VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 18 2004 - 19:48:23 CDT

Josh,
  Which shell does your account use by default, it would appear
that the source command didn't work as I had expected. If you're
using /bin/sh, /bin/bash, or something other than csh or tcsh, then
try doing these steps again, but run /bin/csh first so that you're
in a csh shell when doing the source command etc. Let me know how
it goes. Those warnings you got from the first try were the result
of the source command not working as expected, so if you run it from
a csh shell it ought to work this time.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 16, 2004 at 01:39:06PM -0500, Josh Ward wrote:
> Actually, if I download the file and try to load it from disk it doesn't
> work either. I can load pdb files that I have deleted the header and
> comments from however.
>
> Here's what I got from running your directions:
>
>
> wardjm_at_pablo [1] source ~postlab/bin-linux/postvmd
> [1] 1166
> wardjm_at_pablo [2]
> [1] Done exec xterm -T vmd console -geometry
> 80x11-0-0 -sb -sl 1000 -e ...
> wardjm_at_pablo [2] gdb ~postlab/bin-linux/lib/vmd-1.8.2/vmd_LINUX
> GNU gdb 5.3-debian
> Copyright 2002 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for details.
> This GDB was configured as "i386-linux"...(no debugging symbols found)...
> (gdb) run
> Starting program:
> /.automount/terry/usr/terry4/postlab/bin-linux/lib/vmd-1.8.2/vmd_LINUX
> [New Thread 16384 (LWP 1269)]
> Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
> 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, 4 CPUs detected.
> Info) OpenGL renderer: RADEON 9000 DDR Generic
> Info) Features: STENCIL RN MTX TCM
> Info) Textures: 2-D (2048x2048), 3-D (512x512x512), Multitexture (6)
> ERROR) Tcl startup error: Can't find a usable init.tcl in the following
> directories:
> ERROR) /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6
> /usr/local/lib/tcl8.4
> /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6
> /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl8.4
> /.automount/terry/usr/terry4/postlab/bin-linux/lib/lib/tcl8.4
> /.automount/terry/usr/terry4/postlab/bin-linux/lib/tcl8.4
> /.automount/terry/usr/terry4/postlab/bin-linux/lib/library
> /.automount/terry/usr/terry4/postlab/bin-linux/library
> /.automount/terry/usr/terry4/postlab/bin-linux/tcl8.4.1/library
> /.automount/terry/usr/terry4/postlab/tcl8.4.1/library /usr/local/lib/tcl8.4
> ERROR)
> ERROR) /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl:
> version conflict for package "Tcl": have 8.4, need 7.6
> ERROR) version conflict for package "Tcl": have 8.4, need 7.6
> ERROR) while executing
> ERROR) "package require -exact Tcl 7.6"
> ERROR) (file
> "/bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl" line 18)
> ERROR) invoked from within
> ERROR) "source /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl"
> ERROR) ("uplevel" body line 1)
> ERROR) invoked from within
> ERROR) "uplevel #0 [list source $tclfile]"
> ERROR) /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl:
> version conflict for package "Tcl": have 8.4, need 7.6
> ERROR) version conflict for package "Tcl": have 8.4, need 7.6
> ERROR) while executing
> ERROR) "package require -exact Tcl 7.6"
> ERROR) (file
> "/bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl" line 18)
> ERROR) invoked from within
> ERROR) "source /bio/terry4/postlab/bin-linux/nmrpipe/nmrtxt/tcl7.6/init.tcl"
> ERROR) ("uplevel" body line 1)
> ERROR) invoked from within
> ERROR) "uplevel #0 [list source $tclfile]"
> ERROR)
> ERROR)
> ERROR) This probably means that Tcl wasn't installed properly.
> ERROR) Tk startup error: invalid command name "tcl_findLibrary"
> Found 1 plugins or data handlers in directory
> '/bio/terry4/postlab/bin-linux/lib/vmd-1.8.2/plugins/LINUX/molfile'.
> ERROR) Could not read the vmd initialization file -
> ERROR) source
> {/bio/terry4/postlab/bin-linux/lib/vmd-1.8.2/scripts/vmd/vmdinit.tcl}
> ERROR) can't find package http 2.4
> 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"
> vmd > Warning, could not create initialize Tcl Interp
> Could not load http package
> ERROR) Could not read file 1sps
> Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
> Info) Exiting normally.
>
> Program exited normally.
> (gdb)
>
>
>
> John Stone wrote:
>
> >Josh,
> > I've seen webpdb crash on the very new Athlon64 port of VMD, but
> >not on normal linux builds. I assume that if you download the same
> >pdb and load it from local disk it works fine right? What if you run
> >vmd like this:
> > source /usr/local/bin/vmd
> > (exit that VMD session)
> > gdb /usr/local/lib/vmd/vmd_LINUX
> > (type "run" at the gdb prompt)
> > Then load your webpdb structure that crashes it normally.
> > Then type "where" at the gdb prompt, and email me what it says.
> >
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Apr 16, 2004 at 09:24:41AM -0500, Josh Ward wrote:
> >
> >
> >>Is there a precedence for loading files using webpdb to crash the
> >>program? I am running vmd-1.8.2 on Debian Linux. When I try to load a
> >>molecule via webpdb, some messages appear in the console, but the
> >>program crashes and exits too quickly to read them. I was wondering if
> >>you've run across this problem yet, and hoping there is a quick fix.
> >>
> >>Thanks,
> >>
> >>Josh Ward
> >>
> >>
> >
> >
> > 

-- 
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