VMD-L Mailing List

From: Sabuj Pattanayek (sabuj.pattanayek_at_Vanderbilt.Edu)
Date: Wed Mar 09 2005 - 13:12:33 CST

John Stone wrote:

>Sabuj,
> Ok, what happens if you do this:
>setenv VMDSIMPLEGRAPHICS 1
>vmd
>
>
ok that seems to work. One more thing I realized is that this problem is
happening only on machines with ATI radeon >=9600 (don't have firegl to
test) hardware running xorg >=6.8 and fglrx >= 8.8.25. One machine
running the same gentoo distribution but with nvidia quadro4 doesn't
have this problem. Was there some drastic change with the opengl
initialization between 1.8.2 and 1.8.3?

> 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
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>
>