Re: fix atoms in minimisation

From: Leonardo G. Trabuco (
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:

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.


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

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