Installation

Conda

Make a fresh Conda environment

git clone https://github.com/galaxycomputationalchemistry/duck
cd duck
conda env create -f environment.yaml 

Or quickly: conda create -n openduck -c omnia -c bioconda -c conda-forge -c defaults python=3.7 yank=0.25.2 pdbfixer=1.6 openforcefield=0.6.0 parmed=3.2.0 cudatoolkit=10.1.243 openmm=7.4.1=py37_cuda101_rc_1 openduck=0.1.2

Docker

Pull down the latest image

docker pull abradle/duck

Running

Activate conda and run like this:

source activate duck
frag_duck run.yaml

Or with Docker run like this:

docker run -it -v $PWD:/data abradle/duck /bin/bash -c "frag_duck /data/run.yaml"

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: '3'
apo_pdb_file: '1n2v_apo.pdb'
mol_file: ligand.mol