From: Axel Kohlmeyer (
Date: Wed Dec 10 2014 - 10:27:34 CST

On Wed, Dec 10, 2014 at 10:40 AM, Mehdi Bagherpour
<> wrote:
> Dear All,
> I am going to find water mediated hydrogen bond between protein and DNA.
> Unfortunately when I get the hydrogen bond between water-protein or
> water-DNA, the address of water is not defined in VMD.
> Someone know how could I find the water atoms that are interacted (by
> H-Bond) between protein and DNA.

wouldn't it be sufficient to collect a list of water-protein and
water-dna hydrogen bonds and then compare which water oxygen atoms are
present in both lists?

> D --- W --- P ?
> kind regards,
> Mahdi

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.