Charge file not generated/found

[JSLJ23]

FileNotFoundError: [Errno 2] No such file or directory: '1z6e_protein_temp_out.csv'

Running the cell with compute_inp_surface(target_filename, ligand_filename, dist_threshold=10) in the Docking_example.ipynb throws this error.

Is there something that needs to be done with the multivalue binary in ABPS to return the tmp_file_base+"_out.csv"?

The MULTIVALUE_BIN enviornment variable is pointing to the exact path for the multivalue binary and all the steps prior to this works to output files, like the tmp_file_base + ".csv".

Also, may I ask what this three lines of code are actually doing?
multivalue = multivalue_bin + " %s %s %s"
make_multivalue = multivalue % (tmp_file_base+".csv", tmp_file_base+".dx", tmp_file_base+"_out.csv")
os.system(make_multivalue)

Thank you.

[omendezlucio]

hi @JSLJ23,

The three lines you mention are actually running the multivalue package using the files that were generated in previous steps, ie the .csv and the .dx.

The issue you mentioned usually happens when multivalue or any of the previous steps failed. Try to run reproduce the experiment using the docker image please. Hope it works in there.

[jvenderley-lilly]

I faced similar issues when trying to run "compute_inp_surface" in a directory that was different than the target_filename and ligand_filename location (I'm using a singularity image pulled from docker). In my case, the upstream steps failed because some files couldn't be read. It worked fine once everything was in the same directory so I'm guessing there's potential issues with relative path locations somewhere along the way.