Trying to run the conda environment on the cluster (PBS Pro)

[JGBurgess1]

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Hello! Thanks for making the tutorials available!

I'm trying to make a pipeline in python that will make use of MGL Tools as part of the process. I'm trying to: (A) Model mutations in a protein (B) Energy minimize the protein (A and B in schrodinger). (C) Prepare the protein in MGL Tools (to add gasteiger charges) (D) Dock ligands to the mutated proteins using Autodock Vina.

So far, I've managed (A) and (B). But for C, I'm trying to use the code you have from this tutorial, where you install the conda package of MGLTools in your conda envrionment. I was able to do that.

However, when I try to run a job on the cluster (PBS Pro), I'm not able to access my conda environment that I created. Therefore, I can't run the python scripts from MGL Tools.

Any thoughts/ advice?

Regards

Jeremy Burgess

[JGBurgess1]

Here's the code I'm

` module purge module load chpc/BIOMODULES openmpi module load chpc/python/anaconda/3-2021.11

echo $(module list)

source conda

conda init bash conda list

eval "$(conda shell.bash hook)" /apps/chpc/chem/anaconda3-2021.11/bin/conda activate open_docking_env

cd /mnt/lustre/users/jburgess1/mutation_tests/chatgpt/April/

NP=$(cat ${PBS_NODEFILE} | wc -l ) mpirun --mca btl '^openib' -np $NP --machinefile $PBS_NODEFILE python 4_Mpi_Initialize_MGL_TOOLS.py

conda deactivate `

[pb3lab]

I am not sure if you need to put the whole path for conda to activate the docking module, you might just need to indicate

conda activate open_docking_env

As your module loader is loading the conda module potentially in your path