VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 23 2006 - 13:09:02 CDT

If you're getting permission denied errors when running the
VMD startup script, you'll need to check and make sure that you
have access to the directories where you installed it. Can you
cd into /vmd-1.8.4/bin and do an 'ls -l', for example?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 23, 2006 at 10:18:43AM +0800, a a wrote:
> 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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-- 
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