Matt Thompson

See the error at the end of [this](https://github.com/jthorton/de-forcefields/issues/8#issuecomment-1915267210) code block

Amber needs bond force constants, even for rigid water models

2

**Description** Consider starting from GROMACS files of something containing a fixed three-site water model. These files include sufficient information to construct a chemical graph that includes information about which atoms...

Support 4-site water models in Amber export

4

**Description** This should be simpler than implementing all virtual site types i.e. for ligands, I think.

Rigid water models (which, as far as I can tell, comprise every one commonly used in biophysics) constrains the bonds and angles in water. Main-line OpenFF force fields either constrain...

Unclear relationships between intermolecular exclusions, 1-4 pairs, proper torsions, and improper torsions in Amber files

4

A section in the only [prmtop](https://ambermd.org/prmtop.pdf) documentation I can find reads: > If the third atom is negative, then the 1-4 non-bonded interactions for this torsion is not calculated. This...

Incorrect nonbonded energies from Amber if improper torsions are present

4

Something is wrong with the interplay between setting the third atom negative (its 1-4 interaction was already accounted for) and the fourth atom negative (this torsion is an improper). It...

* Show how to set residue names using the toolkit * Ensure residue names are [not overridden](https://github.com/openforcefield/openff-interchange/blame/v0.2.3/openff/interchange/interop/internal/amber.py) when only one residue name is detected in the topology * Use both...

Using the unconstrained version of Sage, a single ethanol molecule, and no OpenEye: ``` Bond Angle Torsion Nonbonded vdW Electrostatics OpenMM 4.186619 43.830074 10.998074 -10.133417 NaN NaN Amber 3.966014 43.673429...

**Description** "out.lmp" is hardcoded, though users may reasonably wish to use different names for their files