I was using relax.linuxgccrelease to relax my protein (442 residues) with 100 outputs:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/relax.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -s /home/lanselibai/Cheng/relax/input/C226S_raw.pdb -out:show_accessed_options -nstruct 100 -relax:quick &> /home/lanselibai/Cheng/relax/output/record.log &
Then I score it using score_jd2.linuxgccrelease:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:l /home/lanselibai/Cheng/score_C226S_relax/input/list_of_pdbs.txt -out:file:scorefile /home/lanselibai/Cheng/score_C226S_relax/output/relax_score_100.sc
Within the 100 outputs, the lowest is -741.147. But the lowest one 737.91 in the largest cluster is selected as my final structure.
Then it was mutated by using ddg_monomer.linuxgccrelease (option file attached), in which "talaris2013" is used. However, by looking at the "ddg.log" file, all of the trajectories (50 before mutation & 50 after mutation) are of scores lower than -1000.
So my question is:
1) When using score_jd2.linuxgccrelease, is "talaris2013" used?
2) If "talaris2013" is used, why the relax.linuxgccrelease cannot achieve structures lower than -1000 REU as ddg_monomer.linuxgccrelease does? Does 100 output for relax too few?
Thank you very much.
Can I also ask what is the default score used for score_jd2.linuxgccrelease? On the website of https://www.rosettacommons.org/docs/latest/score-commands.html, the default score is not explicitly shown.
In addition, why score12 is still used for relax? As shown in https://www.rosettacommons.org/docs/latest/relax.html, "score12" is used instead of "talaris2013". That page was updated on 2015-01-08, so why we still use the old score function?
The default scorefunction across most of Rosetta (unless hardcoded to be otherwise) is talaris2013. This is the default. So relax is using talaris2013, but that option has not been updated. Will update now.
Thank you. I see so it should be talaris2013.