I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.
I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work.
I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.
I'm attaching the log files. Can you help me with these issues? Thank you in advance!