On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <s.neuman...@gmail.com>wrote:
> Dear Gmx Users, > > I want to use distance restraints of 3 atoms which belong to 3 different > proteins. For this purpose I want to create one topology so one > moleculetype: > > I tried to use pdb2gmx -chainsep ter (where i put TER after each chain in > my PDB) > > But 3 separate topologies were created. > > I want to adjust proper charges for each teraminals but pdb2gmx without > -chainsep will treat it as a one molecule. > > Please help. > > Steven > > > 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
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