[gmx-users] Calculating h-bonds frequency along the simulation

[Vered Kunik]

Thank you Justin fro the prompt response.

If I understood correctly you answer to 3) - you would simply use the
default parameters?

Thanks!

Vered



On Wed, Jan 7, 2015 at 6:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/7/15 11:08 AM, Vered Kunik wrote:
>
>> Dear gromacs users,
>>
>> I am rather new to gromacs and would very much appreciate your help. I
>> have
>> several MD runs of an ATP binding protein (WT versus several mutants). I
>> would like to calculate the frequency of H-bonds between the protein and
>> the ATP molecule as well as the frequency of H-bonds between certain
>> residues within the protein.
>>
>>   My questions are as follows:
>> 1) which flags should I use in g_hbond in order to obtain the above
>>
>>
> What you're looking to do is straightforward application of g_hbond
> without any special flags.  You may want special index groups to define
> specific residues or moieties.  All of this is covered in the manuals.
>
>  2) how do I interpret the residues / atoms that form the  H-bond
>>
>>
> If you use index groups, it should be straightforward.  Otherwise, export
> -hbn to map all the groups.
>
>  3) When calculating H-bonds with gromacs, default values are
>> donor-acceptor
>> angle < 30 degrees and donor-acceptor distance is 0.35 nm (or 3.5
>> angstrom).
>> from what I read in the literature, the angle should be between 90-180
>> degrees, thus < 90 degrees. Furthermore, some indicated that a cutoff of
>> 0.39 nm includes within the hydrogen bonds also weaker h-bonds. What do
>> you
>> think should be the cutoff for both angle and distance for the above
>> mentioned type of H-bonds?
>>
>>
> 90 degrees seems a bit unusual; beware of different conventions for the
> order of the atoms in those definitions.  The widest range I usually see is
> 120-180 degrees.  I also doubt there is much of a practical difference
> between 0.35 and 0.39, but it's certainly easy to do and compare.  You'll
> have an answer in moments.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>