We are currently writing back to the GAFF .mol2 file the coordinates from the previous docked file .pdb. However, this is done using the unique atom names: but if they're not unique this breaks down. So first prepare the .pdb file and ensure that they're unique before applying GAFF and so on.
We are currently writing back to the GAFF .mol2 file the coordinates from the previous docked file .pdb. However, this is done using the unique atom names: but if they're not unique this breaks down. So first prepare the .pdb file and ensure that they're unique before applying GAFF and so on.