End-to-end AMBER system builder from PDB
Project description
AABY
Automated AMBER System Builder
Installation
git clone https://github.com/AmandaStange/AABY.git
cd AABY
micromamba env create -n AABY -f environment.yml
Usage
Example:
python Scripts/AABY.py -f INPUT.pdb --chains A --ph 7.4 --coby-yaml coby_input.yaml --antechamber True --mol2 UNK --nc 0
For help use
python Scripts/AABY.py -h
Example of input coby file (coby_input.yaml)
- -box
- 15
- 15
- 15
- -membrane
- lipid:POPC:6
- lipid:CHL:4
- -protein
- file:{protein_pdb}
- charge:0
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