Restraint Ambiguities

From: Neema Salimi <>
Date: Thu 21 Nov 2002 15:56:44 PDT

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
Graduate Student - Biophysics
University of California, San Francisco
Received on Thu Nov 21 2002 - 14:56:44 PST
Custom Search