The protein isnot from PDB
Dear workflow committee,
I would like to know how I can run a screening if the protein is not from PDB and I prepared it myself.
it was written in the workflow that is possible based on following words fromthe wrokflow:
if you want to manually upload target pdb file upload these to in a subfolder of the input dir called "/PDB/receptor"
I tried to do that but I got the following error:
Activating environment modules: bio/Biopython/1.75-foss-2019b-Python-3.7.4 Activating environment modules: bio/Biopython/1.75-foss-2019b-Python-3.7.4 filename in targets CCLA2, A Traceback (most recent call last): File "/lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/big/screening6/.snakemake/scripts/tmp3vy7qaua.prepareReceptor.py", line 62, in prepareRec(snakemake.input[0], snakemake.output[0], snakemake.config["TARGETS"][0]) File "/lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/big/screening6/.snakemake/scripts/tmp3vy7qaua.prepareReceptor.py", line 48, in prepareRec model = structure[0] File "/cluster/easybuild/broadwell/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/PDB/Entity.py", line 42, in getitem return self.child_dict[id] KeyError: 0 [Tue Nov 2 11:51:24 2021] Error in rule prepareReceptor: jobid: 14 output: /lustre/scratch/m2_jgu-smitt/PDB/receptor/CCLA2.pdb
RuleException: CalledProcessError in line 65 of /cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/workflows/life-science/StructureBasedScreening/workflows/preparation.smk: Command 'module purge && module load bio/Biopython/1.75-foss-2019b-Python-3.7.4; set -euo pipefail; /cluster/easybuild/broadwell/software/Python/3.7.4-GCCcore-8.3.0/bin/python /lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/big/screening6/.snakemake/scripts/tmp3vy7qaua.prepareReceptor.py' returned non-zero exit status 1. File "/cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/snakemake-6.0.5-py3.7.egg/snakemake/executors/init.py", line 2347, in run_wrapper File "/cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/workflows/life-science/StructureBasedScreening/workflows/preparation.smk", line 65, in __rule_prepareReceptor File "/cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/snakemake-6.0.5-py3.7.egg/snakemake/executors/init.py", line 568, in _callback File "/cluster/easybuild/broadwell/software/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/concurrent/futures/thread.py", line 57, in run File "/cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/snakemake-6.0.5-py3.7.egg/snakemake/executors/init.py", line 554, in cached_or_run File "/cluster/easybuild/broadwell/software/mflow/0.4.3-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/snakemake-6.0.5-py3.7.egg/snakemake/executors/init.py", line 2359, in run_wrapper
so could you please help me with that,
I would like to know what could I do with the script in the steps such as:
specify target enzyme ID and chains format: ["PDB_ID, <CHAIN_1> <CHAIN_2]
TARGETS: ["TARGET,A B C"]
and also what i should put in the input file, is the protein in PDB or pdbqt? what about the output?
Thank you so much in advance
cordial regards Mona