AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Oct 12 2009 - 14:28:12 CDT

If iwrap wraps, it will do so intothe cavity of an image proten so the
issue is not iwrap, but postprocessing the data. If you center your
protein and image the water (ptraj) it should always stay there unless
it actually diffused out.

On Oct 12, 2009, at 2:55 PM, ben rodriguez <bramber_at_live.com> wrote:

>
> Hello,
>
> I am looking at internal water molecules in protein cavities, in
> witch the starting structure contain a water molecule. Periodically,
> throughout the trajectory, after the water molecule has diffused
> from the cavity, the 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,' not by reimaging water molecules into
> the cavity.
>
> This was not my understanding of how iwrap behaves? Can any shed
> some light on this.
>
> Thanks,
>
> Ben
>
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