Thank you Yanging Fu. I have vmd 1.9. TOPO tools is already built in vmd 1.9 version. I had trouble loading the tcl script file on tk_console. I have written a input tcl script file for the system which I am working on.
The mistake was, I assumed the working directory for vmd is the same directory in which the molecule (xyz file ) is and I was trying to execute the script from the command line of tk_console. Offcourse its not. I forgot to read the line of the manual and was more focussed on whether I made a mistake in tcl commands and after frustration I e-mailed lammps users. I should have read these lines carefully or should have read used tcl scripting before.
“This is very easy to do. Just use any text editor to write your script file, and in a VMD session, use the command source *filename* to execute the file.”
Thanks
Arun