Chapin Cavender

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icon company Open Force Field Initiative icon location Postdoctoral fellow with Open Force Field Initiative and Gilson lab at UC San Diego. Molecular dynamics, computational chemistry, and biopolymer force fields.

Results 4 issues of Chapin Cavender

Carboxylates from mol2 files produced by tleap have incorrect bond orders and formal charges

2 comment

**Describe the bug** Carboxylate functional groups are read incorrectly from mol2 files produced by Amber/tleap. Carboxylate bond orders are specified as 1 such that the total charge of the functional...

interoperability
external dependencies

Support skipping deduplication with dataset factories

It would be helpful to provide an option to skip deduplication in the `create_dataset()` method of dataset factories. Use cases include datasets containing multiple instances of the same molecule with...

Chemically equivalent atoms with delocalized formal charge are assigned different torsions

5 comment

**Describe the bug** Chemically equivalent atoms in which a nonzero charge is delocalized (represented by resonance structures with the formal charge on different atoms) are assigned different torsions by OpenFF...

Residue name conflict with Amber ions and RNA

Many of the ports of the Amber ion parameters use the residue name "U" for the uranium cation U4+, which conflicts with the residue uracil in RNA force fields. This...