AMBER Archive (2005)

Subject: AMBER: mm_pbsa problem

From: Husni Fattayer (fatayer78_at_yahoo.com)
Date: Mon Apr 25 2005 - 15:59:22 CDT


Dear Amber users,
 I have been trying to calculate the binding energy
for peptide ligand (consisting of 7 standard amino
acids) to a protein receptor using mm_pbsa. after
generating the snapshots successfully I ran mm_pbsa.pl
command but it gave me an error message saying "Can't
use an undefined value as an ARRAY reference at
/aspirin/software/amber7/amber7/src/mm_pbsa/mm_pbsa_statistics.pm
line 1234." the log file looks like

=>> Init data
    Presuming executables of amber suite to be in
/aspirin/software/amber7/amber7/exe

=>> Reading input parameters
    Found PREFIX => ELDKWASBE
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ../complex.prmtop
    Found RECPT => ../receptor.prmtop
    Found LIGPT => ../ligand.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 0
    Found MS => 1
    Found NM => 0
    Found FOCUS => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found PERFIL => 80.0
    Found SCALE => 2
    Found LINIT => 1000
    Found BNDCON => 4
    Found CHARGE => ../my_amber94_delphi.crg
    Found SIZE => ../my_parse_delphi.siz
    Found SURFTEN => 0.00542
    Found SURFOFF => 0.092
    Found IGB => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 1.4
    Found RADII => ../atmtypenumbers
    Found DELPHI =>
/home/gohlke/src/delphi.98/exe.R10000/delphi

=>> Checking sanity
    Checking GENERAL
    Checking MM
    Checking GB
    Checking MS

=>> Creating input
    Sander input

=>> Calculating energy / entropy contributions

=>> Doing statistics
=>> Values of global variables
    TEMP = 300
    R = 8.314
    gammaP = 0.00542
    betaP = 0.92
    gammaG = 0.0072
    betaG = 0.00
=>> Reading input
=>> Reordering files
    Final order:
    1. ELDKWASBE_com.all.out: -
    2. ELDKWASBE_rec.all.out: -
    3. ELDKWASBE_lig.all.out: -
=>> Reading files
    Reading ELDKWASBE_com.all.out
    Reading ELDKWASBE_rec.all.out
    Reading ELDKWASBE_lig.all.out
=>> Treat special parameters

I do not know how to solve this problem at all, I have
been trying for a week nothing worked out.
 I appreciate any help
Thanks

Husni Fattayer

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