AMBER Archive (2009)

Subject: Re: [AMBER] Is iwrap mapping water molecules to my protein cavity?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 12 2009 - 14:12:19 CDT

> I am looking at internal water molecules in protein cavities=2C in witch th=
> e starting structure contain a water molecule. Periodically=2C throughout t=
> he trajectory=2C after the water molecule has diffused from the cavity=2C t=
> he original starting water molecule gets reimaged to its starting position =
> inside the cavity. This happened twice as far as I could tell during a 10ns=
> simulation. I looking for this process to occur 'naturally=2C' not by reim=
> aging water molecules into the cavity. =20
>
> This was not my understanding of how iwrap behaves? Can any shed some light=
> on this.

Are you sure the original water is the one that re-appears in the cavity?

My understanding of iwrap is that when a molecule (possibly residue?)
leaves the box on one side, it reappears on the opposite side. So if
your cavity is some distance from the edge of the box, it could not
be re-imaged into; moreover, even if it was on the boundary and was
filled by reimaging, this would be correct behavior.

If the same water molecule is indeed reappearing, can you rule out the
possibility that it is just moving back and forth?

Bill

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