I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:;
~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol docking_stubs.xml
<Ddg name="ddg" confidence="0.0"/>
<Docking name="dock_12" fullatom="1" local_refine="1" score_high="score12"/>
it gives me this error:
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '1czH_1czW_0001'
Error: [ ERROR ] ERROR: Could not find scorefxns and name score12 in Datamap
Error: [ ERROR ]
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 1czH_1czW_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 200 jobs considered, 1 jobs attempted in 6 seconds
Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages
Error: [ ERROR ].
For your information, I had done many docking with previous release and googled this error but I could not find exact answer.
The Rosetta 2017.39.59729 weekly uses REF2015 as the default energy function. This involves more than just changing the weights files -- a bunch of internal settings have changed as well, so using the score12 weights set in a REF2015 environment is not going to give you the same results as running a score12 weights set in an older version of Rosetta. For this reason we added a bunch of checks to make it clearer that you're mis-matching the weights file with the environment. (Well, at least for some of the obvious cases.)
Unless you have a particular need of the score12, I'd recommend using the REF2015 scorefunction instead. If you do need score12, then you should be able to add the `-restore_pre_talaris_2013_behavior` flag to the commandline to re-enable score12.
Thank you for your nice advices.
I have two more questions.
I remember in last numbered release, there were three types of binary files such as default and static forms in /main/source/bin. But in last weekly release, there is just on type; static. What is deferences between static and default forms? is it correctly compiled?
I have an error with placestub mover in rosetta (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PlaceStubMover).
This is error which I faced:
ERROR: Error in core::scoring::RamaPrePro::read_canonical_rpp_tables(): Could not read table for ALA.
ERROR:: Exit from: src/core/scoring/RamaPrePro.cc line: 319
How can solve this error? How can find internal settings which were changed in new release to overcome upcoming errors?
The type of executables in the bin directory (static, dynamic, etc.) are entirely dependent on what has been compiled. For the pre-compiled distributions, we provide only the statically linked forms, as there's often too much issues trying to get the dynamically linked versions to run on a different machine from which they're compiled.
On your second question, that sounds like a code/database mismatch. Make sure you're using the Rosetta database that comes with the version of Rosetta you're using. Check you environment variables (`env | grep ROSETTA`) to see if you have anything set to the older version of the database.