ssdo-lib - SSDO-0.1 pipeline library. Pipeline overview is available via the link.

Installation

Install miniconda

Run the installation script:

source conda_installation.sh

Configure parameters in constants.py file, mainly:

ligand name:

ln = 'L_PI35P'

Configure some parameters in constants.py file:

Catalytic atom pairs from literature:

args.lit_at_pairs = [
    [[17,  'SG',  'C'],  [3632, 'P3']],
]
args.num_threads_em_nvt_npt = 12
args.conv_len_thres = 20
args.B_len_thres = 100000
args.run_hrx_gpu_id = 2

Ligand net charge

args.net_charge = -5

Protein pdb file

args.E_pdb = "/home/user/1xww_prot.pdb"

Ligand pdb file

args.XH_pdb = "/home/user/L_PI35P_E.pdb"

Launch the pipeline:

conda activate py37
ipython launch.py