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 <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-requ...@gromacs.org<mailto:gmx-users-requ...@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-requ...@gromacs.org<mailto:gmx-users-requ...@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-requ...@gromacs.org<mailto:gmx-users-requ...@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-requ...@gromacs.org.