Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear FFFFGF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce and choosing None for both termini I will get the following error >------------------------------------------------------- >Program pdb2gmx, VERSION 4.6.3 >Source code file: /home/johnny/gromacs-4.6.3/src/kernel/pdb2top.c, line: 110 > >Fatal error: >There is a dangling bond at at least one of the terminal ends. Fix your coorate file, add a new >terminal database entry (.tdb), or select the proper exing terminal entry. >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors >-------------------------------------------------------
Has anybody an idea how i can overcome this problem or some kind of tutorial to generate the topologies files for a cyclic peptide ? Thanks in advance Cheers Jan -- View this message in context: http://gromacs.5086.x6.nabble.com/Cyclic-Peptide-Topology-tp5009832.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
