Hi, It sounds like your practical options are to build some larger fragments to use when required, or generate your topology with something else, e.g. a custom script. pdb2gmx was built with slightly-branched polymers in mind, not much else.
Mark On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker <swac...@ucalgary.ca> wrote: > Hi, > > I am parameterizing an artifical ligand. I use small residue-like > fragments and connect them with specbonds in a grid, since I need arbitrary > shapes and sizes. Now, I ran into segmentation faults, when the grid > becomes to large. > Is there an upper limit for the specbonds? How can I fix that or do you > see a better way to solve that issue? > > Thanks > Soren > > -- > 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. > -- 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.