TITLE> * CHARMM> close unit 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> VCLOSE: Closing unit 97 with status "KEEP" RETURNING TO INPUT STREAM 98 CHARMM> OPEN WRITE UNIT 20 CARD NAME "molecule.psf" VOPEN> Attempting to open::molecule.psf:: OPNLGU> Unit 20 opened for WRITE access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\molecule.psf CHARMM> WRITE PSF UNIT 20 CARD RDTITL> * USING CHARMM FORCEFIELD RDTITL> * CHARMM> CLOSE UNIT 20 VCLOSE: Closing unit 20 with status "KEEP" CHARMM> define missing sele .not. init show end The following atoms are currently set: SEGId RESId RESName .. TYPEs .. SELRPN> 0 atoms have been selected out of 50 VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> STREAM "block.stream" VOPEN> Attempting to open::block.stream:: OPNLGU> Unit 98 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\block.stream INPUT STREAM SWITCHING TO UNIT 98 RDTITL> Parameter: IN1 <- "" CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> STREAM "noneSolvation.stream" VOPEN> Attempting to open::noneSolvation.stream:: OPNLGU> Unit 98 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\noneSolvation.stream INPUT STREAM SWITCHING TO UNIT 98 RDTITL> *STREAM FILE FOR CALCULATIONS IN VACUUM (NONE SOLVATION) RDTITL> * Parameter: IN1 <- "" CHARMM> NBONDS CDIE EPS 1 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 15.000 CTEXNB =999.000 CTONNB = 11.000 CTOFNB = 14.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.500 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 147 exclusions and 124 interactions(1-4) found 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1201 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 1077 ATOM PAIRS WERE FOUND FOR ATOM LIST 1 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> STREAM "nonbond.stream" VOPEN> Attempting to open::nonbond.stream:: OPNLGU> Unit 98 opened for READONLY access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\nonbond.stream INPUT STREAM SWITCHING TO UNIT 98 RDTITL> *NONBOND STREAM FILE TEMPLATE RDTITL> * Parameter: IN1 <- "" CHARMM> FAST ON MISCOM> FAST option: EXPANDED (limited fast routines) CHARMM> NBONDS CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.500 EPS = 1.000 NBXMOD = 5 There are 1077 atom pairs and 271 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1201 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 1069 ATOM PAIRS WERE FOUND FOR ATOM LIST 1 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> !Cleans up all previous constraints CHARMM> !clean up all fixed constraint CHARMM> CONS FIX SELE NONE END SELRPN> 0 atoms have been selected out of 50 CHARMM> !clean up all harmonic restraint CHARMM> CONS HARM CLEAR CHARMM> !clean all distance constraints CHARMM> NOE NOE> RESET NOE> END NOE: CURRENT NUMBER OF CONSTRAINTS= 0 CHARMM> !clean up all dihedral constraints CHARMM> CONS CLDH CHARMM> CHARMM> SHAKE OFF SHKCOM> SHAKE constraints removed. CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> MINI SD NSTEP 1000 NPRINT 50 TOLGRD 3 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.500 EPS = 1.000 NBXMOD = 5 There are 1069 atom pairs and 271 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1201 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 1069 ATOM PAIRS WERE FOUND FOR ATOM LIST 1 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 1000 NPRINT = 50 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 3.0000000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 36.25290 0.00000 24.83471 0.02000 MINI INTERN> 20.76345 21.12767 0.00000 22.73297 0.00186 MINI EXTERN> 9.30057 -37.67361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 3.0000000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- STPD> 7 7.90701 28.34590 1.97310 0.00259 STPD INTERN> 1.19868 13.16734 0.00000 23.02233 0.03533 STPD EXTERN> 8.37904 -37.89571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> CHARMM> MINI CONJ NSTEP 2000 NPRINT 50 - CHARMM> TOLGRD 0.1 TOLENR 0.0 TOLSTP 0.000000 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.500 EPS = 1.000 NBXMOD = 5 There are 1069 atom pairs and 271 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1201 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 1070 ATOM PAIRS WERE FOUND FOR ATOM LIST 1 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 2000 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.1000000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 7.90701 28.34590 1.97310 0.00000 MINI INTERN> 1.19868 13.16734 0.00000 23.02233 0.03533 MINI EXTERN> 8.37904 -37.89571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 1.72212 6.18489 0.53675 0.04872 MINI INTERN> 0.97307 12.61350 0.00000 24.36989 0.04174 MINI EXTERN> 4.02313 -40.29921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 1.11824 0.60388 0.20499 0.02614 MINI INTERN> 1.01814 12.20450 0.00000 24.60301 0.02477 MINI EXTERN> 4.11411 -40.84630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 1.11824 0.60388 0.20499 0.00000 MINI INTERN> 1.01814 12.20450 0.00000 24.60301 0.02477 MINI EXTERN> 4.11411 -40.84630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 150 1.00269 0.11555 0.16905 0.01206 MINI INTERN> 0.97244 11.82665 0.00000 25.05838 0.02395 MINI EXTERN> 3.96249 -40.84123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.1000000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- CONJ> 163 0.97763 0.02505 0.08795 0.02000 CONJ INTERN> 0.99233 11.63986 0.00000 25.22069 0.02245 CONJ EXTERN> 4.00237 -40.90006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> IOFOrmat exte MISCOM> Expanded I/O format is used. CHARMM> OPEN WRIT UNIT 51 CARD NAME "3GEN_ligand_mini.crd" VOPEN> Attempting to open::3GEN_ligand_mini.crd:: OPNLGU> Unit 51 opened for WRITE access to D:\Program Files\BIOVIA\PPS\web\jobs\16606\961EECD0-E749-4E37-8617-04B88973ED23\Intermediate\3GEN_ligand_mini.crd CHARMM> WRIT COOR UNIT 51 CARD RDTITL> CLOSE UNIT 51 VCLOSE: Closing unit 51 with status "KEEP" CHARMM> CLOSE UNIT 51 CHARMM> CHARMM> ENERGY NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 0.500 EPS = 1.000 NBXMOD = 5 There are 1070 atom pairs and 271 atom exclusions. There are 0 group pairs and 0 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1201 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 1068 ATOM PAIRS WERE FOUND FOR ATOM LIST 1 GROUP PAIRS REQUIRED ATOM SEARCHES ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 0.97763 0.02505 0.08795 ENER INTERN> 0.99233 11.63986 0.00000 25.22069 0.02245 ENER EXTERN> 4.00237 -40.90006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> STOP VCLOSE: Closing unit 6 with status "KEEP" VCLOSE: Closing unit 99 with status "KEEP" $$$$$$ New timer profile Local node$$$$$ Electrostatic & VDW 0.01 Other: 0.00 Nonbond force 0.01 Other: 0.00 Angle energy 0.00 Other: 0.00 Dihedral energy 0.01 Other: 0.00 INTRNL energy 0.01 Other: 0.00 Energy time 0.02 Other: 0.00 Total time 0.16 Other: 0.14 $$$$$$ Average profile $$$$$ Electrostatic & VDW 0.01 Other: 0.00 Nonbond force 0.01 Other: 0.00 Angle energy 0.00 Other: 0.00 Dihedral energy 0.01 Other: 0.00 INTRNL energy 0.01 Other: 0.00 Energy time 0.02 Other: 0.00 Total time 0.16 Other: 0.14 NORMAL TERMINATION BY NORMAL STOP NO WARNINGS WERE ISSUED $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 0.25 SECONDS CPU TIME: 0.20 SECONDS