AMBER Archive (2007)

Subject: AMBER: mm_pbsa error

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Wed Jan 31 2007 - 03:19:46 CST

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_at_yahoo.com
tarisyed_at_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_at_yahoo.com
tarisyed_at_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_at_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_at_mcg09:~/Working/Tari/Tutorial7/mm_pbsa>

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