Hi Steven, There will be three dihedrals spanning a break. Make sure to remove all of them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you can file it as a bug.
Cheers, Tsjerk On May 25, 2012 3:11 PM, "Steven Neumann" <s.neuman...@gmail.com> wrote: Yes, it works (-chainsep interactive: merge = yes ) but when you process to grompp there is an error: Unknown cmap torsion between atoms 6002 6004 6006 6017 6021 pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with first three residues of chain B. Removing these lines does not solve the problem. Any suggestions appreciated! On Fri, May 25, 2012 at 9:57 AM, Steven Neumann <s.neuman...@gmail.com>wrote: > > > > On Thu, May 24, 2012 at 10:04 PM, Francesca < > francesca.stanzi...@unina.it> wrote: >> >> I checked ... > > Yes, it works (-chainsep interactive: merge = no ) but when you process to > grompp there is an error: > > Unknown cmap torsion between atoms 6002 6004 6006 6017 6021 > > pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A > with first three residues of chain B. Does removing this lines will be > reasonable or some torsions wont be taken into account? > > Steven > > >> >> >> -- >> View this message in context: > http://gromacs.5086.n6.nabble.com/One-molculetype-for-3... > > -- 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
-- 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