Hi All,
I encounter a series problem when running this demo, and past my questions as follows:
(A) About the README file problem, At the second step, I think the command is not right, Is the "@finder_option" should be replaced with "@maker_options" ?
2) Make the potential homodimers
There are two ways to do this. If you are only doing it for one structure is is easy just to use this command line
rosetta/rosetta_source/bin/homodimer_maker.linuxgccrelease -s 2a7b_mpm.pdb.gz -database rosetta/rosetta_database @finder_options > maker_tracers
-run::chain A
-sheet_start 806
-sheet_stop 812
-window_size 5
-ignore_unrecognized_res true
-mute core protocols.moves.RigidBodyMover basic.io.database
(B) About running problem!
Then i run it on my local machine and used the command line as follows:
shenzy@shenzy-pc:/media/shenzy/E6B0120DB011E4B9/rosetta_2014.19.56789_bundle/demos/public/beta_strand_homodimer_design$ /home/shenzy/lib/rosetta_2014.19.56789_bundle/main/source/bin/homodimer_maker.linuxgccrelease -s 2a7b_mpm.pdb -database /home/shenzy/lib/rosetta_2014.19.56789_bundle/main/database/ @maker_options
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed 2a7b_mpm.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/DonStrength.csv
Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/AccStrength.csv
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB 2a7b_mpm.pdb
apps.public.beta_strand_homodimer_design.homodimer_maker: Sheet Length: 7 Window size: 5
apps.public.beta_strand_homodimer_design.homodimer_maker: Sheet from: 104 to 108 Window: 1 Center residue: 106
apps.public.beta_strand_homodimer_design.homodimer_maker: C-O vector on center res is 0.4790000000000001 -0.9649999999999999 0.5760000000000005, Direction of translation is: -0.4790000000000001 0.9649999999999999 -0.5760000000000005
apps.public.beta_strand_homodimer_design.homodimer_maker: Number of RB steps to search: 1
apps.public.beta_strand_homodimer_design.homodimer_maker: Translate step: -1 distance: -7
ERROR: homodimer_maker is incompatible with analytic_etable_evaluation. Please either fix the code or add '-analytic_etable_evalution 0' to the command line.
ERROR:: Exit from: src/apps/public/scenarios/beta_strand_homodimer_design/homodimer_maker.cc line: 226
protocols.jd2.JobDistributor:
[ERROR] Exception caught by JobDistributor for job 2a7b_mpm_0001
[ERROR] EXCN_utility_exit has been thrown from: src/apps/public/scenarios/beta_strand_homodimer_design/homodimer_maker.cc line: 226
ERROR: homodimer_maker is incompatible with analytic_etable_evaluation. Please either fix the code or add '-analytic_etable_evalution 0' to the command line.
protocols.jd2.JobDistributor: 2a7b_mpm_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 6 seconds
apps.public.beta_strand_homodimer_design.homodimer_maker: Complete.
I have two questions about the process,
(1)About the warning info, I really can't find the two files in recently rosetta versions.
Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/DonStrength.csv
Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/AccStrength.csv
(2) ERROR: homodimer_maker is incompatible with analytic_etable_evaluation. How two resolve it? I try to add "-analytic_etable_evalution 0' to the command line.
However, it didn't work.
Hope anybody can help me, thanks !!!!
Regarding the DonStrength.csv and AccStrength.csv files, they're not needed. This is a superfluous warning that has since been removed. Don't worry about it.
The other issue you're running into is a scorefunction version mismatch. The beta_strand_homodimer_design was written about two and a half years ago. During that time we were using score12 as a default scorefunction. Since then, we switched to using talaris2013 as the default scorefunction. This change encompassed a large number of modifications, but amoung them is the use of "analytical etables". (It's a technical change in how things like the LJ terms are calculated.)
An easy fix is to simply add the "-restore_pre_talaris_2013_behavior" flag to the commandline. This should return the behavior of Rosetta to the score12 (pre-talaris) defaults, making the application behave more like the way it would back when the demo was written.
Long term, the application should be updated to the new defaults, but that's something for the developers of the application to do.
Thanks :)