VMD-L Mailing List

From: João Ribeiro KS (jribeiro_at_ks.uiuc.edu)
Date: Sun Feb 12 2017 - 23:32:52 CST

Hi Jrhau,

in principle you don't need to do a docking step after mutate the residues
with QwikMD, just select the residue that you want to mutate to or the
delete the portion of the structure of interest. Possible atom's clash will
be eliminated during the minimization step and you should simulate your
system long enough to enable the structure to adopt to the new most
favorable conformation (reach the equilibrium). QwikMD doesn't allow
residues insertion, only residues deletions and mutate one residue to
another.

As a general statement (not only for QwikMD), insertions and/or deletions
may require a the docking step, depending on the impact and location of
these mutations.

I hope this help

Best

Joao

On Sun, Feb 12, 2017 at 7:15 PM jrhau lung <jrhaulung_at_gmail.com> wrote:

> Dear VMD-I friends:
> If I would like to simulate the binding affinity of an inhibitor with
> a mutant protein structure, do I need to rebuild the mutant protein
> structure and dock the ligand first, or just change the residue "in the e
> Select Residue window. Select Mutate in the Table Mode" in QwikMD?
> Especially if the mutation comes with short amino acid insertion or
> deletion in protein structure? Thanks.
>
> sincerely yours,
>
> Jrhau
> 

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