Science Roadmap 2021

Parsley 1.4 / Sage Release

• LJ Refit

• WBO Torsions

• Beta release by early May

• Looking toward a fuller release candidate early June

N / A

The Parsley 1.3.0 benchmark results have not been broadly shared

@Pavan Behara and / or @Jessica Maat (Deactivated) ?

IN PROGRESS

The benchmarks have been performed but not written up as e.g. a blog post.

LJ Refit

@Simon Boothroyd @Owen Madin

Ready

Mixture feasibility study complete and show’s improvement after benchmarking, both on mixture properties + solvation free energies.

WBO Torsions

@Jessica Maat (Deactivated) @Pavan Behara @David Mobley

DEFERRED

Initial exploratory fits have been performed but not clear that we have seen improvement.

Expanded QM data set

@David Mobley @Hyesu Jang @Simon Boothroyd

IN PROGRESS

Report 2 (2021-04-08)

We should include sulfonic and phosphonic acids

and sulfoximine, sulfonimidamines:

https://www.ncbi.nlm.nih.gov/pubmed/23934828

Change the QM theory level

@Hyesu Jang @Lee-Ping Wang @Pavan Behara

IN PROGRESS

Data should have been generated, but not acted on yet.

Are we considering QM theories which are compatible with ANI?

Repeat Lim + Hahn QM Benchmark

@Pavan Behara ?

UNASSIGNED

Should also include the Open set from Pharma partners?

Free Energy Benchmarks

UNASSIGNED

@Simon Boothroyd will sync up with @David Hahn

The will likely be limited to MNSol, FreeSolv (make these relative solubilities?), and TYK2 with Perses.

The cis / trans amide issue

@Simon Boothroyd @Hyesu Jang

In PROGRESS

Previous work: (wip)A fix of cic-trans preference of amides(for v1.3.1)

Currently generating new TD data for a diverse amide like set which exercises the parameters @Hyesu Jang identified in previous work as potentially being problematic:

Initial bio-polymer parameter refit - likely will be similar strategy to small molecule but with bio-polymer data / fragments.

Chapin

proposed

Mostly blocked by infrastructure side of things.

Cap QM bio-polymer fragments?

Chapin

proposed

Refit BCC Parameters

@Simon Boothroyd @Owen Madin

In PROGRESS

Virtual Sites

@Simon Boothroyd @Trevor Gokey

In PROGRESS

@Trevor Gokey is currently working on extending openff-recharge to facilitate fitting these.

Potential collaboration with @Danny Cole?

Refit of Select Impropers

@Jessica Maat (Deactivated)

In PROGRESS

An initial study on exploring the WBO dependency of the aniline improper is being explored.

Re-evaluate whether WBO interpolated parameters are now feasible after other FF improvements.

@Pavan Behara

Fuzzy charges / polarisability?

Reduced LJ Types?

@Michael Gilson @Willa Wang @Tobias Huefner

proposed

The rationale and methodology for selecting the bio-polymer data sets is currently undocumented.

@Michael Shirts

@Michael Shirts will follow up with Dave to get an explanation of the rationale and methodology for why these sets where chosen + how.

These are the selected data sets:
2020-07-06-OpenFF-Protein-Fragments-Initial

2020-07-27-OpenFF-Benchmark-Ligands

2020-08-12-OpenFF-Protein-Fragments-version2

2020-09-16-OpenFF-Protein-Fragments-TorsionDrives

2020-10-27-OpenFF-Protein-Fragments-Unconstrained

2020-10-26-PEPCONF-Optimization

Explore different non-bonded functional forms

@Daniel Cole

Being supported in our infrastructure using plugins: Consider rolling this into the toolkit instead?