VMD-L Mailing List

From: CPMAS Chen (cpmasmit_at_gmail.com)
Date: Thu Jun 25 2015 - 15:44:09 CDT

Now, vmd started to run. but here is another error

Command = zcat setp1.dx.Z

Filename.Z = setp1.dx.Z

Command = gzip -d -c setp1.dx.gz

Filename.gz = setp1.dx.gz

FATAL ERROR: Problem reading grid force potential file

------------- Processor 0 Exiting: Called CmiAbort ------------

Reason: FATAL ERROR: Problem reading grid force potential file

Any hints?

Thanks!

Charles
On Tue, Jun 16, 2015 at 4:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
***************************************************
Charles Chen
Research Associate
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************