Using customized force field for small molecules

[wenchangzhou-qtx]

Hey @IAlibay @mikemhenry,

For small molecules, can we now using customized force fields provided by users like myself, other than gaff or espaloma?

Thanks

[mikemhenry]

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.

[aminsagar]

@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.

[mikemhenry]

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 openmm/openmmforcefields#336

[wenchangzhou-qtx]

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

[mikemhenry]

Yes that should work, if it doesn't please let me know!

[wenchangzhou-qtx]

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

[IAlibay]

@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.

[wenchangzhou-qtx]

[like] Wenchang Zhou reacted to your message:

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________________________________ 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-qtx<https://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. — Reply to this email directly, view it on GitHub<#851 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5FJXJJ4WJOMMOCPJQARGMLZCGW55AVCNFSM6AAAAABHQ3QEYCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBZGQYDEMRXG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>