Ahoy, What I have here is a 100% precisely set up periodic ssdna chain of six residues without termini. The goal is to get the 'polymerization' across the box. So, I boxed the chain and set up the periodicity pretty much perfectly.
To test, translation in the direction of periodicity by the periodicity constant results in bonds perfectly recognized by things like VMD or pymol (in the concatenated structure). When running pdb2gmx on the boxed structure, the periodicity seems to be ignored and then expectedly I get a fatal error with a custom FF that works fine on finite chains. x2top sees pbc, but we're not using it here. So, no topology in sight. Any ideas? Thanks, Alex p.s. I can post the test structure if there's any doubt about periodicity of the structure itself. -- 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.
