Re: [AMBER] distance restraints

From: Jason Swails <>
Date: Wed, 2 Jun 2010 13:56:38 -0400

On Wed, Jun 2, 2010 at 1:24 PM, Bill Ross <> wrote:

> > It depends on what you want to learn. If you're looking to confirm your
> > suspicions about how a ligand docks in your protein, then adding a
> restraint
> > to force the ligand to adopt the position you expect hardly constitutes
> > evidence that the ligand binds that way.
> However it might help you decide if such binding is possible, so
> I don't think it's a wrong move to try. E.g. you could equilibrate
> with the restraints in place, then drop them and see if the ligand
> stays put.

That's true, but my point was that in the end, the restraints have to come
off to make any statements about binding conformation, etc. Everybody's
interpretation of an email differs, I suppose... I would agree with Bill's

All the best,

> Bill
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Jun 02 2010 - 11:00:14 PDT
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