On 20 Mar 2012, at 12:34, Eleanor Dodson wrote: > I would like to use this to check an existing ligand. I have the PDB refined > according to a cif file, and that cif file used for input to REFMAC and > phenix. > > I dont want to lose the atom names assigned there so is it possible to start > GRADE with one of those inputs or do I have to convert it to a MOL2 file (I > guess thsat is a SYBIL file?)
You will have to convert it to a mol2 file; we have had very acceptable results doing this using openbabel, simply obabel ligand.pdb -Oligand.mol2 at least in the case where the ligand has all its hydrogen atoms present and named. If the ligand doesn't have hydrogen atoms, you will have to use obabel ligand_noH.pdb -h -Oligand_H.mol2 then edit ligand_H.mol2 so that all the hydrogen atoms have different names (I appreciate this is tedious, it will be automatic in the next version), then use that as input. Ton
