AMBER Archive (2002)

Subject: Re: How to define a sphere to minimize?

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Mon Oct 21 2002 - 06:00:03 CDT

On Monday 21 October 2002 08:46 am, Guillermo Mulliert Carlín wrote:
> Hello,
> I am using sander_classic in Amber 6, I would like to define a sphere
> of 10 A with centre in an alpha carbon, and minimize (or make some
> dynamics) only on this sphere.
> Is it possible?
>
> With the belly option I must define all the residues I want.
>

Hi,

My solution to this problem was to use the CUTRES feature of carnal.

eg:

FILES_IN
 PARM p1 sphere.top ;
 STREAM s1 sphere.crd ;
FILES_OUT
DECLARE
 GROUP g1 (RES NAME PYR) ;
 CUTRES c1 g1 34.0 ;
OUTPUT
END

This "analin" file gives me an "analout" file with all the residues within 34
Angstroms from a residue called "PYR". It is already nicely arranged in
"group" format so you can basically stick it at the end of your "mdin" file
and use ibelly=1.

Hope this helps.

---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 7740
Fax.: +49 (0)89 2180 7738
e-mail: David.Smith_at_cup.uni-muenchen.de
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