Hi Jason, I wonder if you could send me (off-line) some SDF specifications for ligands and I'll see if I can fix up ligandfit to take them as a list. (Perhaps you could send me exactly what you want to be able to give to ligandfit). Thanks! -Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Phan, Jason [[email protected]] Sent: Monday, July 21, 2014 4:32 PM To: [email protected] Subject: [phenixbb] phenix.ligandfit does not recognize a list of SDF file names Hi All, I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb