VMD-L Mailing List

From: Alisha \ (jonesan_at_muohio.edu)
Date: Tue Jul 19 2011 - 16:14:56 CDT

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