From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Jun 25 2015 - 16:29:42 CDT

This indicates that something is going wrong during the map generation
process. In your working directory there should be a "map.log" file. There
should be some sort of error somewhere in that file. Could you send that
file or copy the error here?

On Thu, Jun 25, 2015 at 4:25 PM CPMAS Chen <cpmasmit_at_gmail.com> wrote:

> 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
>
> ******************************************************
>
>