PMX ligand mutation tutorial - jupyter notebook - missing protein part?

Hi all,

I’m following the ligand mutation pmx tutorial in the jupyter notebook (pmx/tutorials/ligand_tutorial.ipynb at develop · deGrootLab/pmx · GitHub). And aside from preloading the data from completed calculation it seems to work just great.

Except it seems to be missing the part for protein transition computations. The ligand transition is prepared and jobscripts generated, so its easy to do, but protein is not.

Has anyone done this tutorial before? Am I missing it somehow?



P.S. are there any other tutorials I could follow to learn ligand mutation? (I’m aware of this one: Ligand modification free energy calculations, but it’s in CLI so i’ll try to do it after im done with python version)

Hi Dom,

The protein transition computation was not performed to keep the size of the input files minimal (as it would required the trr files for protein-ligand in water simulation). You could do that by bProt=True in fe.prepare_transitions() if you generate the trr files.

I suggest sticking to the Jupyter Notebook tutorial, as it’s the most recent one.