Setting up Dual Topology Files for Mutation Alchemical Free Perturbation

[Pujan Ajmera]

Hi,

I am interested in setting up an alchemical free energy perturbation in OpenMM, where I introduce a mutation. I have psf and crd files for the protein in its wild-type and mutated states. How can I make a dual-topology and set up the corresponding OpenMM calculation?

[Peter Eastman]

https://github.com/choderalab/openmmtools might be able to do what you want.