VMD-L Mailing List

From: phubbard_at_post.its.mcw.edu
Date: Wed Jan 22 2003 - 16:04:25 CST

Thanks. That fixed it!

AGS

> 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