leifseute / grappa-data-creation Goto Github PK

Scripts used to create the peptide datasets 'uncapped_amber99sbildn', 'tripeptides_amber99sbildn', 'hyp-dop_amber99sbildn' and 'dipeptide_rad' from grappa-1.1.

For all of these, the workflow was:

• Generate PDB files from sequences using the pepgen package (generate_pdbs.py)
• Sample states from MD at 300K using a traditional forcefield (amber99sbildn for peptides, an early version of grappa for radicals). To reach a larger conformational space, we simulate at 500K and reduce the temperature back to 300K before sampling a state (generate_states.py)
• Calculate single point energy and gradient with DFT (single_points.py)
• Save energy, gradient, sequence, pdb-string and atomic numbers as npz file that can be read by grappas data.MolData class (to_grappa_format.py)