[gmx-users] hbond hydroxyl oxygen, both acceptor and donor?

[Jeremy T First]

Ah thank you! This fixed the problem.

Jeremy Todd First
Webb Research Group
University of Texas at Austin
Jeremy_First at utexas.edu

On Mon, Jul 18, 2016 at 3:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/18/16 4:27 PM, Jeremy T First wrote:
>
>> Hello,
>>
>> I am attempting to quantify the amount of hydrogen bonding environment a
>> certain residue experiences during the course of a simulation. To do this,
>> I am using gmx hbond to plot the number of hydrogen bonds between the
>> solvent (water) and the hydroxyl oxygen of the residue as a function of
>> simulation time.
>>
>> According to the help information for gmx hbond, hydroxyl oxygens are
>> classified as hydrogen bond donors. When I select this oxygen and the
>> Water
>> group in gmx hbond, gromacs finds one less donor than acceptor, leading me
>> to believe that the hydroxyl oxygen is classified only as a donor, and not
>> also as an acceptor.
>>
>> Many frames of my simulation show the hydroxyl oxygen (as calculated by
>> VMD) donating and accepting a hydrogen bond, but gmx hbond only reports 1
>> hydrogen bond for the frame.
>>
>> Is there any reason that a hydroxyl oxygen can not simultaneously donate
>> and accept a hydrogen bond? If not, is there a way to let gromacs allow
>> the
>> hydroxyl oxygen to be an acceptor as well?
>>
>> Any help would be greatly appreciated!
>>
>>
> You can't use just the oxygen atom; the analysis group must contain both O
> and H to be considered a donor.  If you're just selecting an O and the
> entire water group, the O in the hydroxyl can only be considered an
> acceptor.
>
> -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.
>