Re: AMBER: How to build a dimer using amber

From: David A. Case <>
Date: Mon, 14 Jan 2008 23:51:50 -0800

On Tue, Jan 15, 2008, Reena ..... wrote:
> I have tried placing the "ter" card and the combine command in xleap.

You need to be a *lot* more specific in what you did. Please give the exact
commands, what try to say precisely what was wrong with the result.

> I have also used Hex, wherein the resulting file had two monomers in
> antiparallel geometry as the most stable structure. This file was used as
> input structure for the minimisation n dynamics run in Amber.

Sounds fine to me. Are you trying to say that you are satisfied or
dis-satisfied with using this Hex structure?

Again, please tell us exactly what you did, in as much detail as possible.
Don't just say "the resulting file...": what kind of file is it? how exactly
did you input this into Amber?

I'm not trying to be critical here, just trying to point out what sort of
information you will need to provide if anyone is going to be able to help.

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Received on Wed Jan 16 2008 - 06:07:23 PST
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