[AMBER] How to calculate water density around the certain residue or ligand

From: mish <smncbr.gmail.com>
Date: Tue, 15 Mar 2011 15:47:54 +0100

Hello all:

I have a small problem of computing water density around the certain amino
acids/ ligand of the system. Can any of you tell me some way to do it in
ptraj? or any other program ?
I tried to use grid command in ptraj like in fallowing input file (201 and
202 are the residue number of the ligand),
trajin production.traj
center :1-200
image center familiar
grid wat.xplor 50 0.5 50 0.5 50 0.5 :WAT

What I can see in the output is not clear to me. The Either the grid was
placed in the center of the protein molecule (when i use center origin) or
far away from ligand, somewhere in water. Can any of you clear me out, where
am I doing wrong ?

How can I compute the number of water molecules within 2-3A from a certain
amino acid residue/lignad for each snapshot in the trajectory ?

Thanking you

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Received on Tue Mar 15 2011 - 08:00:09 PDT
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