AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa problem

From: Husni Fattayer (fatayer78_at_yahoo.com)
Date: Wed Apr 27 2005 - 10:09:40 CDT

Hi guys,

as I read in one of the messages , I commented the
line "unlink $sanout" in mm_pbsa.pl file. but still I
got the same error message.

--- Husni Fattayer <fatayer78_at_yahoo.com> wrote:

> 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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