VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Dec 10 2014 - 17:57:40 CST

Hi Mahdi,

There are two options: if you use the GUI version of the h-bonds plugin,
ask for the more detailed files. This has the problem that they are not
resolved in time, and that is probably what you care about. If you don't
use the GUI, (and this is the better alternative), you can the hbond
interaction lists back as an output. Take a look at the documentation
for the "measure hbonds" command
(http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html), read it
thoroughly, and then you can use the simultaneous list comparisons like
Axel described.

Basically, this is your pseudocode:
-Make your selections (one each for protein, DNA, and water)
-Iterate through your trajectory
--update the frame each selection is using (eg. $sel frame $i)
--get the list of hbond interactions at each frame (using measure hbonds
repeatedly to catch all the different permutations)
--check the lists that are returned to see if a water molecule appears
to interact both with protein and DNA simultaneously.
--write out your results to a file

If you need help filling in the details, make a solid attempt first so
we have code to work with, and then the list can make suggestions if
appropriate.

-Josh Vermaas

On 12/10/2014 04:33 PM, Mehdi Bagherpour wrote:
>
> ---------- Forwarded message ----------
> From: *Mehdi Bagherpour* <mehdi.bpour_at_gmail.com
> <mailto: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 <mailto: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
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Wed, Dec 10, 2014 at 10:40 AM, Mehdi Bagherpour
> <mehdi.bpour_at_gmail.com <mailto: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 <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia
> PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>