martimunicoy / peleffy-benchmarks

A compilation of benchmarks to validate the parameterization of peleffy (PELE Force Field Yielder).

MIT License

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Structural benchmark #11

Open martimunicoy opened 4 years ago

martimunicoy commented 4 years ago

Description

This benchmark evaluates the geometries resulting from a PELE minimization.

Remarks

Dataset

Several sources are available:

Machinery to download graph molecules from newer OpenFF QCArchive datasets (Must have CMILES)
Full molecule dataset, with energies, in mol2 format for recent forcefield fits. Will be inside fb-fit/targets folders. Technical details of fit here

Molecule alignment and RMSD calculation

We need to find a way to align the structure with reference and calculate the RMSD. There are several ways that could be employed for this purpose:

OpenEye: RMSD + alignment code is in benchmarkFF
Example of aligning multiple CONFORMERS of a SINGLE molecule in RDKit
Method to align multiple RDKit molecules