VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 10 2014 - 18:06:44 CST

On Dec 10, 2014 5:59 PM, "Mehdi Bagherpour" <mehdi.bpour_at_gmail.com> wrote:
>
>
> ---------- 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.

You have to provide more details. It is not clear to me, what kind of file
you are talking about. In any case, since you want to do a custom analysis,
you will likely have to write your own analysis script utilizing the
measure command of the vmd script interface.

Axel

>
> 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.
>
>
>