Hello! Right now I am having trouble saving my system topology using parmed. The error message seem to indicate that some bonded parameters are missing, but I cannot identify any missing parameters.
My set up is the following:
- I parameterize my small molecule with the Espaloma force field and transfer to an openmm topology.
- I used openmm's Modeller object + addSolvent() method to solvate my system with Tip3P.
- I convert the OpenMM topology to a ParmED Structure
- I attempt to save the ParmED structure as Amber PRMTOP, but this fails.
- (If I save just the small molecule as a ParmED structure as Amber PRMTOP, this works)
As far as I can tell, there is an issue combining the ligand force field with solvent/counter ion forcefield, since the same problem is raised if I use openff.
Any tips on resolving this?
Hello! Right now I am having trouble saving my system topology using parmed. The error message seem to indicate that some bonded parameters are missing, but I cannot identify any missing parameters.
My set up is the following:
As far as I can tell, there is an issue combining the ligand force field with solvent/counter ion forcefield, since the same problem is raised if I use openff.
Any tips on resolving this?