NOTE - worked has moved to OpenBPMD2, so this is no longer maintained
OpenBPMD is an open source implementation of binding pose metadynamics (BPMD). Based on work by Clark et al, 2016. Primarily built for reranking docked poses out of a list of candidates generated by a docking program. OpenBPMD biases ligands using metadynamics and evaluates how stable they are during the simulation. Recommended to be used in conjunction with grand to optimise water networks around the ligand before subjecting it to metadynamics.
The dependencies needed for running the scripts can be installed with conda:
conda create -n openbpmd -c conda-forge openmm mdanalysis mdtraj parmed pytest cudatoolkit=11.8
conda activate openbpmd
Once the dependencies have been installed, running OpenBPMD involves simply running one of the Python scripts. Have a look at the examples/ directory for further instructions on how to run and analyse the OpenBPMD results.
- A. J. Clark, P. Tiwary, K. Borrelli, S. Feng, E. Miller, R. Abel, R. A. Friesner, B. J. Berne, J. Chem. Theory Comput. 2016, 12, 6, 2990–2998, DOI:https://doi.org/10.1021/acs.jctc.6b00201
- D. Lukauskis, M. L. Samways, S. Aureli, B. P. Cossins, R. D. Taylor, F. L. Gervasio, J. Chem. Inf. Model. 2022, 62, 23, 6209–6216, DOI:https://doi.org/10.1021/acs.jctc.6b00201