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Problems met when do H3_modeling in the antibody design protocol

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Problems met when do H3_modeling in the antibody design protocol
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Hi! I am trying to run the antibody design protocol. But when I try to do H3 modeling using the abH3.flags downloaded from the Rosetta3.13 whose content shown below:

#how to run antibody mode -- these are the current best-practices
-antibody::remodel              perturb_kic
-antibody::snugfit              true
-antibody::refine               refine_kic
-antibody::cter_insert          false
-antibody::flank_residue_min    true
-antibody::bad_nter             false
-antibody::h3_filter            false
-antibody::h3_filter_tolerance  5
-antibody:constrain_vlvh_qq

#more standard settings, for packages used by antibody_H3
-ex1
-ex2
-extrachi_cutoff 0

#these are standard settings for kic/ngk
-loops:legacy_kic false
-loops:kic_min_after_repack true
-loops:kic_omega_sampling
-loops:allow_omega_move true    ### remove 'true' and loop::?
-kic_bump_overlap_factor 0.36
-loops:ramp_fa_rep
-loops:ramp_rama
-loops:refine_outer_cycles 5

#These enable the kink constraints.  Increase the weight if you want tighter kink constraints.
-antibody:constrain_cter
-constraints:cst_weight 1.0

The first problem I met is: [FILE]: src/utility/options/OptionCollection.cc [LINE]: 1468 [START_MESSAGE]

Option matching -antibody:remodel not found in command line top-level context

Did you mean: -loops:remodel

                            -remodel

[END_MESSAGE] [END_CRASH_REPORT]

After I deleted "-antibody::remodel", another error occurred:

[FILE]: src/utility/options/OptionCollection.cc [LINE]: 1468 [START_MESSAGE] Option matching -antibody:refine not found in command line top-level context

Did you mean: -RBSegmentRelax:rb_file

                           -SSrbrelax:rb_file

                           -antibody:refine_h3

                            -loops:refine

                            -packing:resfile

                            -smhybrid:fa_refine

                            -smhybrid:refine

[END_MESSAGE] [END_CRASH_REPORT]

I changed "-antibody :: refine" to "-antibody::refine_h3" as it shows in the ROSETTA_CRASH.log and rerun again, but the third problem came out: Error: Illegal value for boolean option -antibody:refine_h3 specified: refine_kic

This is my command line:

nohup /home/gaon/biosoftware/rosetta313/main/source/bin/antibody_H3.hdf5.linuxgccrelease @abH3.flags -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint -out:file:scorefile H3_modeling_scores.fasc -multiple_processes_writing_to_one_directory -out:path:pdb H3_modeling > h3_modeling-0.log 2>&1

I used rosetta version 3.13 and I used antibody_H3.hdf5.linuxgccrelease. I would appreciate if anyone could tell me how to fix those errors and what should I changed to continue the protocol. Thank you!

AttachmentSize
h3_modeling-0.log104 bytes
ROSETTA_CRASH.log8.57 KB
Category: 
Post Situation: 
Sun, 2024-05-12 18:40
ng98

-antibody:refine and -antibody:refine_h3 are different options.

The protocol changed a bit, and now, like the -antibody:remodel flag, the -antibody:refine is no longer necessary -- simply delete it from your command line.

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P.S. We're updating the site, and as part of that we're moving the forums to Github Discussions.

If you have additional questions or are still having issues, please feel free to open up a thread over there.

Thu, 2024-06-20 13:11
rmoretti