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Topologies with combined forcefields? #6

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chabi-fin opened this issue Nov 12, 2024 · 0 comments
Open

Topologies with combined forcefields? #6

chabi-fin opened this issue Nov 12, 2024 · 0 comments

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@chabi-fin
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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:

  1. I parameterize my small molecule with the Espaloma force field and transfer to an openmm topology.
  2. I used openmm's Modeller object + addSolvent() method to solvate my system with Tip3P.
  3. I convert the OpenMM topology to a ParmED Structure
  4. I attempt to save the ParmED structure as Amber PRMTOP, but this fails.
  5. (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?

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