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 14:00:43 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> * 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> 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 = 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 CHARMM> CHARMM> AUTOGENereate 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 = 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 CHARMM> CHARMM> ic param CHARMM> ic seed 1 C1 1 C2 1 C3 CHARMM> ic build CHARMM> CHARMM> print coor COORDINATE FILE MODULE TITLE> * MAKE PSF AND BUILD COOR FROM IC IN THE RTF TITLE> * 47 EXT 1 1 BGLCA C1 0.0000000000 0.0000000000 0.0000000000 S 1 0.0000000000 2 1 BGLCA H1 -0.3874220603 0.4619170171 0.9086952550 S 1 0.0000000000 3 1 BGLCA O1 -0.3848214360 -1.3557581573 -0.0785145296 S 1 0.0000000000 4 1 BGLCA HO1 0.0408847699 -1.7424439977 -0.8514232222 S 1 0.0000000000 5 1 BGLCA C5 -0.0661870764 2.1458561496 -1.0483067465 S 1 0.0000000000 6 1 BGLCA H5 -0.3276292635 2.6137818327 -0.0962204595 S 1 0.0000000000 7 1 BGLCA O5 -0.5111250234 0.7780122348 -1.0535800764 S 1 0.0000000000 8 1 BGLCA C2 1.5218000000 0.0000000000 0.0000000000 S 1 0.0000000000 9 1 BGLCA H2 1.8687740081 -0.4996218624 -0.9035173891 S 1 0.0000000000 10 1 BGLCA O2 2.0473909648 -0.7326643603 1.0956815563 S 1 0.0000000000 11 1 BGLCA HO2 1.5207364300 -0.4634828896 1.8600758177 S 1 0.0000000000 12 1 BGLCA C3 2.0415368244 1.4248693005 0.0000000000 S 1 0.0000000000 13 1 BGLCA H3 1.7426826275 1.9183087933 0.9315375064 S 1 0.0000000000 14 1 BGLCA O3 3.4532518440 1.4562093717 -0.1480221040 S 1 0.0000000000 15 1 BGLCA HO3 3.8083316862 0.8624988751 0.5234799153 S 1 0.0000000000 16 1 BGLCA C4 1.4463617356 2.1938823160 -1.1554607893 S 1 0.0000000000 17 1 BGLCA H4 1.7548592190 1.7125713356 -2.0919525847 S 1 0.0000000000 18 1 BGLCA O4 1.8424648232 3.5534441632 -1.1309736996 S 1 0.0000000000 19 1 BGLCA C6 -0.7572985846 2.8551131464 -2.1880950627 S 1 0.0000000000 20 1 BGLCA O61 -1.5687678713 3.9176344441 -1.7206854151 S 1 0.0000000000 21 1 BGLCA O62 -0.4663884336 2.3759439880 -3.1279145622 S 1 0.0000000000 22 2 AGLCNA C1 3.1648667145 3.8756183730 -1.4738293201 S 2 0.0000000000 23 2 AGLCNA H1 3.8221536348 3.4749379334 -0.6801029315 S 2 0.0000000000 24 2 AGLCNA C5 2.7902988755 3.6708900954 -3.8680911715 S 2 0.0000000000 25 2 AGLCNA H5 1.7216085156 3.5002587306 -3.7178892671 S 2 0.0000000000 26 2 AGLCNA O5 3.5205827709 3.2074713884 -2.7187769873 S 2 0.0000000000 27 2 AGLCNA C2 3.3471979499 5.3691449505 -1.5491681060 S 2 0.0000000000 28 2 AGLCNA H2 4.4077099513 5.6053363144 -1.6258790854 S 2 0.0000000000 29 2 AGLCNA N 2.8811583569 6.0154256231 -0.3749920586 S 2 0.0000000000 30 2 AGLCNA HN 3.2109809979 5.4809898540 0.3596627475 S 2 0.0000000000 31 2 AGLCNA S1 1.3596786784 6.3353760892 -0.0363938789 S 2 0.0000000000 32 2 AGLCNA O2 1.5722072322 7.1228027603 1.1937958835 S 2 0.0000000000 33 2 AGLCNA O7 0.8820707153 5.0263612974 0.1593133477 S 2 0.0000000000 34 2 AGLCNA O8 0.9150451309 7.0453912484 -1.1859160589 S 2 0.0000000000 35 2 AGLCNA C3 2.6218361087 5.8954306922 -2.8267898018 S 2 0.0000000000 36 2 AGLCNA H3 1.5459004912 5.7454669819 -2.6838495254 S 2 0.0000000000 37 2 AGLCNA O3 2.9192176898 7.2642399176 -3.0586465240 S 2 0.0000000000 38 2 AGLCNA HO3 2.7348168982 7.7243681015 -2.2317443457 S 2 0.0000000000 39 2 AGLCNA C4 3.0421903370 5.1528580590 -4.0728203983 S 2 0.0000000000 40 2 AGLCNA H4 4.1155938068 5.3154524580 -4.2316155257 S 2 0.0000000000 41 2 AGLCNA O4 2.2948615961 5.5705860153 -5.2010529973 S 2 0.0000000000 42 2 AGLCNA HO4 2.3059946461 6.5348509908 -5.1829046585 S 2 0.0000000000 43 2 AGLCNA C6 3.2798978565 2.8283641160 -5.0214518358 S 2 0.0000000000 44 2 AGLCNA H61 2.7494313289 3.1173604046 -5.9255025525 S 2 0.0000000000 45 2 AGLCNA H62 4.3476660772 3.0186161033 -5.1669430665 S 2 0.0000000000 46 2 AGLCNA O6 3.0248899614 1.4525399121 -4.8023983646 S 2 0.0000000000 47 2 AGLCNA HO6 3.4290145955 1.2478487085 -3.9526020412 S 2 0.0000000000 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 $$$$$$ New timer profile $$$$$ Total time 3.54 Other: 0.00 NORMAL TERMINATION BY NORMAL STOP MOST SEVERE WARNING WAS AT LEVEL 2 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.55 SECONDS CPU TIME: 3.46 SECONDS