[AMBER] Watershell

From: fernando <fmgarcia.cbm.uam.es>
Date: Mon, 15 Nov 2010 10:18:23 +0100

Dear Amber users:

I have some problems when i measure the solvation shell of some atoms. I
want to define the number of waters of my simulation around an specific
atom using the rmsd of my MD simulation. The command line of my ptraj
script is:

watershell :1671.O2G ${MOL}${j}.watshell lower 2.5 upper 2.9 :WAT.O

The script run well, but when i check the structure, sometimes the
number of water molecules doesn't match with what i see in my structure
in the pdb file.

is there any mistake in the line above?


Fernando Martín García.
Centro de Biología Molecular "Severo Ochoa".
C/ Nicolás Cabrera, 1.
Campus UAM. Cantoblanco, 28049 Madrid. Spain.
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Received on Mon Nov 15 2010 - 01:30:02 PST
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