VMD-L Mailing List

From: Recep adyaman (radiyaman_at_nku.edu.tr)
Date: Tue Apr 15 2014 - 03:49:01 CDT

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 Tekirda-TRKYE
recepadiyaman2244_at_gmail.com
radiyaman_at_nku.edu.tr
radiyaman.nku.edu.tr <radiyaman_at_nku.edu.tr>