Hi,
I would also suggest looking at the file pbsa_com.1.out to see what errors
are in it because that will give you insight as to why the calculation
stopped as well.
On Wed, Oct 27, 2010 at 6:58 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Hello,
> When I run the binding_energy.mmpbsa, it showed error and stopped:
> /usr/local/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out
> -c
> ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
> This is the output in the log file:
> =>> Init data
> Presuming executables of amber suite to be in /usr/local/amber10/exe
>
> =>> Reading input parameters
> Found PREFIX => snapshot
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT => ./com_vac.prmtop
> Found RECPT => ./ricin.prmtop
> Found LIGPT => ./antibody_vac.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 PROC => 2
> Found REFE => 0
> Found INDI => 1.0
> Found EXDI => 80.0
> Found SCALE => 2
> Found LINIT => 1000
> Found PRBRAD => 1.4
> Found ISTRNG => 0.0
> Found RADIOPT => 0
> Found NPOPT => 1
> Found CAVITY_SURFTEN => 0.0072
> Found CAVITY_OFFSET => 0.00
> Found SURFTEN => 0.0072
> Found SURFOFF => 0.00
> 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
>
> =>> Checking sanity
> Checking GENERAL
> Setting START to default 1
> Setting STOP to default 10e10
> Setting OFFSET to default 1
> Setting VERBOSE to default 0
> Checking MM
> Checking PB
> Checking GB
> Checking MS
>
> =>> Creating input
> Sander input
> PBSA input
>
> =>> Calculating energy / entropy contributions
> Calc contrib for ./snapshot_com.crd.1
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
>
> I set MM, GB, PB, and NM to 1. It that right?
> BTW, I don't know how these terms related to the binding energy
> calculation. The
> manual is too brief. I can't find much helpful information.
>
>
>
>
>
>
>
> ________________________________
> From: Bill Miller III <brmilleriii.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wed, October 27, 2010 11:57:58 AM
> Subject: Re: [AMBER] cannot generate snapshot_statistics.in file
>
> The extract_coords.mmpbsa input file is designed to simply make the
> snapshots that binding_energy.mmpbsa uses to actually calculate the
> energies. You will need to turn on (set equal to 1) MM, GB, PB, etc in
> order
> to get the files you described below.
>
> -Bill
>
> On Wed, Oct 27, 2010 at 11:52 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > Dear all,
> > When I run extract_coords.mmpbsa for a protein-antibody complex, the log
> > file
> > didn't show any error message, but I didn't get snapshot_com.all.out,
> > snapshot_lig.all.out, snapshot_rec.all.out, and
> snapshot_statistics.infile.
> > Could anybody give me some suggestions?
> >
> > I got 200 snapshot file for the complex, ligand, and receptor, but no
> > all.out
> > files. The script worked for other molecules, I don't know why it didn't
> > work
> > this time.
> >
> > Thank you very much.
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Oct 27 2010 - 16:30:04 PDT
