targeted molecular dynamics

Date: Thu Oct 14 2010 - 17:22:30 CDT

I try to write a script in order to do targeted molecular dynamics, but I do not
understand some things:
the TMDFile must be the initial pdb or the pdb that refers to the target
structure(final structure)?
Also, this segment will be part of a minimization script, how can I run it?
Thank you in advance.

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