RosettaCommons - Design

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Error about using BuildDeNovoBackboneMover

ng98 — Wed, 29 May 2024 08:47:05 +0000

Hi! I am sorry for asking about the segementation fault problems because this be caused by many things. It is the first time I wrote a Rosetta scripts and I really stuck on the script.

I tried to use BuildDeNovoBackboneMover to generate backbones based on the antibody structure I got, I wrote the xml file but it shows:

[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]
[END_CRASH_REPORT]

This is my XML file:

<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn_16" weights="beta_nov16"/>
                <ScoreFunction name="sfxn" weights="beta_nov16"/>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <AntibodyRegion name="Abselect" region="cdr_region" cdr_definition="Chothia"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <AddCDRProfileSetsOperation name="AddCDRs" cdrs="all cdrs" include_native_restype="true" picking_rounds="3"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ScoreType name="score_filter" score_type="sfxn_16" threshold="0" confidence="0"/>
                <ResidueCount name="res_count_all" max_residue_count="9999" confidence="0"/>
        </FILTERS>
        <MOVERS>
                <BuildDeNovoBackboneMover name="dn_backbone" dump_pdbs="false" >
                        <BlueprintArchitect name="bp_arch" blueprint="template1.bp"/>
                        <RemodelLoopMoverPoseFolder scorefxn="sfxn_16"/>
                </BuildDeNovoBackboneMover>
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
                <Add mover="dn_backbone"/>
        </PROTOCOLS>
        <OUTPUT />
          
         
</ROSETTASCRIPTS>

My input is :rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol blueprint_build.xml -corrections::beta_nov16 -s model-0.relaxed_0003.pdb -out:prefix test_

The model-0.relaxed_0003.pdb file is attached, I think it is because my input pdb or the blueprint file? But I do not know how to modify it based on my purpose. Could anyone please help me solve the problem? Thank you!

Attachment	Size
This is blueprint file.	1.16 KB
model-0.relaxed_0003.pdb	308.96 KB

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Is it impossible to use the ddg_monomer function on a non-monomeric structure?

Wexter300 — Sat, 25 May 2024 21:16:36 +0000

Hi,

I have been working on finding the most stable form of a tetrameric structure with 4 idenitical chains. I tried the ddg_monomer module. I could not get it to work using the original strucutre, but got it to work when I tried it with a single chain. Is there no way to get it to work with a tetramer? I have found an alternative using pmutscan to look for stabilizng mutations, but I would rather use ddg if possible. I was considering using ddg_monomer on a single chain and then just docking 4 of those mutated chains using rosetta_docking, but I don't know if that will take into account any interactions between reisudes in the tetramer structue that would not be accounted for when mutating only a single chain.

Much appreciated,

Wexte300

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Question about blueprint file generation

ng98 — Fri, 24 May 2024 10:02:50 +0000

Hi, I am trying to use Rosetta to design an immunoglobulin structure based on the existing antibody structure. I read the paper :Chidyausiku,Tamuka M.,et al."De novo design of immunoglobulin-like domains".Nature Communications,vol.13,2022,https://doi.org/10.1038/s41467-022-33004-6. And I found in the paper that the backbone generation was made by Rosetta Monte Carlo fragment assembly using blueprints specifying secondary structures and ABEGO tor-
sion bins, together with hydrogen bond constraints specifying β-strand pairing. I used getBluePrintFromCoords.pl to get general blueprint file, but I was confused about following steps.

I got the general blueprint file like this:

1 Q .
2 V .
3 Q .
4 L .
5 V .
6 Q .
7 S .
8 G .
9 S .
10 E .
11 L .
12 K .
13 K .
14 P .
15 G .
16 A .
17 S .
18 V .
19 K .

.......
But I got problems about how to modify this general blueprint file, for example: how to determine which residue could be rebuilt or leave it alone; how to decide which residue shoulld be insert in which place? Are there any tutorials or paper that I could learn to get detailed explanations on how to build blueprint files? Or are there any movers or tools that I could use to help me solve those problems? I would appreciate if someone could help me on these questions. Thank you so much!

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Error about rifdocking step 19 motifgraft mover

ng98 — Wed, 22 May 2024 09:25:18 +0000

Hi I've got provblem with Rifdocking protocol 19 when I test one of commands:

protocols.jd2.JobDistributor: [ WARNING ] mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01900_0001 reported failure and will NOT retry protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MotifGraft - motif_grafting======================= protocols.motif_grafting.movers.MotifGraftMover: Executing Motif Graft Mover protocols.motif_grafting.movers.MotifGraftMover: Target scaffold size: 65 protocols.motif_grafting.movers.MotifGraftMover: Motif size: 7 protocols.motif_grafting.movers.MotifGraftMover: contextStructure size: 211 protocols.motif_grafting.movers.MotifGraftMover: Target scaffold numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Motif numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: contextStructure numChains: 1 protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 7 protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment/size combination there are not fragments that match the size of your motifs. protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job mot_ferr_ems_00043_000000149_0001_58_64_E_HHHH_bc_01944_0001

[ ERROR ]: Caught exception:

File: src/protocols/motif_grafting/movers/MotifGraftMover.cc:546 For this scaffold there are not suitable scaffold grafts within your constrains

I followed the protocol and my command shown below: /home/gaon/biosoftware/rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/gaon/cao_protocol/cao_2021_protocol/paper_motif_graft.xml -beta_nov16 -in:file:silent /home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/scaffold_splits/xah.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/gaon/cao_protocol/cao_2021_protocol @/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/grafting.flags -parser:script_vars motifpdb=/home/gaon/TYRP1/protocol/rifgen63_263/fd_output_splits/motifing/motifs/mot_ferr_ems_00043_000000149_0001_58_64_E.pdb.gz hotspots=1:2:3:4:5:6:7 -out:prefix mot_ferr_ems_00043_000000149_0001_58_64_E_

Could anyone please tell me why this error happened? Could it be fixed or just because something else? I will appreciate for the help. Thank you!

