- This topic has 2 replies, 3 voices, and was last updated 10 years, 6 months ago by Anonymous.
May 25, 2013 at 11:59 pm #1592Anonymous
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
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 (??)
May 27, 2013 at 8:04 am #8828Anonymous
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.
May 27, 2013 at 6:03 pm #8832Anonymous
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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