Streamlines the end-to-end preparation of molecular dynamics simulations using MDClaw CLI tools.
MD Prepare is a specialized capability for computational biophysicists that automates the rigorous workflow of setting up molecular dynamics (MD) simulations. It manages the entire pipeline from structure acquisition—via PDB, AlphaFold, or Boltz-2—to structure cleaning, protonation at specific pH, explicit solvation, and Amber topology generation. By providing intelligent defaults and interactive checkpoints for chain and ligand selection, it ensures reproducible simulation environments and includes a 0.1ns sanity-check MD run to verify system stability before production.
主要功能
01Comprehensive structure preparation including protonation and residue cleaning
02Amber topology generation and quick stability sanity checks
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04Intelligent chain and ligand selection with interactive or autonomous modes
05Automated structure acquisition from PDB IDs, UniProt, or FASTA sequences
06Explicit solvation with OPC/TIP3P water models and ionic strength control
使用场景
01Predicting and preparing protein structures for MD starting from a UniProt ID
02Initializing protein-ligand complexes for simulation directly from a PDB ID
03Automating repetitive solvation and topology generation for batch molecular modeling
