Open wenchangzhou-qtx opened 4 months ago
We support custom force fields if they comply with the smirnoff spec so anything that openff makes or you create with bespoke fit should work.
@mikemhenry I have also been trying to use espaloma as the small molecule force field. #682 It seems it should be possible to use espaloma #229 Can you please give a minimal example of using espaloma?
Thanks.
Ah! Okay yes this is supported, I don't have time right now to test this, but it should be as easy as specifying espaloma-0.3.2
as the forcefeield you want to use, is that what you mean?
OH! I see in #682 it looks like openmmforcefeild needs an update to support espaloma-0.3.2
since it only supports espaloma-0.2.2
currently. Tracking that issue here https://github.com/openmm/openmmforcefields/issues/336
Thanks! @mikemhenry, on this topic, is it possible to change it inside yaml file like this?
protocol:
settings:
forcefield_settings:
small_molecule_forcefield: 'espaloma-0.2.2'
protocol_repeats: 2
Yes that should work, if it doesn't please let me know!
Hey @mikemhenry, thanks for checking, I just tried but in the output json file I still have the default, openff-2.1.1
for small_molecule_forcefield
and 3 for protocol_repeats
, my settings.yaml
file looks like this:
mapper:
method: lomap
# method: kartograf
network:
method: generate_radial_network
settings:
central_ligand: 'lig_ejm_31'
# method: generate_radial_network
# method: generate_maximal_network
# method: generate_minimal_redundant_network
protocol:
settings:
forcefield_settings:
small_molecule_forcefield: 'espaloma-0.2.2'
protocol_repeats: 2
The command I run is openfe plan-rbfe-network -M tyk2_ligands.sdf -p tyk2_protein.pdb -o network_setup -s settings.yaml
@wenchangzhou-qtx, CLI YAML inputs for Protocols is not currently available in the 1.0 release of openfe. It should make it soon but for now if you want non-default settings you'll have to use the Python API.
[like] Wenchang Zhou reacted to your message:
From: Irfan Alibay @.> Sent: Tuesday, May 14, 2024 6:42:38 AM To: OpenFreeEnergy/openfe @.> Cc: Wenchang Zhou @.>; Mention @.> Subject: Re: [OpenFreeEnergy/openfe] Using customized force field for small molecules (Issue #851)
@wenchangzhou-qtxhttps://github.com/wenchangzhou-qtx, CLI YAML inputs for Protocols is not currently available in the 1.0 release of openfe. It should make it soon but for now if you want non-default settings you'll have to use the Python API.
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Hey @IAlibay @mikemhenry,
For small molecules, can we now using customized force fields provided by users like myself, other than gaff or espaloma?
Thanks