[gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

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
>> 
>> 
>> 
>> ‌
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=
>> signaturevirality&>
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request@
>> gromacs.org><mailto:gmx-users-request@
>> gromacs.org<http://gromacs.org/>>.
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request@
>> gromacs.org>.
>> 
>> 
>> 
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> Ph.D Student
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request@
>> gromacs.org>.
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.