RosettaCommons
Not found /software/rosetta/DAlphaBall.gcc
In line 32 of the scripts/get_interface_metrics.py , as follows： init('-corrections::beta_nov16 -holes:dalphaball /software/rosetta/DAlphaBall.gcc -detect_disulf false')
What file is/software/rosetta/DAlphaBall.gcc here? I did not find it in the Rosetta source code.
DAlphaBall is distributed with the regular Rosetta package in source/external/DAlpahBall/. You have to compile it separately, using the Makefile provided in that directory. That should place the DAlphaBall.gcc application into that directory. You can then move/symlink/adjust paths as necessary.
Alternatively, there's a separate distribution of just DAlphaBall, if you don't need the full Rosetta package: https://github.com/outpace-bio/DAlphaBall -- Or you can download it from the original source: https://simtk.org/projects/alphamol
Thank you for your answer. I found the rosetta/main/source/external/DalpahBall/ directory and compiled it to generate DAlphaBall.gcc.
When I run ./get_interface_metrics.py output/run2/trf_relax/, The error is as follows： `ERROR: Failed to run the psipred command, which was "/opt/RFDesign/scripts/psipred/runpsipred_single DCQRKVQEAK_8MMGOTHT.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256 ERROR:: Exit from: /home/benchmark/rosetta/source/src/core/io/external/PsiPredInterface.cc line: 341 protocols.rosetta_scripts.ParsedProtocol: Set filter value for contact_molecular_surface to: 301.156 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:
File: /home/benchmark/rosetta/source/src/core/io/external/PsiPredInterface.cc:341 [ ERROR ] UtilityExitException ERROR: Failed to run the psipred command, which was "/opt/RFDesign/scripts/psipred/runpsipred_single DCQRKVQEAK_8MMGOTHT.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256`
/opt/RFDesign/scripts/psipred is the installation path for psipred4, and the path on line 106 of the interface_metrics.xml file has been modified.