From: Prathit Chatterjee (
Date: Mon Jan 04 2010 - 23:22:16 CST

     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

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
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 format) so that you might check the versions what is wrong.

Thanking you,

--- On Sat, 2/1/10, John Stone <> wrote:

From: John Stone <>
Subject: Re: vmd-l: reply
To: "Prathit Chatterjee" <>
Cc: "Vmd l" <>
Date: Saturday, 2 January, 2010, 8:23 PM

  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: 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.

  John Stone

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:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078