AMBER Archive (2001)

Subject: Re: energies for part of the protein

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 12 2001 - 19:07:32 CDT

        Is it at all possible to get AMBER to output coordinates and
        energies for just a segment of the protein molecule?

Carnal does this, see the group option for OUTPUT COORD. Something like

 ...
OUTPUT
  COORD x1 GROUP g1;
 ...

        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?

Use Anal, defining the group(s) you want.

        Can I ask sander to just write the energies for that piece out to
        a file?

Only by changing the code :-)

Bill Ross