AMBER Archive (2002)

Subject: Re: Restraint Ambiguities

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 21 2002 - 20:08:04 CST

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 

-- 

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