2015-08-04 20:37 GMT+02:00 David Menéndez Hurtado <david.menendez.hurtado@scilifelab.se>:

On Tue, Aug 4, 2015 at 11:07 AM, Pawan K. Gupta
<pawanpharma79@yahoo.co.in> wrote:
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback

That looks like there is a problem with your Modeller installation.
Which operative system are you using?

This is actually an harmless message. Check e.g. https://salilab.org/modeller/release.html point 1 of known issues.

massimo