VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 09 2005 - 13:00:15 CST

Sabuj,
  Ok, what happens if you do this:
setenv VMDSIMPLEGRAPHICS 1
vmd

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 09, 2005 at 12:53:36PM -0600, Sabuj Pattanayek wrote:
> John Stone wrote:
>
> >Sabuj,
> > If running the script opens and closes an xterm immediately, we need
> >to figure out why. VMD will not run correctly if you start the binary
> >manually. What happens when you run VMD like this:
> > vmd -dispdev text
> >
> >
> vmd -dispdev text
> Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> vmd > quit
> Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> Info) Exiting normally.
>
> ..no error messages there
>
> ls -l /bin/csh
> lrwxrwxrwx 1 root root 9 Jun 23 2004 /bin/csh -> /bin/tcsh
> tcsh --version
> tcsh 6.12.00 (Astron) 2002-07-23 (i386-intel-linux) options
> 8b,nls,dl,al,rh,color,filec
>
> >Do you have /bin/csh installed on your machine?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Mar 09, 2005 at 12:41:13PM -0600, Sabuj Pattanayek wrote:
> >
> >
> >>Hi,
> >>
> >>I get this error when I start vmd 1.8.3 (you have to run
> >>/path/to/vmd/vmd_LINUX since just running the vmd script opens a window
> >>and it closes immediately):
> >>
> >>ERROR) Tcl startup error: Can't find a usable init.tcl in the following
> >>directories:
> >>ERROR) /usr/local/lib/tcl8.4 /usr/local/sbin/lib/tcl8.4
> >>/usr/local/lib/tcl8.4 /usr/local/sbin/library /usr/local/library
> >>/usr/local/tcl8.4.1/library /usr/tcl8.4.1/library /usr/local/lib/tcl8.4
> >>ERROR)
> >>ERROR)
> >>ERROR)
> >>ERROR) This probably means that Tcl wasn't installed properly.
> >>ERROR) Tk startup error: invalid command name "tcl_findLibrary"
> >>ERROR) VMDDIR undefined, startup failure likely.
> >>ERROR) Could not read the vmd initialization file -
> >>ERROR) source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
> >>ERROR) couldn't read file "/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl":
> >>no such file or directory
> >>ERROR) The VMDDIR environment variable is set by the startup
> >>ERROR) script and should point to the top of the VMD hierarchy.
> >>ERROR) VMD will continue with limited functionality.
> >>ERROR) invalid command name "vmd_load_extension_packages"
> >>
> >>I installed it according to the instructions (remove old vmd
> >>installtion; modify configure, run ./configure, and cd src; make
> >>install). Just to make sure there isn't anything wrong with the system I
> >>did a fresh install of vmd 1.8.2 and it works. The vmd 1.8.3 script has:
> >>
> >>set defaultvmddir=/usr/local/sbin/vmd
> >>set vmdbasename=vmd
> >>
> >>slocate init.tcl
> >>
> >>/usr/lib/tcl8.4/init.tcl
> >>/usr/local/sbin/vmd/scripts/vmd/vmdinit.tcl
> >>/usr/local/sbin/vmd/scripts/tcl8.4/init.tcl
> >>/usr/local/sbin/pymol/ext/lib/tcl8.4/init.tcl
> >>/usr/local/sbin/chimera1.2065/lib/tcl8.4/init.tcl
> >>/usr/local/sbin/ac3dlx/lib/tcl8.4/init.tcl
> >>/root/vmd-1.8.2/lib/scripts/tcl8.4/init.tcl
> >>/root/vmd-1.8.2/scripts/vmd/vmdinit.tcl
> >>/root/vmd-1.8.3/lib/scripts/tcl8.4/init.tcl
> >>/root/vmd-1.8.3/scripts/vmd/vmdinit.tcl
> >>
> >>Thanks,
> >>Sabuj Pattanayek
> >>
> >>
> >
> >
> > 

-- 
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              
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