[phenixbb] phenix.ligandfit does not recognize a list of SDF file names

Terwilliger, Thomas Charles terwilliger at lanl.gov
Mon Jul 21 17:52:56 PDT 2014

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).
-Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Phan, Jason [jason.phan at vanderbilt.edu]
Sent: Monday, July 21, 2014 4:32 PM
To: phenixbb at phenix-online.org
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.
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