simtk.org

Hi
I wonder if there is a way to do Alanine scaning with openmm as it make a lot of sense here with the very fast openmm, like 10ns MD with each mutation for 200 aa long polypeptide.
Thanks
Omar

It would be pretty easy to do this with PDBFixer (https://github.com/pandegroup/pdbfixer). It has an applyMutations() function that makes this very simple. See https://github.com/pandegroup/pdbfixer/ ... #L729-L761.