Create Mutant Structure

Example on how to create a structure file containing hybrid residues for an alchemical transformation. At the moment, pmx supports the mutation of protein, DNA, and RNA residues.

This is how you can mutate a protein residue.

>>> from pmx.model import Model
>>> from pmx.alchemy import mutate

>>> # load the PDB file
>>> m = Model('protein.pdb', rename_atoms=True)
>>> # perform mutation
>>> m2 = mutate(m=m, mut_resid=9, mut_resname='R', ff='amber99sb-star-ildn-mut')
>>> # save mutant PDB file
>>> m2.write('mutant.pdb')

The Model can also be modified in place:

>>> mutate(m=m, mut_resid=9, mut_resname='R', ff='amber99sb-star-ildn-mut', inplace=True)
>>> m.write('mutant.pdb')

Similarly, you can also mutate DNA with the same pmx.alchemy.mutate() function.

>>> m = Model('dna.pdb', rename_atoms=True)
>>> m2 = mutate(m=m, mut_resid=2, mut_resname='T', ff='amber99sb-star-ildn-bsc1-mut')
>>> m2.write('mutant_dna.pdb')

With the verbose option you can get additional info printed to screen.

>>> m2 = mutate(m=m, mut_resid=2, mut_resname='T', ff='amber99sb-star-ildn-bsc1-mut', verbose=True)
log_> Residue to mutate: 2 | DA | A
log_> Mutation to apply: A->T
log_> Hybrid residue name: DAT
log_> Inserted hybrid residue DAT at position 2 (chain A)

Note that, by default, pmx.model.Model renumbers all residues from 1. If you want to keep the original residue IDs, you can do this by using the renumber_residues argument when loading the Model:

>>> # load the PDB file
>>> m = Model('peptide.pdb', rename_atoms=True, renumber_residues=False)

In this case, however, your residue IDs might not be unique anymore. If pmx finds that your residue ID selection is not unique, it will raise an error. Thus, in this scenario it is safer to also provide the chain ID to pmx.alchemy.mutate(), e.g.:

>>> m2 = mutate(m=m, mut_chain='A', mut_resid=9, mut_resname='R', ff='amber99sb-star-ildn-mut')