AMBER Archive (2002)

Subject: Re: Im lost

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 20 2002 - 10:15:29 CDT

On Tue, Aug 20, 2002, Sankha Subhra Som wrote:

> Im a newbie to Computational Biology.I want to perform a force field
> calculation on a file in PDB format.Please note that I dont have the AMBER
> package with me but have the parameter and the topology files.
> Where do i start from?

You have to find a program package that will perform force field calculations;
the parameter and topology files by themselves will be of little to no help
to you.

This mailing list is for Amber users, which is one possibility. The tutorials
on the web site will give you an idea of what is involved. You still haven't
said what sort of molecule it is that you have "in PDB format": it makes quite
a difference whether it is a small molecule or a macromolecule. Your
selection may also be influenced by the type of computer you have available.
Programs like Hyperchem, PC-Model (and others) are geared towards running on
Wintel PC's with a convenient interface.

A good book describing the foundations and practice of computational chemistry
is that by Andrew Leach. You should expect to spend quite a bit of time
learning both the fundamentals and the practical aspects of molecular
modelling if you want to get useful results.

...hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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