[AMBER] grid action command in ptraj

From: mish <smncbr.gmail.com>
Date: Wed, 9 Mar 2011 13:41:06 +0100

Hi all:

I am interested in looking "water density" around the ligand in in my
system. I used fallowing inputs (167 and 168 are the residue name of the
trajin producrion.traj
center :500-501
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 centre of the protein molecule (when i use centre origin) or
far away from ligand, somewhere in water. Can any of you clear me out, where
am I doing wrong ?

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Received on Wed Mar 09 2011 - 05:00:05 PST
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