Re: [AMBER] Conserving water bridges?

From: Jason Swails <>
Date: Fri, 11 Jun 2010 13:00:21 -0400


On Fri, Jun 11, 2010 at 5:56 AM, Waqas Nasir <>wrote:

> Dear amber users,
> I am working with a protein ligand system with more than 10000 atoms. I use
> a truncated octahedron with the cutoff radius of 10 Angstrom around my
> protein ligand complex. I have noticed from a number of my simulations that
> with the passage of time the water molecules "bridging" the interactions
> between protein and ligand tend to move out of the binding site leaving
> behind only a few of the water molecules (less than 20 in a 12 sphere in
> the binding site) and the number keeps on decreasing. Is there something
> wrong with the system or it is the normal behavior? Is there a way to keep
> the bridging water molecules?

Not without adding restraints.

Do you have the iwrap=1 variable set? What may be happening is that some of
the water molecules that you are visualizing ARE actually in the binding
pocket, just in another periodic box if iwrap is not set to 1. With a
binding pocket that is accessible to water, I would expect the water
molecules to exchange. As long as the pocket is not losing volume, I would
expect the number of water molecules to remain fairly constant.

To re-image the waters, see the image command in ptraj (familiar I believe
is needed if you're trying to re-image to a truncated tetrahedron).

Good luck!

> Responses are highly appreciated!
> Kind regards,
> Waqas.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jun 11 2010 - 10:30:03 PDT
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