MoleculeType

As by design we don’t implement pdb2gmx functionality, the user is responsible to create the ITP files containing [ moleculetype ] blocks for all molecules she wants to use. This typically involves running pdb2gmx and editing the resulting topol.top file to contain only the [ moleculetype ] section. Position restraints should also be inserted in this file. We supply the tool top2itp to aid this conversion.

MoleculeType instances have the following important attributes:

  • name: molecule type name
  • kind: molecule kind: Solute, Solvent, Ion
  • itpfile: the corresponding topology include file
  • count: the number of molecules of this type in the system
  • posresdefine: preprocessor macro for grompp which activates position restraints (e.g. POSRES)
  • atoms: atom information read from the ITP file