Re: [AMBER] problem

From: Jason Swails <>
Date: Tue, 04 Aug 2015 09:22:10 -0400

On Tue, 2015-08-04 at 15:46 +0530, Debodyuti Dutta wrote:
> hello Amber users,
> I am facing a strange problem in MM-PBSA and I would like to know if there
> is any solution to it or
> someone else is also facing the same.
> In MM-PBSA we use the trajectory protein-ligand trajectory. It write 3
> output files, namely, _MMPBSA_complex_pb.mdout.0,
> _MMPBSA_receptor_pb.mdout.0, _MMPBSA_ligand_pb.mdout.0. Problem is that the
> calculation is going on well if there is only 5 frames and the program is
> writing the .dat files at the end of the calculation; but if there is ,lets
> say, 5000 frames the calculation finishes after writing full
> _MMPBSA_complex_pb.mdout.0 and not writing the other mdout files.

Are you sure you are giving it enough time to finish? 5000 frames is a
LOT of frames to analyze -- far too many in my opinion. PB calculations
can take a long time -- if each one takes ~20 seconds, then 5000 frames
will probably take more than 2 days (assuming ~40 seconds per frame for
the complex, receptor, and ligand).

It's possible that there is a bug of some kind, but it will probably be
difficult to reproduce and detect given that you report it only
happening for very long calculations. You will probably be better off
extracting only ~100 to 200 frames for calculation from your trajectory.
Your answers are unlikely to change by adding more.

> There is
> no error message of any kind. Although all 3 sets of mdcrd.0, pdb, inpcrd
> and mdin files are generated by cpptraj before the calculations go through
> Sander. I am using amber14.

What makes you sure that the calculation has finished and is not just
taking a long time? Another thing you can try is to figure out exactly
what frame it is failing on and then setting "startframe" and "endframe"
to analyze *just* that frame and see if you can reproduce the error. I
have never seen this behavior before, so I'm not quite sure what else to
try at this point.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 04 2015 - 06:30:03 PDT
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