VMD-L Mailing List

From: Alan Wilter Sousa da Silva (alan_at_biof.ufrj.br)
Date: Thu Jan 23 2003 - 06:21:18 CST

Hi,

        Respect to the MSMS error. If you're running GNU/Linux, I think
you should define a domain (instead of localhost only) to your computer
and start network, even if you don't have a net card.

On Wed, 22 Jan 2003 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

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil