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Participants

Goals

  • SMIRKS for protein-specific torsions

Discussion topics

Item

Presenter

Notes

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]

Action items

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Decisions

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