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DDG_monomer application

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DDG_monomer application
#1

Hello,

I am new in Rosetta. I would like to compare stability of the wild-type and mutated proteins using DDG_monomer. Since my protein is quite big I use the low resolution protocol for now. The results that I obtained look weird to me. Could you please tell me if they are supposed to be like this or I do something wrong?

I obtained the following output files: ddg_predictions.out (it looks fine to me), wt_S360D.out (all structures and corresponding scores are either the same or have negligible differences), mut_S360D.out (all structures and corresponding scores are either the same or have negligible differences), mutant_trajS360D (empty!), wt_traj (empty!). Please see my flag file and grepped scrores below.

According the application documentation, I expect conformational sampling of sidechains within 9A of the mutated residue for the both wild-type and mutant proteins. But the structures I obtained look like I applied some strong constrains to all atoms. There is no any sampling of rotamer conformations.

Thank you in advance!

Maria.

@flag_ddg_low

-in:file:s input_files/min_cst_0.5.5flz_C_0001.pdb 

-ddg::mut_file input_files/mut_file.dat 

-ddg:weight_file soft_rep_design 

-database /gs/project/ear-065-aa/rosetta_src_2017.45.59812_bundle_12nodes/main/database/ 

-fa_max_dis 9.0 

-ddg::iterations 50 

-ddg::dump_pdbs true 

#-ignore_unrecognized_res 

-ddg::local_opt_only true 

-ddg::suppress_checkpointing true 

-in::file::fullatom 

-ddg::mean true 

-ddg::min false 

-mute all 

-ddg::output_silent true 

-out:level 400

wt_S360D.out SCORES

SCORE:     score     fa_atr     fa_rep ...
SCORE:  -686.234  -3344.916    279.393 ...
SCORE:  -686.234  -3344.916    279.393 ...
SCORE:  -686.234  -3344.916    279.393 ...
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -685.691  -3344.808    278.848
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393
SCORE:  -686.234  -3344.916    279.393             

Category: 
Post Situation: 
Mon, 2018-02-12 12:14
shadrinams