VMD-L Mailing List

From: phubbard_at_post.its.mcw.edu
Date: Wed Jan 22 2003 - 14:45:36 CST

Hello,

Thanks for the quick reply. With reagrds to defining a subset - distance
would be the best (I have used this method in InsightII and it works
well). Could you please tell me how I do this as I've had limited
experience with VMD (just the point 'n' click stuff).

With regards to MSMS: I've tried the following

paul_at_iris10 % > msms
MSMS 2.4.1 started on iris10
Copyright M.F. Sanner (1994)
Compilation flags -O2 -Olimit 660 -xansi -DVERBOSE -DTIMING -DFUNCPROTO
-fullwarn -mips2
MSMS: No input stream specified
paul_at_iris10 % > which msms
/usr10/local/bin/msms
paul_at_iris10 % > setenv MSMSSERVER /usr10/local/bin/msms
paul_at_iris10 % > vmd

Info) Starting MSMS with: '/usr10/local/bin/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
'/usr10/local/bin/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.

Thanks

AGS

>
> 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