Hello
Here is an attached file having the command and its output, that is giving an error.
Kindly guide me to solve it.
Thanks in advance
Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan
tarisyed.yahoo.com
tarisyed.hotmail.com
---------------------------------
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Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan
tarisyed.yahoo.com
tarisyed.hotmail.com
---------------------------------
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9:~/Working/Tari/Tutorial7/mm_pbsa> ./mm_pbsa.pl mm_pbsa.in < mm_pbsa.lo
g &
[3] 6845
zuh.mcg09:~/Working/Tari/Tutorial7/mm_pbsa>
=>> Init data
Presuming executables of amber suite to be in /usr/local/amber8/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./ras_raf_II_wt.prmtop
Found RECPT => ./ras_II_wt.prmtop
Found LIGPT => ./raf_wt.prmtop
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found DCTYPE => 2
Found COMREC => 1-166 254-255
Found COMLIG => 167-253
Found COMPRI => 1-255
Found RECRES => 1-168
Found RECPRI => 1-168
Found RECMAP => 1-166 254-255
Found LIGRES => 1-87
Found LIGPRI => 1-87
Found LIGMAP => 167-253
Found PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 2
Found LINIT => 1000
Found PRBRAD => 1.6
Found RADIOPT => 1
Found FOCUS => 0
Found PERFIL => 80.0
Found CHARGE => ./my_amber94_delphi.crg
Found SIZE => ./my_parse_delphi.siz
Found SURFTEN => 0.005
Found SURFOFF => 0.0
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
Found DIELC => 4
Found MAXCYC => 10000
Found DRMS => 0.0001
Found BOX => YES
Found NTOTAL => 25570
Found NSTART => 1
Found NSTOP => 5000
Found NFREQ => 500
Found NUMBER_LIG_GROUPS => 0
Found LSTART => 0
Found LSTOP => 0
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 2666
Found NUMBER_MUTANT_GROUPS => 3
Found MUTANT_ATOM1 => 1480
Found MUTANT_ATOM2 => 0
Found MUTANT_KEEP => 1486
Found MUTANT_REFERENCE => 1477
Found MUTANT_ATOM2 => 1498
Found MUTANT_ATOM1 => 1494
Found MUTANT_KEEP => 1500
Found MUTANT_REFERENCE => 1492
Found MUTANT_ATOM1 => 1552
Found MUTANT_ATOM2 => 0
Found MUTANT_KEEP => 1562
Found MUTANT_REFERENCE => 1549
Found TRAJECTORY => ../prod_II/md_nvt_prod_pme_01.mdcrd.gz
Found TRAJECTORY => ../prod_II/md_nvt_prod_pme_02.mdcrd.gz
Found TRAJECTORY => ../prod_II/md_nvt_prod_pme_03.mdcrd.gz
Found TRAJECTORY => ../prod_II/md_nvt_prod_pme_04.mdcrd.gz
Found TRAJECTORY => ../prod_II/md_nvt_prod_pme_05.mdcrd.gz
=>> Checking sanity
Checking GENERAL
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.005
betaP = 0.0
gammaG = 0.0072
betaG = 0.00
=>> Reading input
=>> Reordering files
Final order:
1. snapshot_com.all.out: -
2. snapshot_rec.all.out: -
3. snapshot_lig.all.out: -
=>> Reading files
Reading snapshot_com.all.out
Reading snapshot_rec.all.out
Reading snapshot_lig.all.out
=>> Treat special parameters
=>> Calc missing parameters
Processing MM GAS
Processing MM INT
Processing MM ELE
Processing MM VDW
Processing GB GBTOT
Processing GB GBELE
Processing GB GBSOL
Processing PB PBSOL
Processing PB PBELE
Processing PB PBTOT
=>> Calc delta from raw data
Can't use an undefined value as an ARRAY reference at /usr/local/amber8/src/mm_p bsa/mm_pbsa_statistics.pm line 903.
zuh.mcg09:~/Working/Tari/Tutorial7/mm_pbsa>
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Received on Sun Feb 04 2007 - 06:07:05 PST
