VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 05 2005 - 13:56:07 CST

Hi guys,
  The currently available MSMS Linux binaries will crash on some
Linux distributions when run in socket mode. You can determine if
this is the case by running it manually from a shell prompt:
  msms -no_area -socketPort 1357

If MSMS immediately crashes when you run it manually, then the best
thing to do is to work around the problem by telling VMD to run MSMS
with the file-based interface rather than the socket interface (works
in VMD 1.8.3 and newer versions..):
  setenv VMDMSMSUSEFILE 1
  vmd

If VMD can't find your MSMS binary, you may need to addtionally set
the MSMSSERVER environment variable to the full path to the binary, but
hopefully the above step will solve your problem.

The file interface may be a little slower than the socket interface,
but this is surely much faster than using Surf, so it's probably your best
bet until they fix the MSMS binaries that are available.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 05, 2005 at 08:36:33PM +0100, Cojocaru,Vlad wrote:
> Dear Sabuj,
> Thanks a lot for the link regarding the MSMS problem (John's answer to a previous inquiry about MSMS). However, I noticed that in my /etc/hosts there is localhost, so I was trying to look at the ports issue but unfortunately I am not so experienced with that so I didnt know how to check on SuSE whether ports above 1024 are allowed. Also it would be helpful to know how to allow such ports in case they are not allowed. I am using SuSE 10. on a AMD64 CPU.
>
> Best,
> vlad
>
>
> -----Original Message-----
> From: Sabuj Pattanayek [mailto:sabuj.pattanayek_at_vanderbilt.edu]
> Sent: Sun 12/4/2005 9:20 PM
> To: Cojocaru,Vlad
> Cc:
> Subject: Re: vmd-l: MSMS problem
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2500.html
>
> Cojocaru,Vlad wrote:
> > Dear vmd users,
> > I have written previously an email in which I described a problem
> > with MSMS. So, after I install the msms into a directory in the path, I
> > test it and it seems to work fine as standalone application. However I
> > cannot use it to visualize structure surfaces in vmd ... As I said
> > previously this is strange because apllying the same procedure on
> > another computer everything worked fine ... So, now the question is: My
> > computer has a Athlon 64 3500+ processor ... Can it be that this is the
> > problem?? However, I would imagine that if this would be the problem,
> > msms should not work also as a standalone app... But maybe it has
> > something to do with vmd. In the meantime I also tested different
> > versions of vmd and the problem is independent of vmd version.
> >
> > I am using SuSE 10.0 as OS, the msms binary is in ~/bin and if I command
> > "which msms", it gives me the right binary. The error message that I get
> > from vmd is given below:
> > If somebody has also experienced this, I would be grateful for any
> > advices how to fix the problem
> > Best
> > vlad
> >
> > Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
> > 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 variable
> > MSMSSERVER to point to the correct binary.
> > Info) Could not compute MSMS surface
> > Info) Done with MSMS surface.
> >
>
>
>
> 

-- 
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