AMBER Archive (2008)

Subject: Re: AMBER: mm_pbsa error

From: stephane acoca (
Date: Thu Apr 03 2008 - 15:21:29 CDT

Probably ran out of memory. You can use a higher fillratio of 3 and that
might help. you should look at the pbsa output file to have more info on
the error. You can also change the "scale" parameter and put it a little
lower to 1.5 or so.

On Thu, Apr 3, 2008 at 12:28 PM, rams rams <> wrote:

> Dear amber users,
> I am running mm_pbsa moldule for calculating binding free energy for my
> protein with ligand. When I run mm_pbsa, it run well for complex and
> receptor, when it comes to ligand, the program got terminated by complaining
> the following:
> ../amber9/exe/pbsa -O -i -o pbsa_lig.8.out -c ./snapshot_lig.crd.8
> -p ./ not successful
> Could some one tell me what might be the reason and do I need to rerun
> every thing or is there any way I can continue from here for the rest of the
> calculations.
> Please let me know if I need to provide more info regarding the problem
> mentioned above.
> Thanks and Regards,
> Ram.

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