Hi, I'm trying to create a topology for DNA with periodically connected ends. There's a previous message on this, with advice by Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html
I have a single-stranded DNA structure in a pdb file with a phosphate on one end (P, OP1, OP2) and an oxygen on the other (O3'). These are exactly the atoms I want to connect later on. I use pdb2gmx to get the hydrogens + topology and give it -ter "none", which gives me the error message "Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry." I added the flag -missing (according to Justin's advice), but does not help. I guess I'm not understanding what bond is dangling here, and what to add to the tdb file that would help? Of course, I could get most of the topology I need by avoiding selecting -ter 'none' but then I have to fiddle with adding back atoms. Best, Viveca -- 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.