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?

Okay got it, I think then I will do the following (for other users that see this): 1) Get the crd file from the last frame in openmm (parmed can do this nicely) 2) Use charmm to mutate and regenerate psf and crd file, I found some builder scripts that can handle this 3) Reload those corresponding fi...

To clarify then, how would I make sure the psf file is also properly modified? I imagine for example, a MET-->VAL mutation, there would be a significant connectivity change that needs to be specified

Hi, I was wondering how I can mutate a protein residue within or outside of openmm, such that my files are compatible with it? From my trajectory, I yielded a pdb file, as well as an xml state file. I have a psf file with the rest of the parameter files as well from before. My system has too many at...

Hi Peter, Thank you for your response. I did an energy decomposition analysis on my initial structure, and also tried letting parts of the system go iteratively to see which was causing the overly large energies: Initial structure energy decomposition: Force HarmonicBondForce: 697298.8917322994 kJ/m...

Hi all, I am attempting to minimize the lipids in my structure (this is part 1 of a 5 step minimization I'm doing). For some reason, the energies aren't really changing, and the coordinates are barely changing - my initial system is definitely not close to a minimum, but this did run for around an h...