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output.txt~
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output.txt~
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1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 36b1 August 15, 2011
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-71.29.1.el6.x86_64(x86_64)@suga
Created on 4/22/15 at 13:48:02 by user: rumack
Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * CEL48F + BGLC + TIP3
RDTITL> *
CHARMM>
CHARMM> resize chsize 500000
Size Original New
MAXA 360720 500000
MAXB 360720 500000
MAXT 721440 1000000
MAXP 1082160 1500000
MAXIMP 180360 250000
MAXNB 90180 125000
MAXPAD 360720 500000
MAXRES 120240 166666
MAXSEG 45090 62500
MAXATC 500
MAXCB 1500
MAXCT 5500
MAXCP 10000
MAXCI 600
MAXCH 3200
MAXCN 125250
MAXCRT 120240 166666
CHARMM>
CHARMM> bomblev 0
CHARMM>
CHARMM> open unit 12 read form name top_all36_carb.rtf !/home/chen/para/newTOPPAR/
VOPEN> Attempting to open::top_all36_carb.rtf::
OPNLGU> Unit 12 opened for READONLY access to /home/rumack/charmm/top_all36_carb.rtf
CHARMM> read rtf card unit 12
MAINIO> Residue topology file being read from unit 12.
TITLE> * $ID: TOP_ALLXX_SUGAR.INP,V 1.104 2014/01/03 20:55:32 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 12
VCLOSE: Closing unit 12 with status "KEEP"
CHARMM>
CHARMM> open unit 13 read form name par_all36_carb.prm !/home/chen/para/newTOPPAR/
VOPEN> Attempting to open::par_all36_carb.prm::
OPNLGU> Unit 13 opened for READONLY access to /home/rumack/charmm/par_all36_carb.prm
CHARMM> read param card flex unit 13
PARAMETER FILE BEING READ FROM UNIT 13
TITLE> * $ID: PAR_ALLXX_SUGAR.INP,V 1.130 2013/12/11 16:54:47 PRABHU 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> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 13
VCLOSE: Closing unit 13 with status "KEEP"
CHARMM>
CHARMM> open unit 10 read form name top_all22_prot.rtf !/home/chen/para/newtoppar/
VOPEN> Attempting to open::top_all22_prot.rtf::
OPNLGU> Unit 10 opened for READONLY access to /home/rumack/charmm/top_all22_prot.rtf
CHARMM> read rtf card append unit 10
MAINIO> Residue topology file being read from unit 10.
TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"
CHARMM>
CHARMM> open unit 11 read form name par_all22_prot.prm !/home/chen/para/newtoppar/
VOPEN> Attempting to open::par_all22_prot.prm::
OPNLGU> Unit 11 opened for READONLY access to /home/rumack/charmm/par_all22_prot.prm
CHARMM> read param card flex append unit 11
PARAMETER FILE BEING READ FROM UNIT 11
TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> close unit 11
VCLOSE: Closing unit 11 with status "KEEP"
CHARMM>
CHARMM> open unit 9 read card name prot_sequence.txt
VOPEN> Attempting to open::prot_sequence.txt::
