mihaelasmilova/duck

Fork of open-source DUck (Dynamic Undocking) used by Galaxy

Installation

Conda

Make a fresh Conda environment

git clone https://github.com/mihaelasmilova/duck
cd duck
conda env create -f environment.yaml 
conda activate openduck_latest
python setup.py -install

Running

Activate conda and run like this:

source activate openduck_latest
python ./scripts/run_full_duck_pond.py -i inputs_file.txt

where inputs_file.txt contains the paths to directories with openduck input (1 directory = 1 interaction). The input directories need to contain:

• prepared apo protein file
• protonated ligand file
• run.yaml file with DUck parameters

where run.yaml is a file like the following:

prot_code: '1n2v'
prot_int: 'A_ASP_156_OD2'
lig_id: 'BDI'
cutoff: 9
md_len: 0.5
distance: 2.5
init_velocity: 0.00001
num_smd_cycles: 1
gpu_id: 0
apo_pdb_file: '1n2v_apo.pdb'
mol_file: ligand.mol