Re: [AMBER] distance restraints

From: Jason Swails <>
Date: Wed, 2 Jun 2010 09:20:13 -0400


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.

I would run unrestrained MD (heat carefully and equilibrate first), so that
you don't introduce bias into your simulation by additional restraints.

However, to answer your question, you can use nmropt=1 and define distance
restraints to do this. However, I feel like I have to reiterate that
forcing the MD to adopt your "expected structure" does not constitute
evidence that your expectations are valid.

Good luck!

On Wed, Jun 2, 2010 at 9:14 AM, qiaoyan <> wrote:

> Dear amber users:
> I want to simulate a protein and a ligand, there should be four hydrogen
> bonds between them, but in my docked structure, the internuclear distances
> were too large for hydrogen bonds, is there a way to get my expected
> structuer? for example, if I can use distance restraints in the md
> simulation to come to this end?
> 2010-06-02
> qiaoyan
> _______________________________________________
> 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 - 06:30:09 PDT
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