I try to use Rosetta 3.4 to calculate the ddG of a protein.
The command I use is
$ROSETTA/rosetta_source/bin/ddg_monomer.linuxgccrelease -in:file:s test.pdb --ddg::weight_file ddg.wts -ddg::iterations 20 -ddg::dump_pdbs true -database $ROSETTA/rosetta_database/ -ddg::local_opt_only true -ddg::min_cst false -ddg::mean true -ddg::min false -ddg::sc_min_only true -in:file:fullatom -resfile test.resfile
Everything goes well but some proteins have problems.
For example core.pack.task.ResfileReader: On line 2, the pose does not have residue with chain=A, PDBnum=1
One of the pdb has this problem are attached. But if I change the structure from test.pdb to test2.pdb, there is not error. I check the pdb files, I didn't find any format different between these two.
I also try to use the mut_file format, but for the test.pdb, the program allways claims error.
Could you please help me to check that? Thank you!