From: Ajasja Ljubetič (
Date: Tue Apr 15 2014 - 05:22:11 CDT


VMD is just a very powerful and scriptable viewer. Using a combination of
NAMD and VMD (and a lot of TCL scripting) most of what you describe could
be achieved, but it is far from a routine point and click operation.


On 15 April 2014 10:49, Recep adıyaman <> wrote:

> Dear VMD users,
> We are doing mutations in metal binding proteins. We would like to compare
> binding affinites before and after the mutations.
> Can I use VMD to predict the folding after mutation? I did some search but
> couldn't be sure.
> Also, is it possible to calculate stability (in kcal/mol) of a given
> protein?
> We are planning to scan many mutations so how can I do all these
> calculations in batch (scripting maybe?).
> When a mutant is folding, do VMD keep the backbone stable? (Like FoldX's
> repairpdb function). If a metal bound protein is folded, do the software
> reposition the metal ion accordingly?
> Researcher Recep ADIYAMAN
> Namik Kemal University
> Distance Education Center
> +905397611054
> +902822501071 Tekirdağ-TÜRKİYE
> <>