AMBER Archive (2009)

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

From: Tom Joseph (
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

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


2009/10/29 manoj singh <>:
> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list