Reply To: Ab Initio Modelling of Protein with Small-Molecule Cofactor

[Anonymous]

I’m pretty sure that ab initio goes through centroid mode at some point (I actually think it starts off in centroid mode, though I’m not sure). It might not be the full atom ResidueTypeSet which is missing the FAD – it might be the centroid ResidueTypeSet instead. You might want to try generating a centroid topology file with molfile_to_params.py (see command line option “-c”), and then passing it to the ab initio program with -extra_res_cen (so your command line would look something like ” … -extra_res_fa FAD.params -extra_res_cen FAD_cen.params … “