Hi,
I am trying to design a higher affinity interface for my protein-protein heterodimeric complex.But I'm getting the error which says "ddg is 0.246217 failing".I'm using the script similar to minpac_optE_premin.xml in the interface_design_demo folder of rosetta_2015.05.57676.
I really need some help to make this work.
Thank you!
p.s- I'll provide any other information if you need
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The ddg filter in that xml file has a threshold of -15. That is, all poses that don't have a ddg -15 or better are thrown away. If you want to retain more poses--at least to make sure that your protocol is doing what you think it does--temporarily change that filter to a higher value (greater than e.g. 0.246217). Then you can lower it as you learn more about your system. (Maybe the wild type ddg is just -5 or something, so great redesigns might merely be -10!)
Also, how many structures are you making? The -nstruct flag controls how many, and since Rosetta's algorithms are Monte Carlo trajectories, some of them will always pass or fail some given filter.
Thanks for your reply!
1)I was making 50 structure and all of them resulted in the above error. The ddg for them was between -0.3 to -0.7 (I don't know why it is so low). But now I have changed the threshold value of ddg to -0.7 and am running the simulation with -nstruct 100 .
2)I have another question about the scoring function in this script.Is there any difference between using the 'score12' score function versus 'optE_inf_premin' weights that this particular script uses?
3)I have also used the online webserver RosettaDesign and it gave the following output file:
Mutation ddG_bind ddG_partnerA ddG_partnerB #Neighbors ddG_h_bond
187B L>W: -1.8 0.0 1.0 15 0.0
3A V>F: -0.9 -0.1 0.0 11 0.0
3A V>Y: -0.9 -0.1 0.0 11 0.0
3A V>W: -0.6 0.2 0.0 11 0.0
117B R>M: -0.5 0.0 -1.9 16 0.0
Do you know why it might be giving only these many mutations when the interface of the complex has over 20 residues?