Reply To: is it possbile to cluster pdb files?

[Anonymous]

Well, yes, it’s failing because you haven’t supplied the inputs. It’s right in the commentary (marked by #) under the flag with the same name as the error message.

You need to get rid of the flag in-file-silent folding.silent.out, because you don’t have that input. Instead use -s (list your pdbs on the command line) or put the list of pdb inputs in a file called pdblist and do -l pdblist.