Broken protein chain in out put

[DanielLevinLab]

Hi,

I design a protein-ligand interaction with rosetta however the output is comping out as a broken chain while the whole sequence is intact, is there a known reason to what causes it?

The ligand is already placed in the binding pocket and there are no clashes

[ajasja]

Probably not enough information to answer this question. How did you redesign, what does the log say, are there any errors.

[DanielLevinLab]

I used a protocol called COMBS from degrado lab to design binding site and then I use rosetta to design the rest of the protein
I looked just now at the logs and here is a warning I get that I didn't see before hand:
core.optimization.AtomTreeMinimizer: [ WARNING ] ***************************************************************
core.optimization.AtomTreeMinimizer: [ WARNING ] ** WARNING: Non-ideal minimization used with a ScoreFunction **
core.optimization.AtomTreeMinimizer: [ WARNING ] ** which isn't set up for non-ideal minimization **
core.optimization.AtomTreeMinimizer: [ WARNING ] ***************************************************************

[NooraAz]

It would be great if you could provide the code and inputs, or a link to them, so we can reproduce the error. My guess is your protein already has a jump. You can check this with pose.annotated_sequence( ) and pose.fold_tree().

[DanielLevinLab]

Input.zip

Thank you for the quick reply here is my input

[NooraAz]

Thanks! and your command line + flags?

[DanielLevinLab]

-parser:protocol flexbb_design_protocol_ligand_docking.xml
-overwrite
-nstruct 1
-ignore_zero_occupancy false
-s AB6H-5.pdb
-extra_res_fa AXA.params
-out:path:all output/
#-out:file:silent 1.out
-out:file:scorefile score.txt
-packing:linmem_ig 10

/sci/labs/jshifman/sergeib/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /sci/labs/jshifman/sergeib/rosetta_bin_linux_2021.16.61629_bundle/main/database/

[NooraAz]

Sorry I couldn't reproduce your job, because some files like no_met_thr_ser_asn.comp, netcharge.charge, resfile.txt, constraints.cst ... are not provided. But looking at your script, I don't see any obvious faults and the input pose has no jumps as well.

Just a question to help you debugging. Does the break always happen at the same place? if yes, where?

[DanielLevinLab]

oh yeah these are additional files that are needed to roseta but since this is the first round I didn'y add constraints.

The breaks are random I think I guess you could just run relax protocol on in it will have the same effect and you will probably won't need anything else aside from the input

[roccomoretti]

The error with the "Non-ideal minimization used" is due to the bondangle="true" bondlength="true" that you're including in your FastRelax. The way to fix it is to either remove those entries, or alternatively use ref2015_cart instead of ref2015 in your ref15_1 definition. (Either will likely work for you.)

That change could indeed cause arbitrary "broken" backbone chains, as the bond lengths can vary and stretch without being properly penalized.