From: Prathit Chatterjee (
Date: Sat Jan 02 2010 - 05:33:04 CST

     Thanks for your reply. I am mailing you the problems faced by me while installing VMD.

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.

2. I tried the command "VMD -deskdov txt" several times before and after your mail but the response is "bash: command not found".

3. I tried to install the vmd by reading the README file provided along with the software while downloading. The problems which I face are written below:

a. First of all I am attaching the instructions given in the README file:

   For quick installation of the binary distribution for Unix do the following:
  1) Uncompress and untar the distribution into a working directory.
     In this working directory, there are several subdirectories such
     as bin, src, doc, data, as well as this README and a configure script.
     Change to this working directory after the unpacking is complete.

  2) Edit the file 'configure'; change the values for
     the $install_library_dir and $install_bin_dir to a directory in
     which vmd data files and executables should be installed, be sure
     that you installing into a clean target directory and not overwriting
     an existing version of VMD (which would otherwise give problems):

     $install_bin_dir is the location of the startup script 'vmd'.
     It should be located in the path of users interested in running VMD.

     $install_library_dir is the location of all other VMD files.
     This included the binary and helper scripts.  It should not be
     in the path.

  3) A Makefile must be generated based on these configuration variables
     by running "./configure".

  4) After configuration is complete, cd to the src directory,
     and type "make install".  This will install VMD in the two
     directories listed above.  Note that running "make install"
     twice will print error messages because you are attempting to
     overwrite some read-only files.  Similarly, if you have incorrectly
     specified the target installation directories or attempt to overwrite
     an existing VMD installation, you will get error messages.

  5) When installed, type 'vmd' to start (make sure the
     $install_bin_dir directory is in your path).

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"

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.

Halting configuration until VMD plugins are built.

e. still I typed the commands "vmd" and "vmd -deskdov.txt". The same problem is arising saying that Command not found.

f. I typed the cd ../src following the instructions attached above and typed "make install" command. The consequences are:

 if [ ! -d "/usr/local/lib/vmd" ]; then \
        mkdir -p "/usr/local/lib/vmd" ; \
    fi ; \
    if [ ! -d "/usr/local/bin" ]; then \
        mkdir -p "/usr/local/bin" ; \
    fi ; \
    if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
        mkdir -p "/usr/local/lib/vmd"/doc; \
mkdir: cannot create directory `/usr/local/lib/vmd': Permission denied
mkdir: cannot create directory `/usr/local/lib/vmd': Permission denied
make: *** [install] Error 1

Thus, I am in a complete dilemma. If you help me patiently, I shall be highly obliged.
Thanking you,
Yours faithfully

Prathit Chatterjee
Junior Resrach Fellow(CSIR)
under Dr. Neelanjana Sengupta
Molecular Dynamics Simulations of Biomolecules
Electronic Structure Theory Group
Centre for Materials Characterization
National Chemical Laboratory