Re: [AMBER] distortion of the ligand during MD

From: David A Case <>
Date: Wed, 17 Oct 2012 09:44:06 -0400

On Wed, Oct 17, 2012, Mu Xia wrote:
> My recent job is a MD simulation of a ligand-protein complex. The ligand
> is quercetin, a kind of flavonoids. I used GAFF for the ligand and
> ff99SB for the receptor. By examining the trajectories, I found that the
> ligand distort abnormally. What shoud I do to deal with this problem?

> Maybe a proper force filed for the ligand is needed.

You are correct: GAFF does its best to create a reasonable force field, but
its parameters should be considered as a first guess. If your ligand is
distorting abnormally, you may well need to examine the bad configurations by
hand and try to fix parameters to get better results. Without knowing the
nature of the distortions you are seeing, it is hard to say anything more

...good luck...dac

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Received on Wed Oct 17 2012 - 07:00:08 PDT
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