RE: AMBER: trajin and rms

From: a a <>
Date: Mon, 22 May 2006 16:55:03 +0800

Dear Sir/Madam,

I downloaded the following gz file for my PC with red hat linux installed
from the website suggested:

LINUX OpenGL (Linux (Redhat 9 or later) with Mesa or hardware OpenGL)

then, I uncompress the file to a folder vmd-1.8.4

then, I change configure file as follows:

# Directory where VMD startup script is installed, should be in users'

# Directory where VMD files and executables are installed

When I type "./configure linux" Then, I go to src directory to type "make
install" It seems OK. But when I type vmd

[vmd-1.8.4]$ vmd
bash: vmd: command not found

however, when I include the path as follows: (Is it the right file? Is it
the right procedure to include the path?)

[vmd-1.8.4]$ /vmd-1.8.4/lib/vmd/vmd_LINUX

The followings error message comes up:

Info) VMD for LINUX, version 1.8.4 (April 17, 2006)
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, 1 CPU detected.
Info) OpenGL renderer: Quadro FX 1300/PCI/SSE2
ERROR) Unable to locate VMD vertex and fragment shader path, VMDDIR
variable not set
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
ERROR) Tcl startup error: Can't find a usable init.tcl in the following
ERROR) /usr/local/lib/tcl8.4 /vmd-1.8.4/lib/lib/tcl8.4
/vmd-1.8.4/lib/tcl8.4 /vmd-1.8.4/lib/library /vmd-1.8.4/library
/vmd-1.8.4/tcl8.4.1/library /tcl8.4.1/library /usr/local/lib/tcl8.4
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
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.
bad window path name "main"
bad window path name "display"
bad window path name "graphics"
bad window path name "color"
bad window path name "files"
bad window path name "labels"
bad window path name "render"
bad window path name "main"
ERROR) invalid command name "vmd_load_extension_packages"
vmd >

Could you please kindly let me know how to solve this problem?

Best regards,

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Received on Wed May 24 2006 - 06:07:10 PDT
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