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_fi...@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_fi...@utexas.edu
> (443) 243-1187
> 
> On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <erik.markl...@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.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 13:20, Dilip H N <cy16f01.di...@nitk.edu.in<mailto:
>> cy16f01.di...@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.markl...@kemi.uu.se<
>> mailto:erik.markl...@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.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:
>> erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.di...@nitk.edu.in<mailto:
>> cy16f01.di...@nitk.edu.in><mailto:
>> cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@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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