AMBER: Request for addition of a useful command in ptraj module of AMBER #2

From: Cenk Andac <>
Date: Tue, 17 Apr 2007 10:24:37 -0700 (PDT)

Hi again,

This is in addition to my previous E-Mail.
I was also wondering if the ptraj command "contacts" would meet my requirements .

my best regards,


Dear AMBER developers,

I would appreciate it very much if someone in the future add a useful command in ptraj that would enable me to extract only certain snapshots of a trajectory in which one or more water molecules (user should also have an option with numbers, like one to infinity would be nice !) within a H-bonding distance to a defined atom(s) in a binding site or on a bound ligand and recompile those selected snapshots into a new trajectory. This idea would get me a good paper I believe.

best regards,



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Received on Wed Apr 18 2007 - 06:07:37 PDT
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