Hi Leila,
> Since I'm beginner in amber, and I used pdb files without change,
> please explain this way by example or tutorial.
I dont think there is a tutorial for this. It would be a good idea to
become more familiar with the Amber programs before attempting complex
simulations like large scale TI on biomolecules. While we on the list are
always willing to help with specific problems, there is no shortcut from
trying out and learning the works for yourselves. Otherwise, how will you
be able to judge and defend your results?
I suggest to play around with leap to see how it builds Amber units from
pdbs with modified and missing atoms. The 'build your own residue'
tutorials may help as well. The details are not complicated per se but
difficult to explain in an email.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Feb 20 2012 - 01:00:02 PST
