Export to other format about openff-bespokefit

[xiki-tempula]

Ok one need to add the line of parmed_structure.residues[0].name = "Lig"

[jthorton]

Hi @xiki-tempula glad you managed to make a bespoke force field! To export the parameters for a different simulation engine it is recommended that you make an OpenMM system using the OpenFF-Toolkit and then use OpenFF-Interchange or parmed as you have above. Here are some notebook examples using interchange or parmed, I hope this helps let m know if you have any issues.

[xiki-tempula]

@jthorton Thanks. I think this is essentially what I'm doing in this code. I wonder if you mind help me on this?
I have attached the file that I'm using here. Thank you.
Archive.zip

[jthorton]

@xiki-tempula not quite you need to use the OpenFF-Toolkit to read offxml force field files rather than OpenMM directly, see the code attached which should work on your example. Let me know if there is anything else I can help with!

from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.topology import Molecule
import parmed

# load the molecule and the force field using the toolkit
molecule = Molecule.from_file("Archive/lig.sdf")
ff = ForceField("Archive/lig.offxml")

# create an openmm system
openmm_system = ff.create_openmm_system(molecule.to_topology())

# Convert OpenMM System to a ParmEd structure.
parmed_structure = parmed.openmm.load_topology(
    molecule.to_topology().to_openmm(), openmm_system, molecule.conformers[0]
)
parmed_structure.save("system.top", overwrite=True)
parmed_structure.save("system.gro", overwrite=True)

[xiki-tempula]

Thanks.

[xiki-tempula]

Thanks. I wonder if it is possible to add the molecule name?
If you check the gromacs output, it is

[ moleculetype ]
; Name            nrexcl
          3

Which lacks the name of moleculetype.
This should normally be something like

[ moleculetype ]
; Name            nrexcl
lig          3