[AMBER] ptraj / water-medited hydrogen bonds

From: leila karami <karami.leila1.gmail.com>
Date: Thu, 3 Mar 2011 15:56:41 +0330

Dear amber users

my simulation system contains protein, dna and water molecule.

I created a mdcrd file containing protein, dna and 8 interfacial water

I want to know can I obtain information about water-medited hydrogen bonds
using ptraj?

can I know which of interfacial water molecules form water-medited hydrogen
bonds with occupancy?

any help will highly appreciated.

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Thu Mar 03 2011 - 04:30:06 PST
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