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A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.
- Automatically download structures, sequences and metadata from the PDB, PDB-REDO, EMDB and UNIPROT
- Automatically fill missing loops with MODELLER or pdbfixer
- Automatically add missing atoms and fix non-standard residues with pdbfixer
- Automatically resolve steric clashes and minimise structures
- Automatically align and trim together structures to be the same length
- Automatically extract and prepare hetatms\ligands for simulation with rdkit
- Easily run simple MD simulations for testing, validation and minimisation with OpenMM
- Create 'morph' trajectories with metadynamics
- Install using conda:
conda install -c CCPBioSim -c salilab prepmd - Run it:
prepmd 6xov 6xov_processed.pdb - More documentaqtion (including more install info) on readthedocs.
AGPLv3
prepmd is developed by Rob Welch. Thanks to Harry Swift for helping set up the CI, organising a lot of the repo stuff and managing the CCPBioSim conda channel. The logo was created by Jas Kalayan. This project is funded by DRI-IMB and the repo is managed by CCPBioSim.