[gmx-users] Regarding calculation of Hydrogen-Bond

Thu Mar 15 04:58:00 CET 2018

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
> >>
> >>
> >>
> >> ‌
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> >>
> >> DILIP.H.N
> >> Ph.D Student
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student