Re: [AMBER] error

From: Rasha Alqus <>
Date: Thu, 24 Oct 2013 14:31:44 +0000

Dear Jason,

Thank you for the help.

I have checked all files and the onlly error is mention is in the progress.log below.

The Latest patch applied to AmberTools12: 28

Thank you

Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/gridware/apps/intel-12.0/amber12-intel-ib-compflags-axAVX/bin/mmpbsa_py_energy
cpptraj found! Using /opt/gridware/apps/intel-12.0/amber12-intel-ib-compflags-axAVX/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /opt/gridware/apps/intel-12.0/amber12-intel-ib-compflags-axAVX/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
CalcError: /opt/gridware/apps/intel-12.0/amber12-intel-ib-compflags-axAVX/bin/mmpbsa_py_energy failed with prmtop!
Exiting. All files have been retained.

From: Jason Swails []
Sent: 24 October 2013 15:08
To: AMBER Mailing List
Subject: Re: [AMBER] error

On Thu, Oct 24, 2013 at 9:02 AM, Rasha Alqus

> Dear Amber users,
> The error occure during the GB calcualtion. I have attatched the files.

You have attached 3 files, none of which help me figure out what went wrong
since the output file does not have an error message and I cannot run the
calculation myself with just these files. If the error message is not in
the output file you sent, then it is likely in the output from
 Without an error message, I cannot diagnose the problem remotely.

> Am using ambertools12.

How many bug fixes have been applied? The command

cd $AMBERHOME && ./ --patch-level


cd $AMBERHOME && ./update_amber --version

will tell you this information.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 24 2013 - 08:00:02 PDT
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