Member Site › Forums › Rosetta 3 › Rosetta 3 – General › optH flag makes hydrogen bond energy scores worse…
- This topic has 6 replies, 2 voices, and was last updated 12 years ago by
Anonymous.
-
AuthorPosts
-
-
July 13, 2012 at 9:04 pm #1345
Anonymous
I was trying to run rosetta.score with no_optH = false. However, when compared with the energies without hbond optimization, the hydrogen bond energies get worse, while the other components are unchanged. I have attached the input pdb file below.
Here are the command lines:
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH true # Turn off hbond optimization
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH false # Turn on hbond optimizationThe output score file is:
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 allatom_rms gdtmm gdtmm1_1 gdtmm2_2 gdtmm3_3 gdtmm4_3 gdtmm7_4 irms maxsub maxsub2.0 rms description
SCORE: -916.848 -1545.330 129.590 764.708 2.831 0.693 -40.420 -43.866 -235.198 -73.020 -51.481 -9.278 0.432 2.847 1.178 -10.334 41.468 264.591 -56.639 -59.620 0.000 1.000 1.000 1.000 1.000 1.000 1.000 0.000 422.000 422.000 0.000 test_0001 # with no_optH = true
SCORE: -911.639 -1545.330 129.438 764.708 2.818 0.693 -40.420 -43.866 -235.198 -69.964 -49.162 -9.278 0.432 2.847 1.178 -10.334 41.468 264.591 -56.639 -59.620 0.000 1.000 1.000 1.000 1.000 1.000 1.000 0.000 422.000 422.000 0.000 test_0001 # with no_optH = false -
July 16, 2012 at 6:39 pm #7410
Anonymous
This duplicates in developer trunk; I am looking into it further.
-
July 27, 2012 at 7:29 pm #7493
Anonymous
Any update on this?
At the least, I would expect that the optimization would return the starting structure and energies, if a better solution cannot be found.
-
July 27, 2012 at 9:45 pm #7494
Anonymous
I filed a bug report but it hasn’t attracted any interest. We have the big yearly meeting coming up next week so i will try shopping it around there to the packing gurus.
-
July 27, 2012 at 10:46 pm #7496
Anonymous
Great! Thanks a lot for following up. I will wait until after RosettaCon for any updates.
-
August 22, 2012 at 12:39 am #7643
Anonymous
Any updates on this?
Thanks.
-
August 22, 2012 at 1:04 am #7644
Anonymous
The official ruling was “well, packing is stochastic and occasionally packing fails to find a better conformation”. Packing isn’t guaranteed to lower energy if it can’t recover off-rotamer atom placements by using only its database rotamers.
I think we should tweak optH to at least check if the energy is increasing and refuse to return the newly worse-packed sidechains, but as it stands it’s considered not a bug but just an insufficiency of Monte Carlo & rotameric sidechains.
-
-
AuthorPosts
- You must be logged in to reply to this topic.