https://github.com/mlund/pdb2xyz
Convert PDB files to coarse grained XYZ files
https://github.com/mlund/pdb2xyz
coarse-graining molecular-modeling pdb-files protein-structure
Last synced: 11 months ago
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Convert PDB files to coarse grained XYZ files
- Host: GitHub
- URL: https://github.com/mlund/pdb2xyz
- Owner: mlund
- License: apache-2.0
- Created: 2025-06-20T05:10:54.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2025-07-01T12:41:13.000Z (12 months ago)
- Last Synced: 2025-07-01T13:48:13.987Z (12 months ago)
- Topics: coarse-graining, molecular-modeling, pdb-files, protein-structure
- Language: Python
- Homepage:
- Size: 101 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Convert PDB → Coarse Grained XYZ files
`pdb2xyz` is a small tool to convert atomistic protein structures to coarse grained representations where residues
are reduced to one or two interactions siters.
Meant to construct models for use with the Calvados force field in the Duello and Faunus software.
## Features
- Convert PDB to XYZ
- Optional off-center sites for ionizable side-chains
- N and C terminal handling
- SS-bond handling
- Partial charge approximation according to pH using
[average residue pKa values](https://doi.org/10.1093/database/baz024)
- Create Calvados3 topology for [Duello](https://github.com/mlund/duello)
## Install
```sh
pip install pdb2xyz
```
## Usage
It is recommended that you fix your atomistic PDB file before converting
using e.g. [pdbfixer](https://github.com/openmm/pdbfixer?tab=readme-ov-file).
```sh
usage: pdb2xyz [-h] -i INFILE -o OUTFILE [-t TOP] [--pH PH] [--alpha ALPHA] [--sidechains]
Convert PDB files to XYZ format
options:
-h, --help show this help message and exit
-i INFILE, --infile INFILE
Input PDB file path
-o OUTFILE, --outfile OUTFILE
Output XYZ file path
-t TOP, --top TOP Output topology path (default: topology.yaml)
--pH PH pH value (default: 7.0)
--alpha ALPHA Excess polarizability (default: 0.0)
--sidechains Off-center ionizable sidechains (default: disabled)
--chains [CHAINS ...]
List of chain IDs to include (default: all chains)
```