AMBER Archive (2002)

Subject: Re: your mail

From: David Case (case_at_scripps.edu)
Date: Fri Nov 29 2002 - 14:07:19 CST

On Fri, Nov 29, 2002, Narang Manpreet Kaur wrote:

> I am working on drug molecule which has anthracene
> dione structure with side chains. The drug molecule is fully symmetrical.
> I want to know how I can I give chemical shifts restraints to it.
>

It's not clear to me what you want to do. You don't indicate whether or not
this is a drug bound to a receptor, or just the drug by itself. You don't
indicate what kinds of shifts you have (proton, nitrogen, carbon?), or what
sorts of restaints you are thinking about.

The chemical shift restraint capability in Amber is mostly geared towards
proteins and nucleic acids. To work with proton shifts in a fairly
arbitrary drug molecule, you could look at the fit_susc program in the
"shifts" package that you can get from the web site below. But don't expect
this to be easy. If you are not dealing with a macromolecule, there are
more "chemistry"-based programs that might be a better fit: try a google
search.

...hope this helps...dac 

-- 

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