VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Sat Aug 21 2010 - 02:14:19 CDT

Fix or restraint the DNA backbone.
http://www.ks.uiuc.edu/Research/namd/2.7b3/ug/node26.html
<http://www.ks.uiuc.edu/Research/namd/2.7b3/ug/node26.html>Or better yet
solvate the system first and minimize afterwards.

regards,
Ajasja

On Sat, Aug 21, 2010 at 05:39, Janani.S <011213028_at_bioinfo.sastra.edu>wrote:

> How to do prevent distortion of a molecule while doing energy
> minimisation?
> I am trying to minimise a protein-dna sequence invaccuo ( dielectric 1).
> But the dna gets very badly distorted. How can i prevent this?
> - Janani
>