Tutorial:tools: Difference between revisions
Jump to navigation
Jump to search
Created page with " 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" |
No edit summary |
||
| Line 1: | Line 1: | ||
==Structure Conversion== | |||
Convert PDB to xyz | Convert PDB to xyz | ||
Features: | Features: | ||
| Line 5: | Line 5: | ||
* It supports other fragments (user needs provide) besides amoebabio18. This is good for, such as, chemical modified residues | * 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 | * Link: https://github.com/leucinw/TIPTOP/blob/main/IP_PDB2txyz.py | ||
==System building== | |||
* CHARMM GUI https://www.charmm-gui.org/ | |||
* | |||
Latest revision as of 22:18, 19 July 2022
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/