1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 37b2 February 15, 2013 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-3.2.0-52-generic(x86_64)@s Created on 8/23/13 at 14:01:38 by user: tarsis Maximum number of ATOMS: 360720, and RESidues: 120240 RDTITL> * MINIMIZE PDB RDTITL> * CHARMM> open unit 1 card read name "top_all36_carb_NHSHB3.rtf" VOPEN> Attempting to open::top_all36_carb_NHSHB3.rtf:: OPNLGU> Unit 1 opened for READONLY access to top_all36_carb_NHSHB3.rtf CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * $ID: TOP_ALLXX_SUGAR.INP,V 1.98 2011-07-20 15:03:53 PRABHU EXP $ TITLE> *>>>>>>>>>>>> ALL-HYDROGEN TOPOLOGIES USED IN THE <<<<<<<<<<<<<<<< TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<< TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG <<<<<<<<<<<<<< TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<< TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> open unit 1 card flex read name "par_all36_carb.prm" VOPEN> Attempting to open::par_all36_carb.prm:: OPNLGU> Unit 1 opened for READONLY access to par_all36_carb.prm **** Warning **** The following extraneous characters were found while command processing in miscom FLEX CHARMM> read PARA card flex unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * $ID: PAR_ALLXX_SUGAR.INP,V 1.126 2011-03-31 19:17:35 OGUVENCH EXP $ TITLE> *>>>>>>>>>>>> ALL-HYDROGEN PARAMETERS USED IN THE <<<<<<<<<<<<<<<< TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<< TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG <<<<<<<<<<<<<< TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<< TITLE> * PARRDR> Error: Repeated ANGLE parameter ( 106): NC2D CC31 HCA1 is replaced ***** WARNING ***** PARRDR no nonbond parameters for atom type: 338 NG2S NO nonbond interactions will be computed for this atom type. PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ! read the psf and coordinate file CHARMM> read psf card name disa.psf VOPEN> Attempting to open::disa.psf:: MAINIO> Protein structure file being read from unit 90. PSFRD2> Reading PSF in the expanded format. TITLE> * PSF TITLE> * DATE: 8/23/13 14: 0:47 CREATED BY USER: tarsis TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 2 Number of atoms = 47 Number of groups = 10 Number of bonds = 48 Number of angles = 87 Number of dihedrals = 135 Number of impropers = 1 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = -2.00000 VCLOSE: Closing unit 90 with status "KEEP" CHARMM> read coor card name disa.crd VOPEN> Attempting to open::disa.crd:: SPATIAL COORDINATES BEING READ FROM UNIT 90 TITLE> * COORDS TITLE> * DATE: 8/23/13 14: 0:47 CREATED BY USER: TARSIS TITLE> * VCLOSE: Closing unit 90 with status "KEEP" CHARMM> CHARMM> CHARMM> ! set up shake CHARMM> shake bonh param sele all end SELRPN> 47 atoms have been selected out of 47 SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500 19 constraints will held by SHAKE. CHARMM> CHARMM> ! set up electrostatics, since we're not using PME, set up switching CHARMM> ! electrostatics CHARMM> nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10. NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSWItch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 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 135 exclusions and 129 interactions(1-4) found 23 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1082 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 946 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> energy NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSWItch VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 946 atom pairs and 264 atom exclusions. There are 0 group pairs and 23 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1082 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 946 ATOM PAIRS WERE FOUND FOR ATOM LIST 0 GROUP PAIRS REQUIRED ATOM SEARCHES : No torsion parameters for 72 ( CC3162 CC3161 NG2S3 SC ) : No torsion parameters for 101 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 102 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 103 ( CC3161 NG2S3 SC OC2DP ) : No torsion parameters for 108 ( HCA1 CC3161 NG2S3 SC ) : No torsion parameters for 116 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 117 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 118 ( HCP1 NG2S3 SC OC2DP ) : No torsion parameters for 119 ( SC NG2S3 CC3161 CC3161 ) : A TOTAL OF 9 MISSING PARAMETERS ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5 /---------\ / \ / \ / \ ! XXXX XXXX ! ! XXXX XXXX ! ! XXX XXX ! ! X ! --\ XXX /-- ! ! XXX ! ! ! ! ! ! ! I I I I I ! ! I I I I ! \ / -- -- \---/ XXX XXX XXXX XXXX XXXXX XXXXX XXX XXX XXX XXX XXXXX XXX XXX XXX XXX XXX XXX XXXXX XXXXX XXXX XXXX XXX XXX Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.75 SECONDS CPU TIME: 3.70 SECONDS