Hello,
I am trying to do comparative modeling of a mutated protein to a known protein PDB. I followed the tutorial instrutions and it appears the script begins running okay but I run into several warnings which end in an error after about ten minutes. I have attempted to fix the problem based on many of the suggestions online however, I am unable to get the program past the final error which quits the script. Here are several of the warnings and final error. I have included the XML file I use for the script rosetta_scripts.mpi.linuxgccrelease -in:file:fasta input.fasta -parser:protocol **hybridize.xml** -default_max_cycles 200 -dualspace -restore_talaris_behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) [ WARNING ] discarding 4 atoms at position 88 in file 31_4f5b.pdb. Best match rsd_type: ALA
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CEN on residue VAL 104
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) [ WARNING ] can’t find pose atom for file-residue 107 atom 1HG2 (trying to store temperature in PDBInfo)
core.optimization.Minimizer: (0) [ WARNING ] LBFGS MAX CYCLES 5 EXCEEDED, BUT FUNC NOT CONVERGED!
ERROR: Scorefunction not set up for nonideal/Cartesian scoring
ERROR:: Exit from: src/core/optimization/CartesianMinimizer.cc line: 66
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/optimization/CartesianMinimizer.cc:66
[ ERROR ] UtilityExitException
ERROR: Scorefunction not set up for nonideal/Cartesian scoring
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job S_0001
As far as I am understsand some of these warnings are due to the PDB being supplied as fullatom, however Rosetta converts it to centroid. Please let me know if this though is incorrect.
.
