From: John Stone (
Date: Thu Apr 01 2004 - 17:33:35 CST

  From the errors you got below, it looks like your VMD installations
were done incorrectly. Rather than just running ./vmd_LINUX, please
read the install instructions included with the README file to correctly
install VMD on your system. When correctly installed, you'll end up
with a special startup script called 'vmd' which should be in your
executable path. The startup script will launch the vmd_LINUX executable
and setup various directory environment variables which relate to the
error messages you saw when you ran it by hand.
Let us know if you have trouble following the install instructions
in the README document.

  John Stone

On Thu, Apr 01, 2004 at 02:24:14PM -0600, Cheri M Turman wrote:
> Hello all,
> I am having strange problems. I hope someone out there can shed some
> light on these. My first install of VMD left me with the errors seen
> below and unable to use RMSD. RMSD did not even show up under the
> extensions menu. I was able to use tkcon, though. This was all running
> version 1.8.1. Most things worked but I wanted to try to make RMSD work
> so I tried altering vmdinit.tcl but got no good results. Finally, I
> tried upgrading to version 1.8.2. The first install I couldn't get
> tkcon or rmsd to function. I tried installing to a different place and
> still no luck. I went throught this, always modifying bashrc and
> sourcing it, a couple more times. This last install for some reason
> allows both tkcon and rmsd to work but I still get the error messages as
> below. Nothing has changed! Why or how could this happen? I am in the
> process of getting a new computer and I am worried that this might
> happen again so I would like to prevent it. I would also just like to
> know out of curiosity.
> Cheers,
> Cheri Turman
> thinktank:~/Desktop/vmd$ ./vmd_LINUX
> Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
> Info)
> Info) Email questions and bug reports to
> 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.
> Info) OpenGL renderer: Mesa GLX Indirect
> Info) Features: RN MTX
> Info) Textures: 2-D (2048x2048), 3-D (0x0x0), Multitexture (2)
> 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) 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.
> vmd >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Cheri M. Turman
> Graduate Student
> University of Texas-Houston Medical School
> 6431 Fannin
> Houston, TX 77030 USA
> e-mail:
> Ph.: 713-500-6126
> Fax: 713-500-0652

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