Re: [AMBER] How to find conserved coordinated waters?

From: Thomas Cheatham III <>
Date: Mon, 29 Mar 2010 15:57:48 -0600 (Mountain Daylight Time)

> 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?

Three possible ways:

(1) closest (or closestwaters) to save waters in active site; note that
numbering will not be maintained so this may only be useful for looking at
the 1 closest water to each residue of interest.

(2) grid density visualized with Chimera or VMD

center :50 mass origin
image origin center familiar
rms first mass :50
grid wat.dat 100 0.5 100 0.5 100 0.5 :WAT.O

(3) hbond command and use of solventdonor/solventacceptor. Search
archives for examples...


AMBER mailing list
Received on Mon Mar 29 2010 - 15:00:03 PDT
Custom Search