dcambie
commented
1 year ago Bash error 127 is command not found, judging on your error message (Command '/utilities/sdconvert) you have not set the location of Schrodinger in settings.cfg (or SCHRODINGER=)
SetupMacroModel was called in PyDP4 at line 278, inspecting the code there suggests that settings.MM == 'm' i.e. macromodel (argparser default if no -m option is specified) is used as molecular mechanics program and the path to the program has not been provided.
Most likely you meant to use TKINTER, if so you should provide the command line option -m set to t.
Replying here as I stumbled upon the same issue ;)
When I ran PyDP4_GUI, it showed this error and stopped working.
QLayout: Attempting to add QLayout "" to CalculationTab "", which already has a layout QLayout: Attempting to add QLayout "" to CalculationTab "", which already has a layout QLayout: Attempting to add QLayout "" to CalculationTab "", which already has a layout QLayout: Attempting to add QLayout "" to CalculationTab "", which already has a layout libGL error: MESA-LOADER: failed to open crocus: /usr/lib/dri/crocus_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: crocus libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast /bin/sh: 1: /utilities/sdconvert: not found Traceback (most recent call last): File "/home/duc/DP5/PyDP4_GUI.py", line 2600, in runPyDP4 self.NMRData, self.Isomers, self.settings, self.DP4Data,self.DP5Data = PyDP4.main(ui.table_widget.Tab1.settings) File "/home/duc/DP5/PyDP4.py", line 278, in main MacroModelInputs = MacroModel.SetupMacroModel(settings) File "/home/duc/DP5/MacroModel.py", line 59, in SetupMacroModel outp = subprocess.check_output(convinp + f + '.sdf -omae ' + f + File "/home/duc/anaconda3/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/home/duc/anaconda3/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '/utilities/sdconvert -isd Compound_O1.sdf -omae Compound_O1.mae' returned non-zero exit status 127. Aborted (core dumped)Where Compound_O1 is one among of the three conformers saved from the optimization results of Gaussian 9 (named O1-O3). I put these files within the DP5 folder, however it showed that file not found. I tried 1 file or 3 files at the same time, move all files to DP5 folder (without any subfolder), but the results were the same. Could you please give me any suggestion? Thank you very much!