AMBER Archive (2001)

Subject: energies for part of the protein

From: Elizabeth K. White (ekwhite_at_goober.cs.colorado.edu)
Date: Wed Sep 12 2001 - 17:21:10 CDT

Is it at all possible to get AMBER to output coordinates and energies for
just a segment of the protein molecule? The NTWPRT flag seems to do some
of this, but how to make it consider atoms 300-500, as opposed to atoms
1-500? More to the point, what if I want to consider, say, the dihedral
angle energies over a certain piece of the folding protein, and ignore the
rest? Can I ask sander to just write the energies for that piece out to
a file? Does anyone have any helpful insights about doing this?

Thanks, Elizabeth