From: Maria Gonzalez (mela_dn_at_yahoo.co.uk)
Date: Tue May 02 2006 - 20:18:50 CDT
Thanks for this. I had assumed the fix option was only
available within a 'proper' MD (and not a
minimisation).
Maria
--- "Leonardo G. Trabuco" <ltrabuco_at_ks.uiuc.edu>
wrote:
> 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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