[gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds

leila karami karami.leila1 at gmail.com
Thu Feb 24 15:43:14 CET 2011

Dear Justin

very thanks for your reply.

I used for script two times:

1) between proten and interfacial waters.

2) between dna and same water molecules.

using what I said above, can I obtain what water molecules form
water-mediated hydrogen bond between protein and dna?

if my way is wrong, please guide me about that.

any suggestion 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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