zhang-ivy
commented
1 year ago It definitely supports ion-bound systems, my RBD:ACE2 systems have Zn ions bound.
It should also handle GTP, though I've never tried it myself. I would just supply the apo and complex PDBs to the PointMutationEngine as normal (if the mutating protein is bound to GTP, GTP should be in both apo and complex PDBs, otherwise just the complex PDB). You may need to also supply the relevant forcefield that for parametrizing GTP. Happy to help debug any errors and suggest changes to the code if necessary
Basically my question is: Can perses handle mutation predictions in complexes that involve a cofactor/ligand bound in one chain?
I have a system involving the study of Protein:Protein complex, using protein mutations, but one of the proteins is bound to a GTP cofactor, and both proteins in the PPI also have Ion cofactors (one Mg2+ and one Ca2+). Neither the cofactor nor ions would be mutating during the transformations.
Does perses currently support cofactor-bound systems? I assume that the Ions will be managed automatically, but looking for some guidance on how I can set up an htf file where I've parameterized the GTP cofactor as well.