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

From: <steinbrt.rci.rutgers.edu>
Date: Mon, 14 Jun 2010 07:39:59 -0400 (EDT)

Hi,

lookup the ptraj 'image' and 'center' commands. If you do not already
apply them in your ptraj script, modify it accordingly and redo your
pdb-generation. If the problem persists after that, it is at least not
caused by imaging ;-)

Kind Regards,

Thomas

On Mon, June 14, 2010 6:20 am, Waqas Nasir wrote:
> 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.
>
> Regards,
> Waqas.
>
> --- On Fri, 6/11/10, steinbrt.rci.rutgers.edu <steinbrt.rci.rutgers.edu>
> wrote:
>
> From: steinbrt.rci.rutgers.edu <steinbrt.rci.rutgers.edu>
> Subject: Re: [AMBER] Conserving water bridges?
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, June 11, 2010, 3:18 AM
>
> 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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Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Mon Jun 14 2010 - 05:00:13 PDT
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