[gmx-users] Regarding calculation of Hydrogen-Bond

[Jeremy T First]

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..??
>
>
>
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> 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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