From: samantha hughes <>
Date: Thu 30 Nov 2000 08:05:22 +0000

Hi Christine, AMBER users

> We plan to use the MM-PBSA module for calculating the post-production energies
> of a few of our structures after we first run them through the sander module.
> We were wondering if there were any variables in the input file for a sander
> production run that needed to be specified in order to later use the
> production results in MM-PBSA (other than setting up a trajectory file printed
> at appropriate timepoints). Thanks again for your help.

As far as I know there are no sander input variables that are
necessary for MM-PBSA, but I have related advice: if calculating
ligand binding energies, make sure that the ligand is either at
the beginning or the very end of the topology file. The
post-processing scripts for MM-PBSA are set up for these two
cases only.

Hope this helps.

Received on Thu Nov 30 2000 - 00:05:22 PST
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