AMBER Archive (2009)

Subject: Re: [AMBER] pairwise per-residue decomposition

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Thu Oct 29 2009 - 19:30:51 CDT

I had the same problem with this script for ~1000 frames of my ~700
residue system on a machine with 8GB of RAM. It would just sit there.
I don't know what the problem is, but I gave up on it and now just run
sander manually and postprocess its output outside of MM_PBSA.pl.

You can try running "top" in another terminal session on the same
machine while your 1000-frame calculation is attempting to run to get
an idea of its memory usage. Look at the "RES", "RSS", or similar
column.

--Tom

2009/10/29 manoj singh <mks.amber_at_gmail.com>:
> Hi all,
>
> I am trying to do pairwise per-residue decomposition of MM-GBSA binding free
> energy for a protein ligand system. My calculation is crashing (the computer
> stop responding) on the "=>> Calc delta from raw data", probably due to the
> memory issue. I will be very thankful if some one can tell me a fix of this
> problem.
>
> Manoj
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> AMBER_at_ambermd.org
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>

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