Hi Steven, Doesn't -chainsep take an argument?
Cheers, Tsjerk On May 24, 2012 5:33 PM, "Steven Neumann" <s.neuman...@gmail.com> wrote: On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > > Dear Gmx Users,... It is stated: The separation of chains is not entirely trivial since the markup in user-generated PDB files frequently varies and sometimes it is desirable to merge entries across a TER record, for instance if you want a disulfide bridge or *distance restraints* between two protein chains or if you have a HEME group bound to a protein. In such cases multiple chains should be contained in a single molecule_type definition. To handle this, pdb2gmx has an option -chainsep so you can choose whether a new chain should start when we find a TER record, when the chain id changes, combinations of either or both of these or fully interactively. And if I use: pdb2gmx -chainsep In my topology: ; Include chain topologies #include "topol_Protein.itp" #include "topol_Protein2.itp" #include "topol_Protein3.itp" [ molecules ] ; Compound #mols Protein 1 Protein2 1 Protein3 1 So how can I have one [moleculetype] for the usage of distance restraints? Why do they state that this option will allow to have one [moleculetype] ? Please, help Steven -- 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
