Open Modk1996 opened 3 hours ago
Hi!
You should be able to mix IDPs and MDPs by adding multiple components.add()
lines in the prepare.py
script:
residues_file = f'{cwd}/input/residues_CALVADOS3.csv'
components = Components(
molecule_type = 'protein',
charge_termini = 'both',
fresidues = residues_file,
)
components.add(name='my_favorite_IDP', nmol=100, restraint=False, ffasta = 'input/fastalib.fasta')
components.add(name='my_favorite_MDP', nmol=100, restraint=True, pdb_folder = f'{cwd}/input', fdomains = f'{cwd}/input/domains.yaml')
The first (IDP) component will be read and built from a sequence fasta file (input/fastalib.fasta
), and the second component will read in a PDB in the specified folder pdb_folder
(make sure to have the pdb named the same as the component name). The domain boundaries are specified in domains.yaml
.
Potentially you have to change the topology to 'grid' rather than 'slab'.
I noticed that the provided examples include systems containing only IDPs and systems containing only MDPs, but I want to simulate a system that includes both MDPs and IDPs. How should I modify the prepare.py file?