Welcome to pdbtop’s tutorial!

Hint

The best way to support the development of pdbtop is that in any published works using pdbtop, please include the following references:

• Zhang, J. Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? J. Chem. Phys. 2022, 156, 204108.

The latest information of pdbtop can be found at: http://www.zhjun-sci.com/pdbtop

We suggest that users go over the tutorials and try the examples. The tutorials are designed to be simple and easy to follow.

Note that not all options are discussed in tutorials. If you want to know more about the details of pdbtop, please refer to the manual. The manual is designed to describe all options.

Tutorials

• Tutorial 0: Install pdbtop
  • Installation
• Tutorial 1: A Standard Protein
  • Download Structure
  • check Structure
  • remove Structure
  • Generate topology
  • solvate System
• Tutorial 2: Ligand Preparation
  • Get Structure
  • Generate Topology
  • Generate Charges
• Tutorial 3: A Protein and its Covalently Bonded Ligand
  • Combine Protein and Ligand
  • solvate System
• Tutorial 4: Modifications and Mutations
  • Modifications
  • Mutations
• Tutorial 5: Get A Better PDB File
  • Using PSF Information
  • Wrapping Molecules into a box
• Tutorial 6: Define Your Own Modification
  • To Do
• Tutorial 7: Supercell of a Molecule
  • A Human-Friendly Structure
  • Build Supercells

Manual

• 1. check
  • 1.1. Arguments
  • 1.2. Theoretical Background
• 2. remove
  • 2.1. Arguments
• 3. topol
  • 3.1. Arguments
• 4. modify
  • 4.1. Arguments
• 5. ligand
  • 5.1. Arguments
  • 5.2. Theoretical Background
• 6. pdb
  • 6.1. Arguments
• 7. psf
• 8. solvate
  • 8.1. Arguments