score_jd2.linuxgccrelease documentation

[Anonymous]

Hi all,

I would like to get documentation about the calculation and the output of the score application, e.g. what each of the parameters exactly mean and how it is calculated, and about if it is better to add hydrogens to run score.

SCORE: score fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref linear_chainbreak overlap_chainbreak time description
SCORE: 543.861 -484.056 361.440 250.604 2.126 17.217 -10.404 -37.398 -1.490 -7.204 -2.149 0.000 0.000 0.000 0.000 25.441 5.337 464.560 -9.804 -30.360 0.000 0.000 0.000 test_in_0001
SCORE: 471.075 -450.241 188.664 309.225 0.999 47.919 -10.519 -22.192 -7.392 -7.877 -5.649 0.000 0.000 0.000 0.000 3.662 17.352 430.963 -3.040 -20.800 0.000 0.000 0.000 1d66_atom_0001

Thanks!!

Fabian

[Anonymous]

As far as the energy function: poke around the other topics and you’ll find it’s reasonably well covered already (or at least, any answers that aren’t linked to here aren’t written down.) Read the Rohl 2004 MIE review paper and Kuhlman’s top7 paper supplemental, plus look at the Meiler lab documentation http://www.meilerlab.org/index.php/jobs/resources (rosetta tab).

As far as hydrogens: Rosetta adds them automatically. For total scores of positive hundreds, there are significant clashes in the structures anyway, so it hardly matters how hydrogens are added. For some structures, you may see some score difference using hydrogens from an external program; assuming their PDB atom names are correct (this is not the common state, sadly) Rosetta will read them in and use them. Use the -no_optH flag for this.

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