[AMBER] How to find conserved coordinated waters?

From: Sasha Buzko <obuzko.ucla.edu>
Date: Mon, 29 Mar 2010 14:51:30 -0700

Hi all,
does anyone know if there is a way to detect spatially conserved water
molecules in a protein binding site? The usual clustering with ptraj is
tied to specific residues, but what if waters at a certain position keep
swapping, but there is always a water presense there?
Is there a way to check for that? And if that's possible, how could I
cluster possible water orientations at that position?

Thanks in advance for any hints


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Received on Mon Mar 29 2010 - 15:00:03 PDT
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