VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 14 2005 - 10:27:58 CDT

Hi,
  It sounds like there's some sort of problem with the network
setup on your Linux machine. We didn't change anything noteworthy
in the MSMS sockets interface for VMD, and it still works fine for us
on all of our Linux machines here, so there may be some other problem
occuring there. We have added a new VMD environment variable that may
make it easier for you to get around this problem. Try setting this
environment variable prior to running VMD:
 setenv VMDMSMSUSEFILE 1

Try that and let us know if you still have trouble with MSMS.
This forces VMD to talk to MSMS through the file-based interface
rather than with the sockets interface, it should work even in the case
that you are having trouble with the sockets interface.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 14, 2005 at 05:17:40PM +0300, Dr. Daniel James White PhD wrote:
> Hi John,
>
> I am trying to make movies of viral capsids.
>
> So... I am using msms to make low resolution triangle surfaces,
> so I dont run out of memory,
> and I'm using the biological unit pdb file
> 1c8g.pdb1 which has 60 "states"
>
> Problems:
>
> 1) On fedora core 3 linux,
> I have downloaded and installed correctly msms 2.5.5. and vmd 1.8.3
> msms works from the command line with command
> msms
> and alo I have pointed $MSMSSERVER to /usr/local/bin/msms
> but VMD gives this error when I try to make an MSMS surface.
>
> ERROR) Could not connect to MSMS server ...... etc. etc etc.
>
> my /etc/hosts file contains
>
> 127.0.0.1 modeling.bio.jyu.fi modeling
> localhost.localdomain localhost
> 127.0.0.1 localhost localhost
>
> commenting out the top line still gives the same error.
>
> same version of MSMS seems to work just fine with VMD 1.3.8 on my OSX
> machine.
>
> 2) I was using VMD 1.8.3b on linux to do the
> Graphical Reprsentations-trajectory-draw multiple frames
> thing to show all sixty subunits of the virus.
>
> today I updated it to 1.8.3
> now on linux and OSX VMD 1.3.8 this no longer seems to work.
>
> I type in
> 0:59
> in the box as before,
> and hit return,
> but nothing happens.
> In 1.8.3b doing this showed all the 60 molecules.
>
> What am i doing wrong!?
>
> cheers
>
> Dan
>
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and
> Department of Biological and Environmental science
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
>
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi 

-- 
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