Re: Restraint Ambiguities

From: David A. Case <>
Date: Thu 21 Nov 2002 18:08:04 -0800

On Thu, Nov 21, 2002, Neema Salimi wrote:

> 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?

This sounds correct, if I understand you. Have atom 1 be the side
chain atoms of the trp, and atom 2 be the side chains atoms of the val.
Then, the restraint will ensure that some atom of trp is within 5 ang. of
some atom of val, i.e. that there is at least one such contact. If that
sounds like what you want, give it a try.

.good luck..dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Thu Nov 21 2002 - 18:08:04 PST
Custom Search