AMBER Archive (2008)

Subject: Re: AMBER: Need help... High energies for complex...

From: David A. Case (
Date: Thu Sep 04 2008 - 09:36:37 CDT

On Thu, Sep 04, 2008, Waqas Nasir wrote:
> Well, I have tried straight single point md on the complex,sugar and protein
> separately, and what I have found is as follows;

This is not what you should do, at least until you understand what is
going on. My suggestion (and Carlos'):

Make a single prmtop file for the complex. Use this prmtop file for
a single point calculation with two sets of coordinates: one with the ligand
(sugar) in its binding location, and a second set of coordinates where you
manually move the ligand to someplace distant from the protein, (but keep the
protein coordinates identical to what they were in the complex.

Once you see and understand how that works, you will be ready to try and
interpret other experiments.


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