Hi, The list cannot accept attachments, so please find another way to share your inputs, e.g. a file sharing service. The pdb on its own would not be enough for anyone to help, because that doesn't tell us what atoms are concerning you.
By design, pdb2gmx will not try to generate a dihedral if there's no bond-like interaction in an .rtp building block, so I suspect the issue is that there is a bond. Distance is not relevant. Mark On Thu, Jul 12, 2018 at 12:01 PM Momin Ahmad <momin.ah...@kit.edu> wrote: > Hi, > > is there a reason why gromacs demands parameters for dihedral angles > that are not bonded? For example i,j, and k are bonded but l is not. The > distance of k and l is about 2.7 Angstroem. How can i tell gromacs to > ignore these dihedrals during pdb2gmx. I did no define a bond in the > .rtp file. The .pdb i used for pdb2gmx is attached. > Thanks in advance. > > Cheers, > Momin > > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 <+49%20721%2060824286> > E-Mail: momin.ah...@kit.edu > > -- > 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.