Tutorial:tools

Structure Conversion

Convert PDB to xyz Features:

• It does not change atom order so good for post-MD processing. so it is a one-to-one mapping
• It supports other fragments (user needs provide) besides amoebabio18. This is good for, such as, chemical modified residues
• Link: https://github.com/leucinw/TIPTOP/blob/main/IP_PDB2txyz.py

System building

• CHARMM GUI https://www.charmm-gui.org/