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-3.2.0-51-generic(x86_64)@pinhole Created on 8/21/13 at 22:28:55 by user: tarsis Maximum number of ATOMS: 360720, and RESidues: 120240 RDTITL> * MAKE PSF AND BUILD COOR FROM IC IN THE RTF 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> * **** WARNING from RTFRDR **** The total charge of the residue, AMIN, -1.0000000, does not equal the expected charge, -2.0100000. There were 1 warning(s) from RTFRDR. 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> * ***** 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> read sequ card MAINIO> Sequence information being read from unit 5. RDTITL> * SEQUENCE RDTITL> * SEQRDR> 2 SEQRDR> BGLCA AGLCNA RESIDUE SEQUENCE -- 2 RESIDUES BGLCAGLC CHARMM> CHARMM> gener S setup warn 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 S. 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 = 52 Number of groups = 12 Number of bonds = 52 Number of angles = 91 Number of dihedrals = 139 Number of impropers = 3 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = -1.00000 QXFORM> Expanded format used. More than 4 character residue name used. CHARMM> read coor univ unit 1 offset 0 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> NONE TITLE> * ** WARNING ** NO COORDINATES FOR 1 1 BGLCA C1 ** WARNING ** NO COORDINATES FOR 2 1 BGLCA H1 ** WARNING ** NO COORDINATES FOR 3 1 BGLCA O1 ** WARNING ** NO COORDINATES FOR 4 1 BGLCA HO1 ** WARNING ** NO COORDINATES FOR 5 1 BGLCA C5 ** TOTAL OF 52 MISSING COORDINATES *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> patch 14ab S 1 S 2 setup ATOM S 1 BGLCA HO4 AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA HO1 AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA O1 AND ALL REFERENCES TO IT DELETED. Message from MAPIC: Atom numbers are changed. DELTIC: 3 bonds deleted DELTIC: 5 angles deleted DELTIC: 10 dihedrals deleted PATCH: Check angles and dihedrals autogenerated. 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 = 49 Number of groups = 12 Number of bonds = 50 Number of angles = 86 Number of dihedrals = 129 Number of impropers = 3 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> autogen angl dihe 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 = 2 Number of atoms = 49 Number of groups = 12 Number of bonds = 50 Number of angles = 90 Number of dihedrals = 139 Number of impropers = 3 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> patch amin S 2 setup ATOM S 2 AGLCNA C AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA O AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA CT AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA HT1 AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA HT2 AND ALL REFERENCES TO IT DELETED. ATOM S 2 AGLCNA HT3 AND ALL REFERENCES TO IT DELETED. ATOM S AGLCNA 2 S1 ADDED. ATOM S AGLCNA 2 O2 ADDED. ATOM S AGLCNA 2 O7 ADDED. ATOM S AGLCNA 2 O8 ADDED. Message from MAPIC: Atom numbers are changed. DELTIC: 6 bonds deleted DELTIC: 11 angles deleted DELTIC: 13 dihedrals deleted DELTIC: 2 improper dihedrals deleted PATCH: Check angles and dihedrals autogenerated. 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 = 79 Number of dihedrals = 126 Number of impropers = 4 Number of cross-terms = 0 Number of HB acceptors = 0 Number of HB donors = 0 Number of NB exclusions = 0 Total charge = -2.00000 CHARMM> CHARMM> ic param CHARMM> ic seed 1 C1 1 C2 1 C3 CHARMM> ic build CHARMM> CHARMM> write psf card name disa.psf unit 1 VOPEN> Attempting to open::disa.psf:: RDTITL> * PSF RDTITL> * VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> write coor pdb name disa.pdb unit 1 VOPEN> Attempting to open::disa.pdb:: RDTITL> * PDB COORDS RDTITL> * Write CHARMM-pdb format VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> write coor card name disa.crd unit 1 VOPEN> Attempting to open::disa.crd:: RDTITL> * COORDS RDTITL> * VCLOSE: Closing unit 1 with status "KEEP" VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> stop $$$$$$ New timer profile $$$$$ Total time 0.14 Other: 0.00 NORMAL TERMINATION BY NORMAL STOP MOST SEVERE WARNING WAS AT LEVEL 2 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 0.14 SECONDS CPU TIME: 0.14 SECONDS