VMD-L Mailing List

From: Mehdi Bagherpour (mehdi.bpour_at_gmail.com)
Date: Wed Dec 10 2014 - 16:33:25 CST

---------- Forwarded message ----------
From: Mehdi Bagherpour <mehdi.bpour_at_gmail.com>
Date: Wed, Dec 10, 2014 at 6:13 PM
Subject: Re: vmd-l: How find water mediated hydrogen bond
To: Axel Kohlmeyer <akohlmey_at_gmail.com>

Dear Mr. Kohlmeyer,

Thanks for your reply.
The problem is in protein-water and DNA-water hydrogen bonding file that
are computed by VMD, there are not any about address (Name, Chain, resid
number ... ) of water molecules and we could not find which water atoms are
interacted with both of them.

Best,
Mahdi

On Wed, Dec 10, 2014 at 5:27 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Dec 10, 2014 at 10:40 AM, Mehdi Bagherpour
> <mehdi.bpour_at_gmail.com> 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>