Re: [AMBER] distortion of the ligand during MD

From: Mu Xia <>
Date: Wed, 17 Oct 2012 22:02:42 +0800 (CST)

Hi David,

Thanks for your reply.

As you know, quercetin has A, B and C ring. For example, if I want the three rings to be plane or the dihedral angle of CA-CB-CC-CD to be near 180 degree during the MD,
how should I fix the parameters? Modify the .frcmod file or something else?

Mu Xia,
Zhejiang Univesity, China
At 2012-10-17 21:44:06,"David A Case" <> wrote:
>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 - 07:30:04 PDT
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