I'm running the high-res protocol of the ddg_monomer on a 439 residue enzyme structure (following the the Kellogg paper and online docs protocols) and I'm seeing some odd score outputs.
There are three types of odd outputs in the ddg_predictions.out file:
1: Residues with one to two mutations with extreme total score(s):
On the whole, the total score for most mutations are around 0 +/- 4. However, throughout the protein there are a significant number of residues with one or two mutations that have a total score of -60 to -80 or +80 to +120. An example of a residue with one of these mutations (D to Y) is in the first output file.
2: Residues with completely extreme negative or positive scores:
As above, most residues have mutations total scores around 0, there are some residues that all of their mutations are completely extremely negative or positive (around -80 or +90). The second output file is an example of this.
3: Inconsistent results from the two cluster runs:
I'm splitting the mutation alphabet for each residue in half (ie: A to L and M to Y) such that each residue has two ddg_monomer runs (due to walltime limits at my cluster). While rare, I'm finding that there are some residues with mutations in one run with a total score on the order of 0 to 4 and the second run with mutations on the order of +80 or -80 for each total score. An example of this is in output file three.
I've run this protocol with this structure on Rosetta 3.5, 3.4, and currently 3.3 and have seen similar results. I've played with setting a constant seed and that has helped the third output (ie: using the random seed from the low scoring run in the other run). And played with -use_input_sc but no improvement with that flag.
Is this behavior normal? Should I set a constant seed for all runs? Is it just that the structure is too big?
Thank you in advance!
Command line (For Rosetta 3.3):
/mnt/home/rosetta_source/bin/ddg_monomer.linuxgccrelease -in:file:s /mnt/home/min_cst_0.5.L_PMF1_0001.pdb -resfile mutations.res -ddg:weight_file soft_rep_design -database /mnt/home/rosetta_database/ -fa_max_dis 9.0 -ddg::iterations 50 -ddg::dump_pdbs false -ignore_unrecognized_res -ddg::local_opt_only false -ddg::min_cst true -constraints::cst_file /mnt/home/input.cst -ddg::suppress_checkpointing true -in::file::fullatom -ddg::mean false -ddg::min true -ddg::sc_min_only false -ddg::ramp_repulsive true -unmute core.optimization.LineMinimizer -ddg::output_silent true -use_input_sc