2022-06-30 Protein FF meeting note

Strategy for protein FF torsion fits

Chapin Cavender

• ELF10 library charges and Sage LJ parameters

• QC data

  • Sage optimization datasets and TorsionDrives

  • Optimization dataset for capped 1-mers (Ace-X-Nme)

  • 2-D TorsionDrives on (phi, psi) for capped 1-mers

  • TorsionDrives on (chi1) or (chi1, chi2) for capped 1-mers

• Outstanding questions

  • Fit torsion and valence parameters sequentially or simultaneously?

  • Fit torsion parameters to TorsionDrives only or TorsionDrives and optimizations?

  • Weight all sidechains equally (total weight 20) or all protomers equally (total weight 26)?

    • Alanine has one protomer. It’s weight is 1.

    • Glutamate has two protomers. Should each protomer be weighted 1/2 or 1?

    • Histidine has three protomers. Should each protomer be weighted 1/3 or 1?

SMIRKS for protein-specific torsions

Chapin Cavender

• Backbone torsions

  • General protein backbone: [#6X4]-[#6X3](=O)-[#7X3]-[#6X4]-[#6X3](=O)-[#7X3]-[#6X4]

  • Glycine: [#6X4]-[#6X3](=O)-[#7X3]-[#6X4H2]-[#6X3](=O)-[#7X3]-[#6X4]

  • Proline: [#6X4]-[#6X3](=O)-[#7R1X3]-[#6X4R1]-[#6X3](=O)-[#7X3]-[#6X4]

  • Beta-branched (Ile, Thr, Val): [#6X4]-[#6X3](=O)-[#7X3]-[#6X4H1](-[#6X4H1])-[#6X3](=O)-[#7X3]-[#6X4]

• Sidechains torsions

  • General protein chi1: [#7X3]-[#6X4](-[#6X3]=O)-[#6X4]-[!#1X4]

  • General protein chi2: [#7X3]-[#6X4](-[#6X3]=O)-[#6X4]-[#6]~[!#1X4]

  • Beta-branched chi1: [#7X3]-[#6X4](-[#6X3]=O)-[#6X4H1]-[!#1X4]

  • Beta-branched chi2: [#7X3]-[#6X4](-[#6X3]=O)-[#6X4H1]-[#6]~[!#1X4]