OPNLGU> Unit 9 opened for READONLY access to /home/rumack/charmm/prot_sequence.txt
CHARMM> read sequence card unit 9
MAINIO> Sequence information being read from unit 9.
TITLE> * WATER PORE SEQUENCE
TITLE> *
SEQRDR> 639
SEQRDR> SER
SEQRDR> TYR
SEQRDR> ASP
SEQRDR> GLN
SEQRDR> ALA
SEQRDR> PHE
SEQRDR> LEU
SEQRDR> GLU
SEQRDR> GLN
SEQRDR> TYR
SEQRDR> GLU
SEQRDR> LYS
SEQRDR> ILE
SEQRDR> LYS
SEQRDR> ASP
SEQRDR> PRO
SEQRDR> ALA
SEQRDR> SER
SEQRDR> GLY
SEQRDR> TYR
SEQRDR> PHE
SEQRDR> ARG
SEQRDR> GLU
SEQRDR> PHE
SEQRDR> ASN
SEQRDR> GLY
SEQRDR> LEU
SEQRDR> LEU
SEQRDR> VAL
SEQRDR> PRO
SEQRDR> TYR
SEQRDR> HSD
SEQRDR> SER
SEQRDR> VAL
SEQRDR> GLU
SEQRDR> THR
SEQRDR> MET
SEQRDR> ILE
SEQRDR> VAL
SEQRDR> GLU
SEQRDR> ALA
SEQRDR> PRO
SEQRDR> ASP
SEQRDR> HSD
SEQRDR> GLY
SEQRDR> HSD
SEQRDR> GLN
SEQRDR> THR
SEQRDR> THR
SEQRDR> SER
SEQRDR> GLU
SEQRDR> ALA
SEQRDR> PHE
SEQRDR> SER
SEQRDR> TYR
SEQRDR> TYR
SEQRDR> LEU
SEQRDR> TRP
SEQRDR> LEU
SEQRDR> GLU
SEQRDR> ALA
SEQRDR> TYR
SEQRDR> TYR
SEQRDR> GLY
SEQRDR> ARG
SEQRDR> VAL
SEQRDR> THR
SEQRDR> GLY
SEQRDR> ASP
SEQRDR> TRP
SEQRDR> LYS
SEQRDR> PRO
SEQRDR> LEU
SEQRDR> HSD
SEQRDR> ASP
SEQRDR> ALA
SEQRDR> TRP
SEQRDR> GLU
SEQRDR> SER
SEQRDR> MET
SEQRDR> GLU
SEQRDR> THR
SEQRDR> PHE
SEQRDR> ILE
SEQRDR> ILE
SEQRDR> PRO
SEQRDR> GLY
SEQRDR> THR
SEQRDR> LYS
SEQRDR> ASP
SEQRDR> GLN
SEQRDR> PRO
SEQRDR> THR
SEQRDR> ASN
SEQRDR> SER
SEQRDR> ALA
SEQRDR> TYR
SEQRDR> ASN
SEQRDR> PRO
SEQRDR> ASN
SEQRDR> SER
SEQRDR> PRO
SEQRDR> ALA
SEQRDR> THR
SEQRDR> TYR
SEQRDR> ILE
SEQRDR> PRO
SEQRDR> GLU
SEQRDR> GLN
SEQRDR> PRO
SEQRDR> ASN
SEQRDR> ALA
SEQRDR> ASP
SEQRDR> GLY
SEQRDR> TYR
SEQRDR> PRO
SEQRDR> SER
SEQRDR> PRO
SEQRDR> LEU
SEQRDR> MET
SEQRDR> ASN
SEQRDR> ASN
SEQRDR> VAL
SEQRDR> PRO
SEQRDR> VAL
SEQRDR> GLY
SEQRDR> GLN
SEQRDR> ASP
SEQRDR> PRO
SEQRDR> LEU
SEQRDR> ALA
SEQRDR> GLN
SEQRDR> GLU
SEQRDR> LEU
SEQRDR> SER
SEQRDR> SER
SEQRDR> THR
SEQRDR> TYR
SEQRDR> GLY
SEQRDR> THR
SEQRDR> ASN
SEQRDR> GLU
SEQRDR> ILE
SEQRDR> TYR
SEQRDR> GLY
SEQRDR> MET
SEQRDR> HSD
SEQRDR> TRP
SEQRDR> LEU
SEQRDR> LEU
SEQRDR> ASP
SEQRDR> VAL
SEQRDR> ASP
SEQRDR> ASN
SEQRDR> VAL
SEQRDR> TYR
SEQRDR> GLY
SEQRDR> PHE
SEQRDR> GLY
SEQRDR> PHE
SEQRDR> CYS
SEQRDR> GLY
SEQRDR> ASP
SEQRDR> GLY
SEQRDR> THR
SEQRDR> ASP
SEQRDR> ASP
SEQRDR> ALA
SEQRDR> PRO
SEQRDR> ALA
SEQRDR> TYR
SEQRDR> ILE
SEQRDR> ASN
SEQRDR> THR
SEQRDR> TYR
SEQRDR> GLN
SEQRDR> ARG
SEQRDR> GLY
SEQRDR> ALA
SEQRDR> ARG
SEQRDR> GLU
SEQRDR> SER
SEQRDR> VAL
SEQRDR> TRP
SEQRDR> GLU
SEQRDR> THR
SEQRDR> ILE
SEQRDR> PRO
SEQRDR> HSD
SEQRDR> PRO
SEQRDR> SER
SEQRDR> CYS
SEQRDR> ASP
SEQRDR> ASP
SEQRDR> PHE
SEQRDR> THR
SEQRDR> HSD
SEQRDR> GLY
SEQRDR> GLY
SEQRDR> PRO
SEQRDR> ASN
SEQRDR> GLY
SEQRDR> TYR
SEQRDR> LEU
SEQRDR> ASP
SEQRDR> LEU
SEQRDR> PHE
SEQRDR> THR
