The use of GAFF1 vs GAFF2 with the pmx ff99SB*-ILDN forcefield

pmx
1

Hello everyone,

I have found some conflicting indications in literature on the recommended GAFF version for use with the modified Amber99sb*ILDN force field shipped with PMX.

The 2019 article ‘Large scale relative protein ligand binding affinities using non-equilibrium alchemy’ indicates the use of GAFF2, while the article on the SAMPL7 challenge mentions some issues with GAFF2 dihedral parameters.

Given these indications, what is currently the recommended parametrisation protocol: Amber99sb*ILDN with GAFF1 or with GAFF2?

Kind regards,

Olivier

2

Hey Olivier,

the issues mentioned in the SAMPL7 challenge were specific to the sugar specific dihedrals in Gaff 2. If your ligands do not make use of those particular dihedrals, it should be fine to use Gaff 2.

Vytas

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3

Crystal clear, thanks!