​​B​3​-protein design using rosettaScript movers

[Anonymous]

​
Hello everyone,
I am tryi​ng to perform a ​​B​3​protein​ design tests ​using ​rosettascript (rosetta demo model). I have 3 ​designable ​positions ​and I am interested in the functionalit​ies​ of ​the movers:​”RandomMutation” and “GreedyO​ptMutationMover​”

Using these movers, none of my design positions have been taken into account as a designable! In the log file, there are warnings
indicating that there is no design position.

Does anyone have any ideas?
I have attached the log file, the resfile, input pdb I have used.
My command line is:

startpdb=rosetta_inputs/redesign/acdy_LLLL_LLLL.pdb

rosetta_scripts.default.linuxgccrelease -database $rosetta_database
-in:file:s $startpdb
-parser:script_vars resfile=resfile_gdOptMC
-parser:script_vars pos=2A,5A,8A
-score:weights mm_std
-out:file:scorefile gdOptMC.fasc
-out:file:silent gdOptMC.dat
-resfile resfile_gdOptMC
-parser:protocol gdOptMC.xml
-overwrite
-multi_cool_annealer 10
-reinitialize_mover_for_new_input
-in:file:fullatom true
-out:file:fullatom true
-use_input_sc
-no_optH false
-ex1
-ex2
-packing::pack_missing_sidechains false
-packing::extrachi_cutoff 0
-in:file:repair_sidechains
&>gdOptMC.log

Thanks,

Seydou

[Anonymous]

I believe that the RandomMutation and GreedyO​ptMutation movers are set up in such a way that they will only recognize designable residues for cannonical amino acids – non-canonical amino acids aren’t treated by them.

Instead, what you probably just want to do is use the PackRotamersMover with your resfile. (The one you already have is probably great.) Slightly contrary to its name, the PackRotamersMover will design if it’s given a resfile which allows for design at that position. (Design is really just packing with the identity of the sidechain allowed to change in addition to the conformation.)

[Anonymous]

Thanks for your reply.

[Author]

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