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
Mish
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 15 2011 - 08:00:09 PDT
