AMBER Archive (1999)

Subject: Refining docking

From: Andrea (andrea_at_neriserv.chim.unisi.it)
Date: Fri Nov 19 1999 - 05:21:13 CST

I beg pardon if this is a trivial question, but I have to end this work
in a very short time and I'm not familiar with amber (v4.1) yet:
I want to improve the complex quality of a protein docked to an
antibody, and I want to run minimisation or md on this complex
mantaining the structure of each molecule fixed (at least the backbone),
but allowing one to move respect the other. How can I get this?

Thanks in advance, Andrea.

Dr. Andrea Bernini, Ph.D.
Dip. Biologia Molecolare
University of Siena, Italy