Approach I: looser torsion priors

One reason our protein force field candidates may not approach the performance of AMBER force fields may be because we are getting stuck in a nearby local minimum. Loosening torsion priors may help us move away from this minimum. Torsion priors have not yet been updated in this investigation so far. This is related to the different optimization algorithms approach.

Not started In progress Completed Won't progress

Fit Sage from small molecule and protein data with looser torsion priors

Starting from an up-to-date version of the protein-param-fit FF ( ), run a re-fit with the same data but increasing the torsion priors to 10 kcal/mol (up from 5 in previous fits)

@Brent Westbrook (Unlicensed)

Dec 01

In progress

Check how much torsions changed in new and previous re-fits

Check parameter changes

@Brent Westbrook (Unlicensed)

Not started

Small molecule benchmarks

Run small molecule QM benchmarks

@Brent Westbrook (Unlicensed)

Passed Failed

Protein stability benchmarks

Run GB3 benchmarks. Can likely decide whether to progress based on performance over 5 us

 @Brent Westbrook (Unlicensed)

@Lily Wang

Not started

Helix folding benchmark

Run helix folding benchmark

 @Brent Westbrook (Unlicensed) @Lily Wang

Not started

Smaller peptide benchmarks

Smaller peptide NMR scalar coupling benchmarks

 @Brent Westbrook (Unlicensed) @Lily Wang

Not started