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
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Received on Wed Oct 27 2010 - 16:00:02 PDT