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PDB file showing error - missing heavyatom: OXT on residue LYS:CtermProteinFull 59

intomybioverse — Thu, 16 May 2024 06:38:57 +0000

Hello everyone!

I am redesigning the specificity of a protein and make it interact with a DNA sequence. I am trying to run the RosettaDNA application program based on the demos. However, I am getting this error.

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 89 in file myfile.pdb. Best match rsd_type: ADE:UpperDNA
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 59

The PDBfile that I am using is a docked protein-DNA complex (prepared using HADDOCK). The arg file and script file are attached for your reference. Can you please help me to troubleshoot?

Attachment	Size
Arg file	627 bytes
rosettascript file	1.72 KB

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Rosetta 3 - Applications

Problems met when do H3_modeling in the antibody design protocol

ng98 — Mon, 13 May 2024 01:40:19 +0000

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!

Attachment	Size
h3_modeling-0.log	104 bytes
ROSETTA_CRASH.log	8.57 KB

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Rosetta 3 - Applications

Question about computer specifications requirement of RFdiffusion

ng98 — Mon, 06 May 2024 09:18:54 +0000

Hi! I would like to use RFdiffusion for binder design, but I wonder if there is any computer specifications requirement for running this deep learning model? Thank you for your help.

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Issues with rosetta numbering and keeping ligand when relaxing molecule.

Wexter300 — Sun, 28 Apr 2024 21:37:22 +0000

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:52:25.363712
[APPLICATION]: /pub/erikps/Rosetta3.14/main/source//bin/cartesian_ddg.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-39)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
 -in:file:s=relax/RNaseH_raw_0002.pdb -in:file:extra_res_fa=PC3.params -score:weights=ref2015_cart -score:fa_max_dis=9 -ddg:mut_file=mutations -ddg:iterations=1 -ddg:dump_pdbs=false -ddg:cartesian -ddg:bbnbrs=1

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x63e45f0]
[0x63e3373]
[0x648e4f6]
[0x90451f]
[0x655101]
[0x419b9d]
[0x6c05e04]
[0x6c06081]
[0x6549b6]

[END_BACKTRACE]

[FILE]: src/core/conformation/Conformation.hh
[LINE]: 509
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.



[END_MESSAGE]
[END_CRASH_REPORT]

I have been trying to perform some DDg calculations on a structure with a heme in the middle. I followed the tutorial for DDG and relaxed the structure. I then used the relaxed structure accompanied with a mutations file to perform the DDg caluclations. There are two Issues:

1. The relaxed structure is missing the heme molecule, no heme is present at all

2. A rosetta numbering error occours

I have tried modifying my mutations file to include a chain ID, but the error persists. I have a parameter file that should account for the heme.

The structure is a tetramer with a heme in the middle, each chain of the tetramer is identical to the other chains.

This is the content of the rosetta crash log file. I have also uploaded my mutations file, parameters file, and the original structure as well as the relaxed structure misisng the heme.

Attachment	Size
PC3.txt	10.6 KB
Original protein structure	166.61 KB
Structure rosetta relax protocol made; missing heme	143.12 KB

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Segmentation fault (core dumped) in rosettaDNA.static.linuxgccrelease

intomybioverse — Sun, 28 Apr 2024 11:51:34 +0000

Hello everyone!

I am trying to redesign the protein-DNA interface to introduce novel interactions between a protein and a DNA molecule using the RosettaDNA application suite.

I am getting this error after running the program. Can you help to fix this?

There are 19 dna positions:
60 (pdb B 1) DT <=> DA 96 (pdb B 37)
61 (pdb B 2) DA <=> DT 95 (pdb B 36)
62 (pdb B 3) DA <=> DT 94 (pdb B 35)
63 (pdb B 4) DT <=> DA 93 (pdb B 34)
64 (pdb B 5) DA <=> DT 92 (pdb B 33)
65 (pdb B 6) DC <=> DG 91 (pdb B 32)
66 (pdb B 7) DG <=> DC 90 (pdb B 31)
67 (pdb B 8) DA <=> DT 89 (pdb B 30)
68 (pdb B 9) DC <=> DG 88 (pdb B 29)
69 (pdb B 10) DT <=> DA 87 (pdb B 28)
70 (pdb B 11) DC <=> DG 86 (pdb B 27)
71 (pdb B 12) DA <=> DT 85 (pdb B 26)
72 (pdb B 13) DC <=> DG 84 (pdb B 25)
73 (pdb B 14) DT <=> DA 83 (pdb B 24)
74 (pdb B 15) DA <=> DT 82 (pdb B 23)
75 (pdb B 16) DT <=> DA 80 (pdb B 21)
76 (pdb B 17) DA <=> DT 79 (pdb B 20)
77 (pdb B 18) DG <=> DC 78 (pdb B 19)
81 (pdb B 22) DA (unpaired)

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Rosetta 3 - Applications

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