From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Apr 15 2014 - 05:22:11 CDT

Hi!

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.

Regards,
Ajasja

On 15 April 2014 10:49, Recep adıyaman <radiyaman_at_nku.edu.tr> 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
> recepadiyaman2244_at_gmail.com
> radiyaman_at_nku.edu.tr
> radiyaman.nku.edu.tr <radiyaman_at_nku.edu.tr>
>