Re: [AMBER-Developers] mmpbsa tests (perl and python)

From: Mengjuei Hsieh <>
Date: Tue, 30 Mar 2010 14:41:43 -0700

On Tue, Mar 30, 2010 at 01:07:30PM -0700, Ray Luo wrote:
> The large memory usage is probably due to the fact that both scripts are
> setting fillratio = 4 right now so the grid setting error will never get
> triggered. This leads to a grid too large except for small organic
> molecules.
> MJ is in the process of making the grid setting routine more
> intelligent. The routine will try to use a larger fillratio if the
> current fillratio is too small. This will be done successively until a
> large enough fillratio is found. This is a minor enhancement and can be
> done today.


Please find the attached patch file in the email. Basically 2 features
were added to make it more failsafe.

1. it automatic adjust fillratio if fillratio is not large enough.
2. it reject cap water in pb computation, since it's not supported
   in current version.

Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
University of California Irvine.

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Received on Tue Mar 30 2010 - 15:00:02 PDT
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