I ran stand-alone version of Edock (prepare.py script) but received the following error message
ERROR efopen: Unable to open ../../parameters/vdw_AMBER_parm99.defn. Terminating execution.
This file is indeed present under two of the subfolders of my Edock folder.
sysadmin@draco:/vol1/software/edock/2019.03$ find . -name "vdw_AMBER_parm99.defn"
./script/beforedocking/parameters/vdw_AMBER_parm99.defn
./parameters/vdw_AMBER_parm99.defn
Looks like the prepare.py cannot find that file under ../../parameters. Would the error be resolved if that path is corrected as ../parameters/vdw_AMBER_parm99.defn?
After this error not all outputs are produced in the output file. Attached you can find the data folder and SLURM output. I will appreciate if you can help.