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Goodman-lab / DP5

Python workflow for DP5 and DP4 analysis of organic molecules
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subprocess.CalledProcessError: Command '/utilities/sdconvert -isd /home/xu/Desktop/AT1_1.sdf -omae /home/xu/Desktop/AT1_1.mae' returned non-zero exit status 127. #62

Closed vvvvike closed 1 year ago

vvvvike commented 2 years ago

settings.cfg is missing! ['/home/xu/Desktop/AT1_'] /home/xu/Desktop/NMR_folder/ NMRpath Current working directory: /home/xu/Desktop/DP Initial input files: ['/home/xu/Desktop/AT1'] NMR file: [PosixPath('/home/xu/Desktop/NMR_folder/Proton'), PosixPath('/home/xu/Desktop/NMR_folder/Carbon')] Workflow: gmns

Generating diastereomers... Getting inchi from file /home/xu/Desktop/AT1.sdf Getting inchi from file /home/xu/Desktop/AT1.sdf Number of diastereomers to be generated: 2 Isomer 0 inchi = InChI=1S/C10H19NO/c1-5-9-8(4)10(12)11(9)6-7(2)3/h7-9H,5-6H2,1-4H3/t8-,9-/m0/s1/f/ Isomer 1 inchi = InChI=1S/C10H19NO/c1-5-9-8(4)10(12)11(9)6-7(2)3/h7-9H,5-6H2,1-4H3/t8-,9+/m0/s1/f/ Generated input files: ['/home/xu/Desktop/AT1_1', '/home/xu/Desktop/AT1_2']

Assuming all computations are done? ... False Using preexisting DFT data? ... False MacroModel

Setting up MacroModel files... Could not find Schrodinger folder, please fill in PyDP4.py Settings with the path. /bin/sh: 1: /utilities/sdconvert: not found Traceback (most recent call last): File "PyDP4.py", line 841, in main(settings) File "PyDP4.py", line 278, in main MacroModelInputs = MacroModel.SetupMacroModel(settings) File "/home/xu/Desktop/DP/MacroModel.py", line 60, in SetupMacroModel '.mae', shell=True) File "/home/xu/miniconda3/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/home/xu/miniconda3/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '/utilities/sdconvert -isd /home/xu/Desktop/AT1_1.sdf -omae /home/xu/Desktop/AT1_1.mae' returned non-zero exit status 127. —————————————————————————————— hello， I run data downloading from https://www.repository.cam.ac.uk，but encounter some issues as shown above , thank you!

Jonathan-Goodman commented 1 year ago

You are setting up files for MacroModel and this requires the sdconvert program which is in the $SCHRODINGER/utilities folder. The program MacroModel.py tries to set the $SCHRODINGER directory automatically. In your example, it seems to be set to "/" which is implausible. You could edit line 27 of MacroModel.py to change the default setting from '/usr/local/shared/schrodinger/current' to whatever it is on your system