AMBER Archive (2009)

Subject: Re: [AMBER] How to create parameter file for unknown residue

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Fri Apr 03 2009 - 05:50:30 CDT

For a user point of view, AMBER is one of the few programs that I know that
besides an extensive manual has a very nice series of tutorials (
http://ambermd.org/tutorial/). Related to your question you might take a
look at this one
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/ .
Marius

On Fri, Apr 3, 2009 at 12:33 PM, nicholus bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

> Dear community members,
>
> As you may noticed in the tutorial
> named "Loop dynamics of the HIV-I integrase core domain" provided with the
> manual a addition parameter file named MG.off for MG residue. Otherwise
> leap
> dose not recognize MG. Can someone help me out with creating parameter
> files
> for unknown residue like ZN, Fe etc. etc. Without these parameter files
> leap
> does not recognize the unknown residues and does not create the topology
> and
> co-ordinate files. Please help me out.
>
> Thank you in advance.
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
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