GitLab

Add new 'smirnoff' mode to ForceField improper torsion handling behaviors to allow SMIRNOFF trefoil torsions to be added correctly

The following lipid were added to the addMembrane() method: DLPC,
DLPE, DMPC, DOPC, DPPC.

Original pdb files were taken from
http://www.fos.su.se/~sasha/SLipids/Downloads.html .

Original files were obtained at temperatures between 293K and 303K.
NPT MD simulations were run for all the systems at 298K for ~10 ns
and the last simulation  step was used to create the pdb files.

Within Modeller.addExtraParticles(), add the ability to pass down
an option to modify compiled.matchResidueToTemplate() 's
ignoreExternalBonds parameter.

https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=11264&p=0&start=0&view=&sid=e384beeb08f3bfd767dcfb546006ad63

Fixes writing invalid PDBx/mmCIF files when residue insertion codes are blank (not empty) in Topology

From @peastman:

> Test cases are failing. I believe it's because the parent for a ScaledUnit needs to be a Unit, not another ScaledUnit. So in the line
>
> ```
>  hartree_base_unit = ScaledUnit(4.3597447222071e-18, joule_base_unit, "hartree", "Ha")
> ```
>
> replace joule_base_unit with joule.

This is of immediate need to QCEngine, in particular MolSSI/QCEngine#151