Re: how to set harmonic constraints to alpha carbon

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 07 2003 - 10:37:51 CST

Hi,

You need a little VMD incantation to generate the input file, the
structure building hands-on includes this and is avaialble at
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/

This is the VMD code:

# STEP 8: Restrain CA

# Put harmonic restraints on the CA atoms for heating and unit cell
# equilibration. Use the coordinates from the last simulation frame.

set all [atomselect top all]
set sel [atomselect top "protein and name CA"]
$all set beta 0
$sel set beta 0.5
$all writepdb restrain_ca.pdb

And this is the NAMD code:

constraints on
consRef restrain_ca.pdb
consKFile restrain_ca.pdb
consKCol B

-Jim

On Thu, 6 Nov 2003, Brian Bennion wrote:

> Hi Zhilei,
>
> The manual at:
> www.ks.uiuc.edu/Research/namd/current/ug/node27.html#7074
>
> gives the commands.
> you need to make a copy of a pdb file for your system and modify the
> columns to constrain CA atoms.
>
> Brian
>
>
> On Thu, 6 Nov 2003, Zhilei Chen wrote:
>
> > Hi,
> >
> > I want to set harmonic constraints to the alpha carbon of my protein during
> > energy minimization. Can anybody tell me how to do it?
> >
> > thanks
> >
> > zhilei
> >
>
> --
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 422-6605 **
> *****************************************************************
>
>

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