On Thu, May 24, 2012 at 6:05 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Steven, > > Doesn't -chainsep take an argument? > > Cheers, > > Tsjerk > It does, I used option: -chainsep ter And I had in my pdb file after each chain TER and thus 3 itp files were created corresponding to my top file and representing different moleculetype (protein, protein2, protein3). In order to use distance restraints I want to have one moleculetype with 3 chains which are not connected via bonds and adjust proper charges to each of 6 terminals. Any suggestions? Steven > 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 >
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