From: phubbard_at_post.its.mcw.edu
Date: Wed Jan 22 2003 - 14:01:37 CST

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