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.