Input Generator

• PDB Reader
• Solvator
• Quick MD Simulator
• Membrane Builder
• Boundary Potential Utilizer
• PBEQ Solver
• Implicit Solvent Modeller
• Normal Mode Analyzer
• NMR Structure Calculator
• User Space

PDB Reader

The PDB Reader is the most basic, yet powerful tool. It allows you to download a PDB file from RCSB PDB (with PDB entry ID) or upload it from your machine, and convert it to CHARMM readable format with the following options:

• partial selection of protein chains,
• modification of engineered residues,
• terminal group selection,
• protonation selection,
• disulfide bond selection,
• phosphorylation selection,
• generation of a biologically functional unit, and
• crystal generation.

There is a PDB Reader demo in Video Demo to illustrate how to use this module. Please note that all the residues in the PDB structure you want to read must be defined in the CHARMM topology file (top_all27_prot_na.rtf). Otherwise, CHARMM will be terminated abnormally.