PBRadii

[Valdes-Tresanco-MS]

Sorry for the previous PR, for some reason Pycharm was always creating the new branch from v3.4.

Fix #1223

This is a contribution of @marioernestovaldes

Add mbondi_pb2, mbondi_pb3 and charmm_radii.

The implementation has a large number of comments and the definitions are explicit and redundant, which helps us to do a better follow-up. After doing more tests we will optimize the code

[swails]

Thanks!

It is probably also worth adding a few tests here to support any future efforts to refactor. That can be added later, though.

[Valdes-Tresanco-MS]

Sure. We'll be working on that a bit later. Now we are preparing some examples for a possible problem that we have found in the conversion of topologies from Gromacs to Amber when cysteines are forming S-S. This is critical since the VDWAALS energies obtained using the tleap and parmed topologies differ considerably (~7000 kcal for the system in which we noticed the problem). The good news is that the delta (Complex - Receptor - Ligand) is the same for both cases.

I'll write this homework down to do later :)

[swails]

Sounds like it's not creating the S-S bond

[Valdes-Tresanco-MS]

Sounds like it's not creating the S-S bond

In order to be able to discuss in more detail, identify the problem and solve it, we are verifying in some systems that the problem is indeed in the CYX. As soon as we have it, we will open an issue with the details and examples. And as always, if possible a PR.