AMBER Archive (2009)
Subject: [AMBER] Query regarding watershell command
From: Mannan (malie_03_at_yahoo.co.in)
Date: Mon Aug 31 2009 - 05:38:08 CDT
Hi AMBER people,
I have used WATERSHELL in ptraj for set of trj files.
In the first frame I got number of water molecules as 400 for a distance cutoff of 3.5 A for any atoms.
But when I see in VMD I could see only 5 water molecules within 3.5 for a set of residues.
How come this big difference. Do i miss anything.
Is that possible to writeout pdb with water molecules within 3.5 for a set of residues from traj.
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