From: Corey Fugate (
Date: Fri Nov 27 2009 - 20:59:51 CST

        Going through the NAMD tutorial (again, since I haven't touched the
program in months) I am having troubles running VMD (1.8.7) in text
mode as described in page 11.

1) If I use the command listed in the Apple box on page 11 I see this -

Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
ERROR: Unable to open pdb file ubpq.pdb to read residues

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed while building segment

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
vmd >

2) I had this problem on my old Macbook 10.4 using VMD 1.8.6, it was
suggested that I include the following lines in my bash_profile -

export VMDDIR=/Applications/VMD_1.8.7app/Contents/vmd !!!!! I have
1.8.7 here because I am using 1.8.7, not 1.8.6
alias vmd="$VMDDIR/vmd_MACOSXX86" $*
alias psfgen='/Users/fugate/NAMD/psfgen'

The problem with this is that VMD has some error -
corey-fugates-macbook-pro:~ fugate$ /Applications/
Contents/MacOS/startup.command ; exit;
Info) VMD for MACOSXX86, version 1.8.7 (August 1, 2009)
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: NVIDIA GeForce 9400M OpenGL Engine
ERROR) Failed to open OpenGL shader source files: /Applications/
VMD_1.8.7app/Contents/vmd/shaders/vmd.vert, /Applications/VMD_1.8.7app/
Warning) GPU driver failed to compile shader:
Warning) /Applications/VMD_1.8.7app/Contents/vmd/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (2048x2048x2048), Multitexture
ERROR) Could not read the vmd initialization file -
ERROR) source {/Applications/VMD_1.8.7app/Contents/vmd/scripts/vmd/
ERROR) couldn't read file "/Applications/VMD_1.8.7app/Contents/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) Color definitions file '/Applications/VMD_1.8.7app/Contents/vmd/
scripts/vmd/colordefs.dat' does not exist.
ERROR) Parsing color definitions failed.
ERROR) Material definitions file '/Applications/VMD_1.8.7app/Contents/
vmd/scripts/vmd/materials.dat' does not exist.
ERROR) Parsing material definitions failed.
ERROR) Residue types file '/Applications/VMD_1.8.7app/Contents/vmd/
scripts/vmd/restypes.dat' does not exist.
ERROR) Parsing residue types failed.
ERROR) Atomselection macro file '/Applications/VMD_1.8.7app/Contents/
vmd/scripts/vmd/atomselmacros.dat' does not exist.
ERROR) Parsing atomselection macros failed.
ERROR) invalid command name "vmd_load_extension_packages"
vmd >

So how am I supposed to run VMD in text mode?

                        Thanks for the help,

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