VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jul 20 2011 - 16:57:49 CDT

Hi,

I think psfgen <http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf> does
not have any three letter restrictions and supports a mutate command.
Another more manula way of mutating a residue is to delete it's side chain
then rename it to the new residue and let psfgen's guesscord do all the
work.

Hope this helps,
Ajasja

On Tue, Jul 19, 2011 at 23:14, Alisha "Jonesy" Jones <jonesan_at_muohio.edu>wrote:

> Hello,
>
> I am attempting to mutate a residue in my peptide to a nonstandard amino
> acid using VMD, however I have noticed the using the "mutator" option, only
> standard three letter amino acid codes are permitted. Is there any way to
> edit the "bank" of amino acids mutator uses to add in the nonstandard amino
> acids? Or, is it possible to upload residues for purposes of mutating them
> in?
>
> I attempted to use molefacture, however in selecting the atoms, I was only
> able to "create" the nonstandard amino acid as a single molecule, in
> contrast to in my peptide. I noticed quite a few tutorial files online but
> I couldn't find one for molefacture... I found one that helps with the
> basics but doesn't exactly help me with what I need to do; Is there a
> tutorial for this or is anyone familiar with this extension?
>
> I would really appreciate some help,
> Jonesy
>