[gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

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>
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>
>
> On 13 Mar 2018, at 11:03, Dilip H N <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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-- 
With Best Regards,

DILIP.H.N
Ph.D Student