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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
- Coming soon: integration with other MD\EM workflows!
For more detailed info, check the readthedocs page.
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.