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!
Your test.pdb has zero occupancies for chain A residue 1 atoms. By default, Rosetta discards atoms with zero occupancies. The loaded pose will therefore not have a chain A residue 1 atom. This will cause the resfile reader to throw an error when you try to specify that residue, and other portions of the code will have issues if there are sequence mismatches.
There’s two ways of fixing it. The first is to edit the PDB file to place a value of 1.00 in the occupacy column. The second is to pass the flag “-ignore_zero_occupancy false” to the commandline, telling Rosetta that it shouldn’t ignore atoms with zero occupancy.