[AMBER] Conserving water bridges?

From: Waqas Nasir <nasirwaqas1983.yahoo.com>
Date: Fri, 11 Jun 2010 02:56:46 -0700 (PDT)

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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Received on Fri Jun 11 2010 - 03:00:05 PDT
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