[gmx-users] define a new residue

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jul 8 18:43:49 CEST 2012

What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)?


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, July 8, 2012 9:02 PM
Subject: Re: [gmx-users] define a new residue

On 7/8/12 11:29 AM, Shima Arasteh wrote:
> Thanks all.
> So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right?

You can look this up in the force field's .rtp file.  For full parameterization procedures, refer to the primary literature for CHARMM.  It should detail how to derive parameters for new species.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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