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Error in flex ddG tutorial

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Error in flex ddG tutorial
#1
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Hi there

I'm trying out the flex ddG tutorial availible at github (https://github.com/Kortemme-Lab/flex_ddG_tutorial). When running the analyzation part for example 1 I get this error:

Traceback (most recent call last):
  File "analyze_flex_ddG.py", line 215, in <module>
    analyze_output_folder( folder_to_analyze )
  File "analyze_flex_ddG.py", line 190, in analyze_output_folder
    scores = pd.concat( inner_scores_list )
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 271, in concat
    op = _Concatenator(
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 329, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

 

Any ideas on how to solve this?

Thanks!

 

Category: 
Compilation
Post Situation: 
Unsolved
Sat, 2020-05-16 08:06
wentlewi
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I have encountered this problem, maybe you should check your Rosetta path.The path should be set to the location of the "rosetta_scripts" binary executable.When I follow the tutorial,I didn't find the 'rosetta_scripts.mpi.linuxgccrelease' in my path,so I use the similar executable 'validate_rosetta_script.mpi.linuxgccrelease',then I run the analysis script, there was raised the error like this, and I fond the output folder just product one file 'rosetta.out' ,so the analysis script raised "No objects to concatenate".When I change my path to '/rosetta_scripts.mpi.linuxgccrelease',the error was gone and the output file will have 7 files like this '1JTG_AB_0001_last.pdb 1JTG_AB_0001.pdb rosetta.out struct.db3 1JTG_AB_0001_low.pdb ddG.db3 score.sc ',you should check whether your problem like this. and you also should note your pandas version should lower than 2.0,because the high version no longer support the pd.oncatenate().
Wed, 2023-10-04 02:38
Alvin Yang
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I have encountered this problem, maybe you should check your Rosetta path.The path should be set to the location of the "rosetta_scripts" binary executable.When I follow the tutorial,I didn't find the 'rosetta_scripts.mpi.linuxgccrelease' in my path,so I use the similar executable 'validate_rosetta_script.mpi.linuxgccrelease',then I run the analysis script, there was raised the error like this, and I fond the output folder just product one file 'rosetta.out' ,so the analysis script raised "No objects to concatenate".When I change my path to '/rosetta_scripts.mpi.linuxgccrelease',the error was gone and the output file will have 7 files like this '1JTG_AB_0001_last.pdb 1JTG_AB_0001.pdb rosetta.out struct.db3 1JTG_AB_0001_low.pdb ddG.db3 score.sc ',you should check whether your problem like this. and you also should note your pandas version should lower than 2.0,because the high version no longer support the pd.oncatenate().
Wed, 2023-10-04 03:34
Alvin Yang