[gmx-users] Re: D-amino acids simulation

Kirti Patel kirti at chem.iitb.ac.in
Tue Feb 21 09:49:33 CET 2006

> Message: 3
> Date: Mon, 20 Feb 2006 07:04:05 -0800 (PST)
> From: Arnold Perez Goicochea <sciarnold at yahoo.com>
> Subject: [gmx-users] D-amino acids simulation
> To: gmx-users at gromacs.org
> Message-ID: <20060220150405.76729.qmail at web54601.mail.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>    Dear All,
> I am planning to perform MD simulations with some D-amino acids. I normally use OPLS-AA with
> GROMACS 3.2.1, but I think it won't work if D-amino acids  are used. The FF torsion potential
> would not be suitable for those aminoacids.
> Should I use the OPLS with D-amino acids? or would be better to use another force field?, or in
> the case no FF is suitable, which kind of modifications should I do on it??
You can refer to our recent paper
 Ramakrishnan, V.; Ranbhor, R.; Durani, S., Biopolymers, 78, 96-105 (2005)

> Thank you in advance for your valuable help,
> -Arnold
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Kirti Patel

"Research Scholar"
Bio-organic Lab,
Department of Chemistry,
Indian Inst. of Technology
Ph. No. +91 9869370689
Fax No:-022-25767152

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