VMD-L Mailing List

From: Liu, Zhanwu (LiuxZx_at_anes.upmc.edu)
Date: Wed Jan 22 2003 - 15:37:35 CST

Hi,

I met this problem before, and finally I found out that the "host" file in
my computer do not have this:
127.0.0.1 localhost localhost

In linux, most likely this file will be in /etc/hosts.

Wish this helps.

Zhanwu

-----Original Message-----
From: phubbard_at_post.its.mcw.edu
To: vmd-l_at_ks.uiuc.edu
Sent: 1/22/2003 3:01 PM
Subject: Surfaces/Cavities

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