Re: [AMBER] Conserving water bridges? need help...

From: Waqas Nasir <>
Date: Mon, 14 Jun 2010 03:20:36 -0700 (PDT)

Hi Thomas,

Thanks for the reply... I extract the pdb files using ptraj and then use my own small script to view all the water molecules within the vicinity of 12A of the coordinate point that I give as input. I have checked the script its working fine. I dont know how to cope with this. In my studies the water bridges are of vital importance and as the run goes on the bridges tend to diminish.

Any help is greatly appreciated.


--- On Fri, 6/11/10, <> wrote:

From: <>
Subject: Re: [AMBER] Conserving water bridges?
To: "AMBER Mailing List" <>
Date: Friday, June 11, 2010, 3:18 AM


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?


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.
> _______________________________________________
> AMBER mailing list

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

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Received on Mon Jun 14 2010 - 03:30:03 PDT
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