Dear Gromacs community I am trying to run a simulation of choline molecule but found various errors concerning to bonds, angles and dihedrals during the minimization.
Part of the top file (line number in the first column): ... 29 [ bonds ] 30; ai aj funct 31 1 4 1 ; N CT3 32 1 14 1 ; N CT4 33 1 2 1 ; N CT1 34 1 3 1 ; N CT2 35 2 12 1 ; CT1 HC12 36 2 13 1 ; CT1 HC11 37 2 11 1 ; CT1 HC13 38 3 7 1 ; CT2 HC21 39 3 6 1 ; CT2 HC22 40 3 5 1 ; CT2 HC23 41 4 8 1 ; CT3 HC31 42 4 10 1 ; CT3 HC32 43 4 9 1 ; CT3 HC33 44 14 17 1 ; CT4 HC41 45 14 15 1 ; CT4 CT5 46 14 16 1 ; CT4 HC42 47 15 20 1 ; CT5 HC51 48 15 18 1 ; CT5 OH 49 15 19 1 ; CT5 HC52 50 21 18 1 ; HO OH ... Errors: ERROR 1 [file topol_choline.top, line 49]: No Default Bond type ERROR 2 [file topol_choline.top, line50]: No Default Bond type and so on with some of the angles and dihedrals... Does anybody have a clue on how to fix it? Thanks in advance. Ednilsom -- 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.