AMBER Archive (2009)

Subject: Re: [AMBER] aromatic ring getting distorted

From: case (
Date: Sun Dec 06 2009 - 14:14:45 CST

On Fri, Dec 04, 2009, Jio M wrote:
> I have a ring system like shown in two attached files which is to be
> used as ligands.When I run dynamics the ring system get distorted more
> or less like cyclohexane ring. This should NOT happen according to atom
> types.

It is hard to be of help without knowing what force field parameters you are
using. Did you use antechamber? If so, how?


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