AMBER Archive (2002)

Subject: Restraint Ambiguities

From: Neema Salimi (nsalimi9_at_itsa.ucsf.edu)
Date: Thu Nov 21 2002 - 16:56:44 CST

('binary' encoding is not supported, stored as-is) I was wondering if using ambiguous restraints developed for NOE distances
would be appropriate for use in enforcing hydrophobic side chain
contacts. For example, I define two "atoms" in the MAP file as the heavy
atoms on a certain tryptophan and a certain valine side chain and enforce
an upper limit distance constraint of 5 Angstroms. Would this be
effective in maintaining the contact throughout MD simulation?

Neema Salimi
nsalimi9_at_itsa.ucsf.edu
Graduate Student - Biophysics
University of California, San Francisco