AMBER Archive (2006)

Subject: Re: AMBER: trajin and rms

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon May 22 2006 - 06:58:04 CDT

you are trying to install the program called VMD, it is not a part
of Amber. You might check the VMD web site or post to the
VMD mailing list.

a a wrote:

> 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'
> 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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