htmd.builder.ionize module

htmd.builder.ionize.ionize(netcharge, nwater, neutralize=True, saltconc=None, cation=None, anion=None, ff=None)
htmd.builder.ionize.ionizePlace(mol, anion_resname, cation_resname, anion_name, cation_name, nanion, ncation, dfrom=5, dbetween=5, segname=None)

Place a given number of negative and positive ions in the solvent.

Replaces water molecules al long as they respect the given distance criteria.

Parameters
  • mol (Molecule object) – The Molecule object

  • anion_resname (str) – Resname of the added anions

  • cation_resname (str) – Resname of the added cations

  • anion_name (str) – Name of the added anions

  • cation_name (str) – Name of the added cations

  • nanion (int) – Number of anions to add

  • ncation (int) – Number of cations to add

  • dfrom (float) – Min distance of ions from molecule

  • dbetween (float) – Min distance between ions

  • segname (str) – Segment name to add

Returns

mol – The molecule with the ions added

Return type

Molecule object