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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Received on Mon Apr 25 2005 - 22:53:01 PDT
