2022-03-24 Protein FF meeting note

Project management

• Formal decision-making process

  • Decisions must be made in this meeting

  • Changes to project plan require unanimous consent of project driver and all approvers. Absences are vetos.

• Add Michael Shirts as an approver

Review of fitting strategy

Chapin Cavender

• Charges

  • ELF-10

  • Library charges for water (TIP3P) and 26 canonical amino acids (AM1BCC-ELF10)

• Lennard-Jones

  • Copy from Sage

• Valence and torsions

  • Fit Sage types (null model) or new protein-specific torsions

  • Target Sage QC training dataset and new QC datasets

    • Optimization dataset for capped 1-mers

    • TorsionDrives on (phi, psi) and (chi1, chi2) for capped 1-mers

  • Fit torsions/valence simultaneously or sequentially

Protein FF benchmark

Chapin Cavender

• Validation dataset

  • Used to choose between models (null vs protein-specific torsions)

  • Beauchamp/Pande dataset

    • 32 small peptides (2 to 5 residues)

    • Chemical shifts and scalar couplings

    • 500 ns trajectories

• Sage benchmarks

  • QC test dataset

  • Physical property test dataset - solvation and transfer free energies

• Test dataset

  • Used to demonstrate model performance

  • Continuous trajectories in triplicate

  • Prioritize diversity of protein systems or diversity of force fields tested?

  • Force fields and water models

    • Need

      • OpenFF/TIP3P

      • Amber ff14SB/TIP3P

    • Want

      • Amber ff19SB/OPC

      • CHARMM36m/TIP3P

      • a99SB-disp/TIP4P-D

      • OpenFF/OPC

  • Need: Robustelli/Shaw a99SB-disp dataset

    • 4 folded proteins (largest 120 residues)

      • Scalar couplings

      • 10 μs trajectories

    • 10 disordered proteins (largest 140 residues)

      • Chemical shifts and scalar couplings

      • 30 μs trajectories

  • Want: Mao/Montelione dataset

    • 41 folded proteins

    • Chemical shifts and NOEs

    • 10 μs trajectories

  • Aggregate sampling

    • Need: 700 μs

    • Need + protein want: 1.5 ms

    • Need + FF want: 2 ms

    • Need + protein want + FF want: 4.5 ms