MantisBT - Rosetta
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0000042Rosetta[All Projects] Incorrect Resultspublic2012-07-16 14:322012-09-04 19:33
smlewis 
 
normalminoralways
confirmedopen 
All 
 
all
score_jd2.linuxgccrelease -database rosetta_database -s test.pdb -no_optH [true/false]
0000042: optH code can increase score
http://www.rosettacommons.org/content/opth-flag-makes-hydrogen-bond-energy-scores-worse [^]

The attached PDB provides a case where the score with -no_optH true < -no_optH false. This is true mostly due to the hydrogen bonding terms getting worse when optH is active (-no_optH false).
Run PDB through scoring with/without optH. Tested in 3.4 and SVN 49568.
Here are the scores, clipped to the relevant terms:

    score fa_rep fa_intra_rep hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc
no_optH_false -911.639 129.438 2.818 -43.866 -235.198 -69.964 -49.162
no_optH_true -916.848 129.59 2.831 -43.866 -235.198 -73.02 -51.481
hydrogen, scoring
? test.pdb (428,268) 2012-07-16 14:32
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=3&type=bug
? optH_false_log (16,918) 2012-07-16 14:39
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=4&type=bug
Issue History
2012-07-16 14:32smlewisNew Issue
2012-07-16 14:32smlewisFile Added: test.pdb
2012-07-16 14:35smlewisCommand Line Used~/LOCAL/super_pure_dont_change/bin/score_jd2.linuxgccrelease -database ~/LOCAL/super_pure_dont_change/rosetta_database/ -s test.pdb -no_optH [true/false] => score_jd2.linuxgccrelease -database rosetta_database -s test.pdb -no_optH [true/false]
2012-07-16 14:35smlewisNote Added: 0000028
2012-07-16 14:35smlewisAssigned To => smlewis
2012-07-16 14:35smlewisStatusnew => confirmed
2012-07-16 14:39smlewisFile Added: optH_false_log
2012-08-21 20:05smlewisAssigned Tosmlewis =>
2012-08-21 20:06smlewisNote Added: 0000079
2012-09-04 19:33LabonteTag Attached: hydrogen
2012-09-04 19:33LabonteTag Attached: scoring

Notes
(0000028)
smlewis   
2012-07-16 14:35   
confirmed for trunk; user reports 3.4 vulnerable as well; unclear if it's a property of this input structure or a general problem
(0000079)
smlewis   
2012-08-21 20:06   
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. I'm leaving the bug open in case someone wants to tweak that implementation detail...