Re: [AMBER] How to generate MM/PBSA statistics from recovered Job

From: Jason Swails <>
Date: Mon, 21 Feb 2011 12:08:22 -0500


All threads should be running concurrently (which is why you have the files
for all 4 threads; .0, .1, .2, and .3). You would have to look at each of
those input files separately to see where the calculation died (on which

There is no way of *easily* computing the statistics from *finished* frames,
I don't think. You can try using the same command you used to run the first time and just add the flag "-rewrite-output" to the
command line. I can't remember whether it counts the frames as it adds
them, or parses it from the ptraj output files.

Just be careful and make sure that the output makes sense.

Good luck!

On Mon, Feb 21, 2011 at 10:38 AM, mish <> wrote:

> Hi,
> I was doing Entropy calculation in nabmode. I used parallel version of the
> python script to do so using 4CPU. Unfortunately my calculation got killed
> due to lime limit and now it copied only -
> _MMPBSA_complex_nm.out.[0-3]
> _MMPBSA_receptor_nm.out.[0-3]
> _MMPBSA_ligand_nm.out.[0-3]
> If I look in the progress.log then i can see that calculation were killed
> during last thread so I think It will have the data up to second last
> thread. Is it possible by someway to generate the final results from this
> data stored in these 12 files ?
> Sincerely
> ..mish
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Feb 21 2011 - 09:30:04 PST
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