Open JSLJ23 opened 4 weeks ago
I transferred this issue to openmmforcefields, since that's where the problem is. It seems the template generator is creating multiple atom types with the same name.
https://github.com/openmm/openmm/pull/4531 might fix this
Good point. @JSLJ23 can you test with the latest development code for OpenMM and see if it works?
Overview
I am trying to run a simple NPT simulation with multiple ligands from a single SDF file parameterised with GAFF but I am running into
ValueError
s for multiple definitions for an atom type.May I know if there is a proper / better supported way for something like this to be done (i.e. running a simulation with multiple small molecules as rdkit/openff-Molecule objects)? Or if the current approach is sensible, are there any tweak I should make to allow for unique atom naming to circumvent this "Found multiple definitions for atom type" error?
Code
Full traceback: