AMBER Archive (2008)

Subject: Re: AMBER: mm_pbsa error

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Fri Apr 04 2008 - 11:29:16 CDT

Did the pbsa_lig.8.out file get created? If so, what is the output? There
are several reasons why you might have troubles at this spot and additional
output could help us locate the problem.

On Thu, Apr 3, 2008 at 2:21 PM, stephane acoca <stephane.acoca_at_gmail.com>
wrote:

> 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 <rams.crux_at_gmail.com> 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 pbsa.in -o pbsa_lig.8.out -c
> > ./snapshot_lig.crd.8 -p ./oba2_nowat_leap.top 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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