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gfzhou / OpenVS

Codes and scripts for "An artificial intelligence accelerated virtual screening platform for drug discovery"
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rosettavs failed to install #2

Open skysky-dot opened 3 days ago

skysky-dot commented 3 days ago

Hello,I am trying to install RosettaVS to apply its capabilities in virtual screening. However, I have encountered difficulties during the installation process and was hoping you could provide some guidance or point me to relevant resources that might help me resolve the issue. The step is 1.git@github.com:RosettaCommons/rosetta.git 2.$ cd source 3.$ ./scons.py -j mode=release bin

  1. add path but it doesn't work,it said that the xml is wrong ,i install rosetta from the https://rosettacommons.org/ ,and it also said the xml is wrong I deleted the runmode="eval" turnon_flexscs_at_relax="1" contact_distance="0.0" entropy_method="Simple" from <GALigandDock name="dock" scorefxn="genpot_soft" scorefxn_relax="genpot" runmode="eval" turnon_flexscs_at_relax="1" contact_distance="0.0" entropy_method="Simple" > ,it works. The error i use your xml as followed:

ERROR: Error in CitationManager::get_citation_by_doi(): The DOI "10.1073/pnas.2012800118" was requested, but this is not associated with any paper in the Rosetta database. Has it been added to database/citations/rosetta_citations.txt? (Note that this error can arise if the Rosetta database is out of sync with the binaries compiled from the source code. If you recently pulled or checked out a different version of Rosetta, you might resolve this error by recompiling, if you forgot to do so.) ERROR:: Exit from: src/basic/citation_manager/CitationManager.cc line: 182 Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'eval.complex_1a30_ligand_4_0001' Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:

File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1208 Input rosetta scripts XML file "/data/software/OpenVS/benchmarks/casf_2016/eval_screening_cpp/eval.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema to output the schema to a file to see all valid options. Your XML has failed validation. The error message below will tell you where in your XML file the error occurred. Here's how to fix it:

1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file. 2) If you haven't run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first. The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem. 3) If you are a developer and neither 1 nor 2 worked - email the developer's mailing list or try Slack. 4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum

I would greatly appreciate any advice or assistance you can offer. Thank you for your time and for your contribution to the field.

gfzhou commented 3 days ago

Hello,

Thanks for raising this issue. First, please use the Rosetta distribution from GitHub: git@github.com:RosettaCommons/rosetta.git.

It didn’t give me any error when I ran python run_eval.py in benchmarks/casf_2016/eval_screening_cpp on my end. Could you provide your command to reproduce this error?

Thanks, Guangfeng