VMD-L Mailing List

From: jani sahil (genomejani_at_gmail.com)
Date: Tue Jan 05 2010 - 00:49:00 CST

vmd is executable and just type ./vmd from vmd install folder.
and add to that path.

One more suggestion please learn basics of linux it will help u to solve ur
problem.

On Tue, Jan 5, 2010 at 10:52 AM, Prathit Chatterjee <pc20apr_at_yahoo.co.in>wrote:

>
> John,
> I have almost installed(following the instructions of README file) vmd
> but there remains a small problem.
>
> I have installed the vmd and I am attaching the consequences I faced while
> doing it.
>
> I uncompressed and untarred the vmd 1.8.7 version and there was an
> automatic directory called vmd-1.8.7. Then, according to your instructions,
> I made 2 directories called vmd-exe and vmd-install which I mentioned in my
> comfigure(while editing) file to install my vmd scripts and vmd executables
> respectively.
>
> Then I gave the command "./configure" and the following response was there:
>
> neelanjana_at_linux-3qfw:~/vmd-1.8.7> ./configure
> using configure.options: LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD LIBSBALL
> XINPUT LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
>
> After that, I went to the src directory by giving the command "cd src" and
> then gave "make install" command. The following positive response was :
>
> neelanjana_at_linux-3qfw:~/vmd-1.8.7/src> make install
> Make sure /home/neelanjana/vmd-install/vmd is in your path.
> VMD installation complete. Enjoy!
>
> Then, I went to the vmd-install directory and gave the command "vmd" but
> inspite of installation of vmd, they are telling(I underlined the
> finalconclusion) :
>
> neelanjana_at_linux-3qfw:~/vmd-1.8.7/src> cd ../
> neelanjana_at_linux-3qfw:~/vmd-1.8.7> cd ../
> neelanjana_at_linux-3qfw:~> ls
> 1std.tcl Desktop prathit vmd-exe
> bin Documents test_namd vmd-install
> carAB genes responsible for encoding CPS ig.pdf vmd-1.8.7
> neelanjana_at_linux-3qfw:~> cd vmd-install/
> neelanjana_at_linux-3qfw:~/vmd-install> ls
> vmd
> neelanjana_at_linux-3qfw:~/vmd-install> vmd
> bash: vmd: command not found
>
> I tried the command "source vmd" and it is been told that:
>
> bash: vmd: line 112: syntax error near unexpected token `('
> bash: vmd: line 112: ` foreach i ($path)'
>
> I am attaching the text version of vmd and configure(in openoffice.orgformat) so that you might check the versions what is wrong.
>
> Thanking you,
> Prathit
>
>
> --- On *Sat, 2/1/10, John Stone <johns_at_ks.uiuc.edu>* wrote:
>
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: reply
> To: "Prathit Chatterjee" <pc20apr_at_yahoo.co.in>
> Cc: "Vmd l" <vmd-l_at_ks.uiuc.edu>
> Date: Saturday, 2 January, 2010, 8:23 PM
>
> Hi,
> I have further comments and suggestions for you based on your reply:
>
> On Sat, Jan 02, 2010 at 05:03:04PM +0530, Prathit Chatterjee wrote:
> > 1. First of all, I mention that I have an Intel Core 2 Duo Procesor.
> So,
> > VMD versions of AMD and/or CUDA might not get installed in my laptop.
>
>
> The CUDA versions will work on any machine, whether it contains an NVIDIA
> GPU/chipset or not. The "AMD64" version is for 64-bit versions of linux,
> it's called "AMD64" for historial reasons, not due to any actual
> AMD CPU specificity.
>
> > 2. I tried the command "VMD -deskdov txt" several times before and
> after
> > your mail but the response is "bash: vmd.sh: command not found".
>
>
> Actually, the command I specified was "vmd -dispdev text", the command you
> listed above could not possibly work correctly, so it's not clear to me
> whether the error you got indicates that you typed the wrong command as you
> listed above, or if there's actually an issue with your VMD installation.
>
> > a. First of all I am attaching the instructions given in the README
> file:
>
> I wrote them so I am quite familiar, and don't need to refer to
> them here :-)
>
> > b. Thus following the instructions, I edited the configure file and
> put
> > there the exact paths required. I am mentioning below, what I had
> edited ;
> >
>
> > -> $install_bin_dir="/home/neelanjana/vmd-1.8.7/bin" instead of
>
> > usr/local/bin/vmd
>
> >
>
> > ->$install_bin_dir="/home/neelanjana/vmd-1.8.7/" instead of
>
> > usr/local/library/vmd.
>
> >
>
> > c. I saved the configure option and as mentioned in the readme file,
> I
> > gave the command "./configure"
>
>
> Above you indicated that you set the $install_bin_dir variable twice,
> but this would not result in a correct installation. Did you actually
> mean that in the second line above that you set the $install_library_dir
> variable? Also, in the second line, I see that you set the target to be
> the parent directory of the binary directory. While not necessarily the
> cause of your problem, it is an unusual arrangement. More importantly,
> I wanted to verify that the directory "/home/neelanjana/vmd-1.8.7/" that
> you listed is a _new_ directory and not the directory where you unpacked
> the VMD tar files into when you first downloaded it. If you try to install
> it into the same directory you unpacked into, this will cause problems.
>
> > d. The following reply came which I am attaching below:
>
> >
>
> > VMD plugin directory not found.
>
> > Please compile the VMD plugins and do 'make distrib' to copy them
>
> > into a 'plugins' directory linked or located in this directory.
>
> > Be sure your PLUGINDIR environment variable is set before running
>
> > 'make distrib' in the plugin build area.
>
>
> To me this seems to indicate that you either have a truncated download
> that's missing components, or that you have set the target installation
> directory to the same directory where you initially unpacked the tar file,
> both of which could create problems.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>
>
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