Re: [AMBER] Conserving water bridges?

From: <steinbrt.rci.rutgers.edu>
Date: Fri, 11 Jun 2010 06:18:25 -0400 (EDT)

Hi,

are you sure this is not just an imaging problem? Due to diffusion into
neighboring cells, it looks like waters moving away when you visualize
your raw trajectory in e.g. vmd.

How do ptraj-imaged trajectories look?

Thomas

On Fri, June 11, 2010 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?
>
> Responses are highly appreciated!
> Kind regards,
> Waqas.
>
>
>
>
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>


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Jun 11 2010 - 03:30:03 PDT
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