VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 22 2003 - 14:16:49 CST

Hi,
  For the atom selection, one possibility would be to do a distance
based atom selection, another would be to use any other properties of
the structure that you're aware of to select just the atoms in the
binding site, by index or residue range, chain, or any other useful fields
that would help you distinguish the atoms at the binding site from the rest.

In order to get MSMS to work, VMD needs to be able to find it in your
path. If it cannot, then another way is to set the environment variable
MSMSSERVER to the actual binary, i.e.:
  setenv MSMSSERVER /usr/local/bin/msms

Let us know if you need more help.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 22, 2003 at 02:01:37PM -0600, phubbard_at_post.its.mcw.edu wrote:
> Hi all,
>
> I have 2 pdb files, one of the protein, and one of a ligand bound to the
> protein. Could someone please tell me how I can define a subset of atoms
> in the protein that line the binding site, and have a surface rendered for
> just that part of the protein.
>
> P.S: I have MSMS 2.4.1 instatlled, but VMD (1.8) doesn't recognize it -
>
> Info) Starting MSMS with: 'msms -no_area -socketPort 1357 > /dev/tty &'
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> ERROR) Could not connect to MSMS server. Please check that the program
> 'msms' exists and is executable, or set the environment variableMSMSSERVER
> to point to the correct binary.
> Info) Could not compute MSMS surface
> Info) Done with MSMS surface.
>
> Any tips on how to fix it.
>
> Thanks
>
> AGS
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078