SEQRDR> ASP
SEQRDR> ASP
SEQRDR> GLN
SEQRDR> ASN
SEQRDR> TYR
SEQRDR> ALA
SEQRDR> LYS
SEQRDR> GLN
SEQRDR> TRP
SEQRDR> ARG
SEQRDR> TYR
SEQRDR> THR
SEQRDR> ASN
SEQRDR> ALA
SEQRDR> PRO
SEQRDR> ASP
SEQRDR> ALA
SEQRDR> ASP
SEQRDR> ALA
SEQRDR> ARG
SEQRDR> ALA
SEQRDR> VAL
SEQRDR> GLN
SEQRDR> VAL
SEQRDR> MET
SEQRDR> PHE
SEQRDR> TRP
SEQRDR> ALA
SEQRDR> HSD
SEQRDR> GLU
SEQRDR> TRP
SEQRDR> ALA
SEQRDR> LYS
SEQRDR> GLU
SEQRDR> GLN
SEQRDR> GLY
SEQRDR> LYS
SEQRDR> GLU
SEQRDR> ASN
SEQRDR> GLU
SEQRDR> ILE
SEQRDR> ALA
SEQRDR> GLY
SEQRDR> LEU
SEQRDR> MET
SEQRDR> ASP
SEQRDR> LYS
SEQRDR> ALA
SEQRDR> SER
SEQRDR> LYS
SEQRDR> MET
SEQRDR> GLY
SEQRDR> ASP
SEQRDR> TYR
SEQRDR> LEU
SEQRDR> ARG
SEQRDR> TYR
SEQRDR> ALA
SEQRDR> MET
SEQRDR> PHE
SEQRDR> ASP
SEQRDR> LYS
SEQRDR> TYR
SEQRDR> PHE
SEQRDR> LYS
SEQRDR> LYS
SEQRDR> ILE
SEQRDR> GLY
SEQRDR> ASN
SEQRDR> CYS
SEQRDR> VAL
SEQRDR> GLY
SEQRDR> ALA
SEQRDR> THR
SEQRDR> SER
SEQRDR> CYS
SEQRDR> PRO
SEQRDR> GLY
SEQRDR> GLY
SEQRDR> GLN
SEQRDR> GLY
SEQRDR> LYS
SEQRDR> ASP
SEQRDR> SER
SEQRDR> ALA
SEQRDR> HSD
SEQRDR> TYR
SEQRDR> LEU
SEQRDR> LEU
SEQRDR> SER
SEQRDR> TRP
SEQRDR> TYR
SEQRDR> TYR
SEQRDR> SER
SEQRDR> TRP
SEQRDR> GLY
SEQRDR> GLY
SEQRDR> SER
SEQRDR> LEU
SEQRDR> ASP
SEQRDR> THR
SEQRDR> SER
SEQRDR> SER
SEQRDR> ALA
SEQRDR> TRP
SEQRDR> ALA
SEQRDR> TRP
SEQRDR> ARG
SEQRDR> ILE
SEQRDR> GLY
SEQRDR> SER
SEQRDR> SER
SEQRDR> SER
SEQRDR> SER
SEQRDR> HSD
SEQRDR> GLN
SEQRDR> GLY
SEQRDR> TYR
SEQRDR> GLN
SEQRDR> ASN
SEQRDR> VAL
SEQRDR> LEU
SEQRDR> ALA
SEQRDR> ALA
SEQRDR> TYR
SEQRDR> ALA
SEQRDR> LEU
SEQRDR> SER
SEQRDR> GLN
SEQRDR> VAL
SEQRDR> PRO
SEQRDR> GLU
SEQRDR> LEU
SEQRDR> GLN
SEQRDR> PRO
SEQRDR> ASP
SEQRDR> SER
SEQRDR> PRO
SEQRDR> THR
SEQRDR> GLY
SEQRDR> VAL
SEQRDR> GLN
SEQRDR> ASP
SEQRDR> TRP
SEQRDR> ALA
SEQRDR> THR
SEQRDR> SER
SEQRDR> PHE
SEQRDR> ASP
SEQRDR> ARG
SEQRDR> GLN
SEQRDR> LEU
SEQRDR> GLU
SEQRDR> PHE
SEQRDR> LEU
SEQRDR> GLN
SEQRDR> TRP
SEQRDR> LEU
SEQRDR> GLN
SEQRDR> SER
SEQRDR> ALA
SEQRDR> GLU
SEQRDR> GLY
SEQRDR> GLY
SEQRDR> ILE
SEQRDR> ALA
SEQRDR> GLY
SEQRDR> GLY
SEQRDR> ALA
SEQRDR> THR
SEQRDR> ASN
SEQRDR> SER
SEQRDR> TRP
SEQRDR> LYS
SEQRDR> GLY
SEQRDR> SER
SEQRDR> TYR
SEQRDR> ASP
SEQRDR> THR
SEQRDR> PRO
SEQRDR> PRO
SEQRDR> THR
SEQRDR> GLY
SEQRDR> LEU
SEQRDR> SER
SEQRDR> GLN
SEQRDR> PHE
SEQRDR> TYR
SEQRDR> GLY
SEQRDR> MET
SEQRDR> TYR
SEQRDR> TYR
SEQRDR> ASP
SEQRDR> TRP
SEQRDR> GLN
SEQRDR> PRO
SEQRDR> VAL
SEQRDR> TRP
SEQRDR> ASN
SEQRDR> ASP
SEQRDR> PRO
SEQRDR> PRO
SEQRDR> SER
SEQRDR> ASN
SEQRDR> ASN
SEQRDR> TRP
SEQRDR> PHE
SEQRDR> GLY
SEQRDR> PHE
SEQRDR> GLN
SEQRDR> VAL
SEQRDR> TRP
SEQRDR> ASN
SEQRDR> MET
SEQRDR> GLU
SEQRDR> ARG
SEQRDR> VAL
SEQRDR> ALA
SEQRDR> GLN
SEQRDR> LEU
SEQRDR> TYR
SEQRDR> TYR
SEQRDR> VAL
SEQRDR> THR
SEQRDR> GLY
SEQRDR> ASP
SEQRDR> ALA