iPBSA is a script for docking results rescoring, it minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods. The algorithm is based on a freely-available AmberTools which can be easily installed via conda
#Download and export iPBSA
wget https://github.com/sahakyanhk/iPBSA/archive/refs/heads/main.zip; unzip main.zip; chmod +x iPBSA-main/iPBSA.sh
export PATH=$(pwd)/iPBSA-main/:$PATH
iPBSA.shUsage ./iPBSA.sh -r <.pdb> -l <lig_dir> -n <int> -c <bcc/gas> -o <out_dir>
-r receptor file in pdb format
-l path to the directory with small molecules (ligands should be in pdb format with added hydrogens)
-n number of parallel threads
-c charge method BCC (defolt) or GAS
-o output directory
For more details, please see Improving virtual screening results with MM/GBSA and MM/PBSA rescoring