[phenixbb] [External] RE: phenix.ligandfit does not recognize a list of SDF file names
Terwilliger, Thomas Charles
terwilliger at lanl.gov
Tue Jul 22 11:00:21 PDT 2014
I fixed ligandfit so that it should now be able to take your list of sdf files and run each file sequentially. Starting with tomorrow's build, you should be able test it out with this regression test:
Thanks for pointing out the problem! Let me know if that does not do it.
All the best,
On Jul 21, 2014, at 7:11 PM, Phan, Jason wrote:
> From: phenixbb-bounces at phenix-online.org<mailto: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<mailto: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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> phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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