VMD-L Mailing List

From: João Ribeiro KS (jribeiro_at_ks.uiuc.edu)
Date: Mon Mar 21 2016 - 11:33:43 CDT

Dear Kalyanashis,

VMD can perform DNA and RNA mutations. You can use "mutate" command (
http://www.ks.uiuc.edu/Research/namd/2.11/ug/node19.html) from psfgen to
mutate either protein or nucleic residues.

I would like to also mentioned that there is a new VMD plugin that
streamlines MD simulation preparation, execution and analysis named QwikMD.
If you would like try I would be glad to give you more instructions how to
get it.

Best

Joao

On Sat, Mar 19, 2016 at 3:34 AM, Vlad Cojocaru <
vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:

> Chimera can do that nicely ... the command is "swapna" (see chimera user
> guide) .. I don't think VMD can do it (but I may have missed this feature
> if it exists)
>
> Best
> Vlad
>
>
> On 03/19/2016 08:32 AM, Kalyanashis Jana wrote:
>
> Hi,
> I am Kalyanashis Jana, working under Dr. Bishwajit Ganguly, CSIR-CSMCRI,
> Bhavnagar, India. I used the VMD mutation technique for protein system.
> However, it was not working for some specific amino acid residues e.g.
> histidine, selenocysteine. Otherwise, it is an excellent platform to mutate
> protein or enzyme. Now, I would like to mutate DNA or RNA i.e. I would like
> to replace a single/multiple nucleobase with other DNA/RNA nucleobase(s).
> Can you please tell me, is it possible to mutate DNA/RNA with VMD?
>
> Looking forward to hear from you positively.
>
> Thanks in advance,
> With best regards
> Kalyanashis Jana
>
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.dehttp://www.mpi-muenster.mpg.de/43241/cojocaru
>
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380