hello guys. Alpha Fold has some pretty cool implications for our group, however they produce only “empty” structures, so often metals/metal complexes and co-factors have to be placed manually. This is done by aligning the homology model with an existing crystal structure and just transfering the hetatoms. I thought about using gromacs to energy minimize the structure, to resolve clashes that might occur. For most co-factors this is usually not an issue, i am able to parameterize them, also in an automated fashion. However what i struggle with are metalloenzymes and metal clusters. Right now i am using rosetta to relax the new structure.
Is there a way to automate the parameterize of these complexes easily so i can run an energy minimization for multiple different systems? I dont need them to be perfect, just approximations will do the job just fine i guess.