VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 17 2000 - 09:16:16 CST

Hi,
  Have you tried running MSMS on a small molecule to see if the
problem is related to the size of your molecule? There is a known
problem with the interface between VMD and MSMS that can cause it to
fail when generating surfaces for large molecules, or on slow machines.
We've been working on improving the VMD/MSMS interface recently, and this
should be fixed once and for all in VMD 1.5. What kind of machine are
you using by the way? We are planning on making the first pre-release
version of VMD 1.5 available today. You might try this new version with
your same MSMS 2.4.x binary and see if it works better, we have already
made various improvements to the MSMS interface code in this pre-release
version, but there's still more to be done before VMD 1.5 is finished.

Thanks for your patience,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 17, 2000 at 02:53:22PM +0100, Xiao-Ping Zhang wrote:
> Hi,
>
> I installed VMD 1.4 and MSMS 2.4 on Redhat Linux 5.2. When I draw molecule
> in VMD with MSMS method, the msms calculation works fine (you can see from
> vmd console window), but nothing showed up in the Graphic window. What I
> did was putting the msms executable in /usr/local/bin/ directory. Do I need
> to install something else?
>
> Thank you.
>
> Sincerely,
>
> Xiao-Ping Zhang
>
> ------------------------------------------------
> Xiao-Ping Zhang
> Department of Biochemistry
> Stockholm University
> 106 91 Stockholm
> Sweden
>
> Phone: 46-08-162582 / 162472
> Fax: 46-08-153679
> e-mail: zhang_at_biokemi.su.se
>
> 

-- 
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