AMBER Archive (2009)

Subject: Re: [AMBER] aromatic ring getting distorted

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Dec 07 2009 - 01:04:55 CST

Dear AMBER users;

Sorry, I have to change  the subject to "COOH group troubling" and
given my ligand mol2 and parmchk derived frcmod file there. Now I am
trying with default atom types given by antechamber not changing cc to
cp. But here COOH atoms are troubling.

thanks, pardon and regards;

JIomm

--- On Sun, 12/6/09, case <case_at_biomaps.rutgers.edu> wrote:

From: case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] aromatic ring getting distorted
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Sunday, December 6, 2009, 8:14 PM

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?

....dac

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