Rosetta forcefield terms and interpretation

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  • This topic has 2 replies, 3 voices, and was last updated 11 years ago by Anonymous.
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    • #1592
      Anonymous

        hi, I just spent a bit of time trying to update my rusty knowledge of the reported forcefield terms. I thought I would post the list and see if people can improve on it. I tend to view this as very important info for non-guru users

        cheers,

        -Louis

        fa_atr = full atom attraction
        fa_rep = full atom repulsion
        fa_sol = full atom solvation via Lazaridis-Karplus solvation model
        fa_pair = full atom statistics based pair term, favors salt bridges
        hbond_sr_bb = hydrogen short range backbone-backbone
        hbond_lr_bb = hydrogen short range backbone-backbone
        hbond_bb_sc = hydrogen bond backbone to sidechain
        hbond_sc = hydrogen bond sidechain-sidechain
        dslf_ss_dst = disulfide sulfur-sulfur distance?
        dslf_cs_ang = disulfide carbon-sulfur angle?
        dslf_ss_dih = disulfide sulfur-sulfur dihedral?
        dslf_ca_dih = disulfide alpha carbon related? dihedral
        rama = ramachandran statistical potential to disfavor rare regions
        probability of phi/psi given amino acid
        fa_dun = full atom Dunbrack rotamer statistics potential
        p_aa_pp = probability of amino acid given phi and psi
        ref = res type dependent reference energy for desolvation on folding
        pro_close = pro_close is a term that ensures proline’s ring stays closed
        omega = statistical potential related to omega angle?
        fa_intra_rep = full atom intra (ligand? rotamer?) repulsion (??)

      • #8828
        Anonymous

          Hi All!
          I felt quite confused with all these terms at the very beginning, but it got better. I also had a plan to write in more detail about all scoring terms and adding it to wiki, but due to some reasons I put it on hold. I think it’s really important for new comers.

        • #8832
          Anonymous

            Hi Louis,

            Your summary is correct.

            To clarify the question marks, the dslf_* terms are the disulfide terms, related to the items you indicate, with the dslf_ss_dih term being for the cb-s-s’-cb’ dihedral, and the dslf_ca_dih term being for the ca-cb-s-s’ dihedrals (for both sides). According to the notes I see, the actual parameters are based on gaussians fitted to a database of disulfides found in the PDB.

            omega is a term based off of the omega backbone angle, specifically a spline-fitted statistical potential.

            fa_intra_rep is the Lennard-Jones repulsion term for interactions of atoms within the same residue. fa_atr/fa_rep are only computed between different residues, and the internal attractive/repulsive for a residue is accounted for by the rotamer potential (i.e. fa_dun). However, some things like ligands don’t have the rotamer potential (all rotamers scoring equally), so to keep them from minimizing to the point where atoms overlap, there’s the fa_intra_rep term, which is typically turned on to a very low level (0.004). When on, it applies to all residues, not just ligand residues – but the fa_dun term typically keeps them from giving high fa_intra_rep scores.

            If you have any questions about the scorefunction, or want further details, please ask.

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