I'm trying to run Rosetta in relax mode to do refinement of some protein structures that i've got from an abinitio run.
I did the clustering, and i extracted some decoys from the output silent file with Reconstruct_PDB_by_index .
I used many different lines to do the relaxation but i get an error every time:
A sample line:
/home/Bob/Rosetta/rosetta++/rosetta.gcc ac 1py6 a -relax -s 1py6_start_0001.pdb -paths path.txt -nstruct 1
__"cant' find starting residue in pdb file"__
than it outputs:
__ERROR:: Unable to determine sequence length from pdb file__
Than Rosetta exits in :
__ERROR:: Exit from: pose.cc line: 2013__
Obviously Rosetta can't read the starting structure properly. I've checked the input pdb files, and they are exactly the same as the files from samples provided with in the RosettaExamples.tgz . I also tried using a true native PDB file.
Something is wrong with the pdb_stream but i don't know how to handle it.
If you have any ideas how to solve the problem, i would be very grateful if you shared it.