[gmx-users] Regarding calculation of Hydrogen-Bond
Joe Jordan
e.jjordan12 at gmail.com
Thu Mar 15 07:16:05 CET 2018
The problem you are running into is that the tool you are using is not
designed to be used in this way. As a suggestion for alternatives, you
could use gmx pairdist to find all N and OW atomtypes within some distance
of each other and then run that through gmx angle. You could also consider
e.g. using MDAnalysis where it is pretty easy to redefine the h-bond donors
and acceptors.
On Thu, Mar 15, 2018 at 4:57 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:
> 1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
> also using the command
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg
>
> but still, i am getting the same error as:-
> Specify 2 groups to analyze:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has 511 elements
> Select a group: 0
> Selected 0: 'N'
> Select a group: 1
> Selected 1: 'OW'
> Checking for overlap in atoms between N and OW
> Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
> Found 0 donors and 512 acceptors
> No Donors found
> -------------------------------------------------------
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> 2) I tried to find out the distance between Calpha(Ca) and Ow from the
> command
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg
>
> but still, i am getting the same error as above one.
>
> Any suggestions...
>
> Thank you.
>
>
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>
> On Tue, Mar 13, 2018 at 7:34 PM, Erik Marklund <erik.marklund at kemi.uu.se>
> wrote:
>
> > A shortcut would be to only look at the C-O distance, which can be done
> > with gmx hbond without modification.
> >
> > Kind regards,
> > Erik
> >
> > > On 13 Mar 2018, at 15:01, Jeremy T First <jeremy_first at utexas.edu>
> > wrote:
> > >
> > > Hi Dilip,
> > >
> > > There is quite a bit of literature, especially recently, that considers
> > the
> > > alpha carbon as a hydrogen bond donor. How well this is represented in
> > your
> > > simulation will depend on your force field.
> > >
> > > You will likely need to develop your own gromacs tool to calculate
> this,
> > > but it should be quite easy. We recently wrote a tool that does
> something
> > > very similar, but you would need to edit it for your own purposes. If
> you
> > > are interested in using our code as a template, feel free to contact me
> > off
> > > list.
> > >
> > > Good luck!
> > > Jeremy
> > >
> > >
> > >
> > >
> > > Jeremy Todd First
> > > Webb Research Group
> > > University of Texas at Austin
> > > Jeremy_First at utexas.edu
> > > (443) 243-1187
> > >
> > > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <
> erik.marklund at kemi.uu.se
> > >
> > > wrote:
> > >
> > >> The point is that Calpha don’t form hydrogen bonds.
> > >>
> > >> Erik
> > >> ______________________________________________
> > >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > >> Department of Chemistry – BMC, Uppsala University
> > >> +46 (0)18 471 4539
> > >> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
> > >>
> > >> On 13 Mar 2018, at 13:20, Dilip H N <cy16f01.dilip at nitk.edu.in<
> mailto:
> > >> cy16f01.dilip at nitk.edu.in>> wrote:
> > >>
> > >> Then how can i calculate the hydrogen bonding between C-alpha and
> Oxygen
> > >> atom of water molecules..??
> > >> What are the other possible ways..??
> > >>
> > >>
> > >>
> > >> <https://mailtrack.io/> Sent with Mailtrack
> > >> <https://mailtrack.io?utm_source=gmail&utm_medium=
> > signature&utm_campaign=
> > >> signaturevirality&<https://mailtrack.io/?utm_source=
> > >> gmail&utm_medium=signature&utm_campaign=signaturevirality&>>
> > >>
> > >> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <
> > erik.marklund at kemi.uu.se<
> > >> mailto:erik.marklund at kemi.uu.se>>
> > >> wrote:
> > >>
> > >> Dear Dilip,
> > >>
> > >> The Calpha is not considered a hbond donor.
> > >>
> > >> Kind regards,
> > >> Erik
> > >> ______________________________________________
> > >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > >> Department of Chemistry – BMC, Uppsala University
> > >> +46 (0)18 471 4539
> > >> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se><mailto:
> > >> erik.marklund at kemi.uu.se>
> > >>
> > >> On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.dilip at nitk.edu.in<
> mailto:
> > >> cy16f01.dilip at nitk.edu.in><mailto:
> > >> cy16f01.dilip at nitk.edu.in<mailto:cy16f01.dilip at nitk.edu.in>>> wrote:
> > >>
> > >> Hello,
> > >> I want to calculate Hydrogen bonding between C-alpha of glycine and
> the
> > >> oxygen atom of water molecules.
> > >> So, i gave the command as:-
> > >>
> > >> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
> > >>
> > >> but i got the error as:
> > >> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> > >> Found 0 donors and 511 acceptors
> > >> No Donors found
> > >> -------------------------------------------------------
> > >> Program: gmx hbond, version 2016.2
> > >> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> > >> Fatal error:
> > >> Nothing to be done
> > >>
> > >> So, how can i solve this issue..?? Is there no any Hydrogen bonding
> > between
> > >> this..?? (I think there is some hydrogen bonding present ...)
> > >>
> > >> Any suggestions are appreciated.
> > >>
> > >> Thank you.
> > >>
> > >> --
> > >> With Best Regards,
> > >>
> > >> DILIP.H.N
> > >> PhD Student
> > >>
> > >>
> > >>
> > >>
> > >> <https://mailtrack.io/> Sent with Mailtrack
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> > >> --
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> > >>
> > >> DILIP.H.N
> > >> Ph.D Student
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> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
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--
Joe Jordan
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