VMD-L Mailing List

From: a a (patd_2_at_hotmail.com)
Date: Mon May 22 2006 - 21:18:43 CDT

Dear Prof. Stone,

I tried to call up the vmd by typing

/vmd-1.8.4/bin/vmd

But the outcome is "bash: /vmd-1.8.4/bin/vmd: Permission denied", I tried
to double click the vmd icon in bin folder, but it open up with word files,
instead of callup a program to run.

I find in the last line of the README file comes with the software, said "
5) When installed, type 'vmd' to start (make sure the $install_bin_dir
directory is in your path)." Could you mind to teach me what is the command
line should be using to make sure the /vmd-1.8.4/bin in the path?

Best regards,

>From: John Stone <johns_at_ks.uiuc.edu>
>To: a a <patd_2_at_hotmail.com>
>CC: vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: redhat linux vmd
>Date: Mon, 22 May 2006 16:19:39 -0500
>
>
>Hi,
> Your path should include /vmd-1.8.4/bin, not the lib directory....
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Mon, May 22, 2006 at 04:51:59PM +0800, a a wrote:
> > Dear Sir/Madam,
> >
> > I downloaded the following gz file for my PC with red hat linux
>installed:
> >
> > 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'
> > paths.
> > $install_bin_dir="/vmd-1.8.4/bin";
> >
> > # Directory where VMD files and executables are installed
> > $install_library_dir="/vmd-1.8.4/lib/$install_name";
> >
> > 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) 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, 1 CPU detected.
> > Info) OpenGL renderer: Quadro FX 1300/PCI/SSE2
> > Info) Features: STENCIL MSAA(16) RN MDE CVA MTX PP PS GLSL(OVF)
> > ERROR) Unable to locate VMD vertex and fragment shader path, VMDDIR
> > environment
> > 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
> > directories:
> > 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)
> > 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.
> > 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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>
>--
>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

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