Re: [AMBER] Possible memory leak with LMOD

From: David A Case <>
Date: Tue, 22 May 2018 16:08:59 -0400

On Tue, May 22, 2018, Charo del Genio wrote:

> I'm trying to use LMOD to dock a ligand on a protein, but I'm running
> into some odd behaviour. After the initial TNCG minimization, which
> completes in quite a short time, the amount of memory used keeps
> growing, until the system runs out of memory and the process is
> killed. The protocol I am trying to use computes 15 modes and selects
> 5 of them for the perturbations, doing a total of 100 iterations and
> restarting every 10, using a pool of 10 configurations and keeping up
> to 50 in conflib.dat. For the code, I am using NAB from AmberTools18,
> compiled with gcc 6.4.0.

Thanks for the report. I'm only an occasional user of LMOD, but I can
probably bring in Istvan Kolossvary to help out.

Are you able to send files that would allow us to (try to) reproduce the
problem? That is probably a key first step.


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Received on Tue May 22 2018 - 13:30:03 PDT
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