VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 16 2015 - 15:11:49 CDT

Hi,
  Your cluster is missing the OpenGL-related drivers and libraries that
the standard VMD builds need to be able to run. Instead of using the
full-featured version of VMD, you should download and install the text-mode
version of VMD which is listed on the VMD download page as:
  LINUX_64 Text-mode

It's the 5th item down on the list of platforms. If you install that version
of VMD, you should be able to run it successfully on your cluster.
  http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 11, 2015 at 03:34:51PM -0400, CPMAS Chen wrote:
> Hello:
> I am following the tutorial to set up xMDFF work. when I submitted my job
> to our cluster, it reported error. The message is like this:
>
> TCL: /opt/local/lib/vmd/vmd_LINUXAMD64: error while loading shared
> libraries: libGLU.so.1: cannot open shared object file: No such file
> or directory
> FATAL ERROR: /opt/local/lib/vmd/vmd_LINUXAMD64: error while loading
> shared libraries: libGLU.so.1: cannot open shared object file: No such
> file or directory
>
> I have the log and namd file attached, could you guys give me some
> suggestions?
> 1. I am bugging the cluster administer to to see if this is setup/software
> issues. but VMD/NAMD works just fine in all other jobs.
> 2. I changed 'vmd' in the .namd file to '/opt/local/bin/vmd' to specify
> the location of vmd executable. and it reported the above error message.
> 3. I tried alias vmd="/opt/local/bin/vmd", so I can use the namd file
> without anything changed. it will report error like this:
>
> TCL: couldn't execute "vmd": no such file or directory
>
> FATAL ERROR: couldn't execute "vmd": no such file or directory
>
> Â Â while executing
>
> "exec vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $PDBFILE
> $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKC
>
> UTOFF > map.log"
>
> Thanks!
> Charles
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ****************************************************** 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/