VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 19 2007 - 12:41:10 CDT

Hi Zhenwei,
there are a couple of ways to do this, depending on how big your protein
is and how specific the conformation you want is. What you'll probably
want to do is write a pdb for the single amino acid (or set of a couple)
that you want to add using the molefacture protein builder, and then
paste the resulting pdb ATOM lines above or below those of your protein
to generate a file containing all of the atoms you want; you can then
use VMD to move it to the right place. This process will be much easier
once I've modified the molefacture protein builder to allow residues to
be added to either end of an existing protein (slated for VMD 1.8.7).
Please let me know if you have any questions.

Peter

Zhenwei Lu wrote:
> Hi, I wander if VMD can be used to add residue at start or end of the
> protein. Thanks a lot for any idea about it.
>
> Zhenwei Lu