[gmx-users] Regarding calculation of Hydrogen-Bond

Erik Marklund erik.marklund at kemi.uu.se
Tue Mar 13 11:42:34 CET 2018

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
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:

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,

PhD Student

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