AMBER Archive (2008)

Subject: Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?

From: Edyta Malolepsza (em427_at_cam.ac.uk)
Date: Mon Mar 31 2008 - 08:05:42 CDT

Dear David,

On Wed, Mar 19, 2008 at 10:54 PM, David A. Case <case_at_scripps.edu> wrote:

> Is it possible to revise the libraries so that the "symmetric" prmtop file is
> made in the first place?

I've tried it on the beginning, but it didn't work. The order of atoms
is sorted few times in LEaP according to rules mentioned in previous
posts and it is independent of order in libraries. Therefore I am
playing on ready topology file.

In some post on Amber Archive I have found information that older
version of Amber took order of atoms for IMPROPER from libraries.

> I hope one of the Amber "force field people" has the time to jump in here, as
> I cannot take on any new responsibilities right now.

I hope too :)

All interested in my python program perm-prmtop.py (specially
Francesco Pietra) are welcome to web page of Dr David Wales, where you
can find it and download: http://www-wales.ch.cam.ac.uk/software.html
Please read comments inside.

Best regards,

Edyta Malolepsza
Group of David Wales, University of Cambridge
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