NAFlex ABC Setup Pipeline
NAFlex provides a pipeline to setup structures for the Ascona B-DNA Consortium (ABC) members.
The setup process is made with leap program from AMBER package and ff14SB forcefield, with the new nucleic acids parmbsc1 forcefield, Dang ions parameters and SPC/E Water model.
The steps of the pipeline are:
- Add missing atoms
- Energetically minimize the system
- Solvate structure with a truncated octahedron box, with SCP/E water model
- Neutralize the system with Potassium ions
- Add an ionic concentration of 150mM of Cl- / K+ ions
- Randomize ions around the structure using cpptraj
NAFlex ABC Setup Pipeline:
