I have a PDB of some protein (without ligand), converted to mol2 format, and a mol2 file of a ligand. I would like to have a new file that consists of the union of two molecules, in PDB or mol2 format. I tried to get this with Pymol, so I created a selection of both molecules and saved it, but it is not recognized as a good PDB for the input in Discovery Studio. So I would need a way to create this kind of union of molecules but in a format similar to the one that appears on the PDB database for proteins crystallized with ligands, any hints?
ok, the solution is to open both files with pymol; and then without creating any selection, just use save file.pdb, and the two molecules are correctly stored in the new pdb file