Re: fix atoms in minimisation

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon May 01 2006 - 15:58:26 CDT

On Mon, May 01, 2006 at 04:14:35PM +0100, Maria Gonzalez wrote:
> I have a set of 'unstable' protein structures that
> I have inserted in a lipid membrane. I would like to
> run a minimisation so that the lipids and water
> wrap the proteins, but conserving the initial geometry
>
> of the protein structure intact.
>
> The question is, is there a way to run a minimisation
> on only a set of atoms? In my case, the lipids and
> water.

Yep, you can use fixed atoms. Check out the documentation:
http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node27.html#SECTION00091200000000000000

Basically you specify a PDB file that has one of the columns filled with
0's and 1's, 1 standing for "fix this atom". The default column is the
occupancy field, but you can change that.

Leo

-- 
Leonardo Giantini Trabuco
Ph.D. student
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign

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