Hi there,
I have been trying to submit parameter files (.json) in the “submit file” portal as a part of some tests I am doing, but I think there were some issues in my file and now the run is stuck at 0%. To make sure it wasn’t a server issue I ran another run but manually added the parameters under “Submit” instead of uploading a .json and it is progressing normally. However, I have 4 json files running and they are all stuck and I am getting an error message whenever I try to cancel.
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Thanks for the response!
577261
577263
577271
577272
577332
Would you also be able to tell what is the issue with the param files I have written? I am not sure what may be causing the issue. I had written a .py script to edit the .jsons from a run that I made manually, only changing the second protein and the active residue list. For the first four runs I realized that I had not edited the histidine protonation or passive residues list, so i set those to blank and left auto passive and auto his “true” for run 577332, but that one also seems to have gotten stuck.
Do not touch the name of the PDB files (the pdb_file parameter).
Only replace the coordinates when editing the json file.
This is the issue with your modified json files.
I corrected your files and the runs should start again
That fixed it, thanks for your help Dr. Bonvin!
Hi again Dr. Bonvin,
I am once again working on editing my script and seem to have some problem with my parameter file again that I cannot identify. The run moves from queued to running and never makes any progress, but my manual submissions progress just fine. RunID is 585603
Thanks!