RosettaCommons - Rosetta 3 - Applications

Post Situation:

Solved

Abnormal output of ScoreCutoffFilter

DivingWhale — Fri, 31 May 2024 01:46:14 +0000

Hi everyone!

The output of `ScoreCuoffFilter` looks like this:
ResResE Res1 Res2 fa_atr fa_rep fa_sol fa_intra_r fa_intra_s lk_ball_wt fa_elec pro_close hbond_sr_b hbond_lr_b hbond_bb_s hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planar ref rama_prepr total
ResResE 83_6531 72_6532 -1.663 0.129 1.501 0.000 0.000 -0.424 0.258 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.198
....

The filed of Res1 or Res2 looks strange. In older version, this field will have the one-letter amino acid name, chain ID, and residue index. Why are name and chain ID replaced by numbers? Is there any update on this filter or it's replaced by other filter? I can't find documentation.

Rosetta version: rosetta.binary.linux.release-371

XML file:
<ROSETTASCRIPTS>
<SCOREFXNS>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Neighborhood name="nbrhood" resnums="35A-290A"/>
<Not name="others" selector="nbrhood" />
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="turn_off_others" selector="others">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<RestrictToRepacking name="rtrp"/>
</TASKOPERATIONS>
<FILTERS>
<ScoreCutoffFilter name="scofilter" report_residue_pair_energies="1" cutoff="5000000.0" />
</FILTERS>
<SIMPLE_METRICS>
</SIMPLE_METRICS>

Could you please help me with this?

Category:

Scoring

Forums:

Post Situation:

Error in snugdock application

syntekabio2019 — Tue, 28 May 2024 07:59:54 +0000

Hi all

Recently I;m involved in antibody related project

While I'm running snugdock application with my antibody( H chain: Lchain) and antigen complex

I got following error :

Can't find residue type 'VRT' in type set of mode fa_standard

In my PDB , only standard amino acid residues are there.

and I think VRT means something like virtual related object.

I don't know why this kind of error occur

Attached file is my pdb file with this error

Any kind of comments would be welcomed

Thanks

Attachment	Size
test.pdb	463.79 KB

Category:

Docking

Post Situation:

Forums:

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

Category:

Post Situation:

Forums:

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

Category:

Post Situation:

Forums:

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)

Category:

Forums:

Post Situation:

"Segmentation Fault" error occurred when Running a pilot job

Cooben — Fri, 19 Apr 2024 02:47:02 +0000

Hello everyone! I'm trying to run a command in paper_interface_design_pilot_1000_commands.list generated in step 12 “Running a pilot job”
the commands are as follows:

cd /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/paper_interface_design_pilot_1000/00000

/home/cooben/rosettatest/rosetta_src_2021.07.61567_bundle/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/cooben/rosettatest/cao_2021_protocol/paper_interface_design.xml -beta_nov16 -in:file:silent /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/pilot_splits/xat.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/cooben/rosettatest/cao_2021_protocol @/home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/design.flags > log.log 2>&1

An error occurred after execution:
Segmentation Fault

My design flags：
-script_vars patchdock_res=97,98,99,100,101,102,103,104
-script_vars runpsipred_single=/home/cooben/rosettatest/psipred/runpsipred_single
-dalphaball /home/cooben/rosettatest/rosetta_src_2021.16.61629_bundle/main/source/external/DAlpahBall/DAlphaBall.gcc
-indexed_structure_store:fragment_store /home/cooben/rosettatest/ss_grouped_vall_all.h5
-dunbrack_prob_buried 0.8
-dunbrack_prob_nonburied 0.8
-dunbrack_prob_buried_semi 0.8
-dunbrack_prob_nonburied_semi 0.8

I'm using Rosetta version rosetta-3.13 with GCC 6.3.0 as the compiling environment (while separately building rosetta-3.9 with GCC 6.1.0). Has anyone encountered this error before? How should I resolve it?
Thank you for your suggestions！

Attachment	Size
log.log	59.87 KB
ROSETTA_CRASH.log	5.43 KB

Category:

Post Situation:

Solved

Forums:

Error in rosetta minimization

syntekabio2019 — Wed, 17 Apr 2024 14:04:17 +0000

Hi all

Recently I'm now doing large scale protein ligand docking using rosetta

while I'm doing , I got the following warning not error

This should never happen after extending the interface
protocols.ligand_docking.ligand_options.MinimizeBackbone: (6) [ WARNING ] for backbone minimization to work properly, a stretch of at least 4 residues needs to be allowed to move. Stretch between 298 and 299 is too short. This should never happen after extending the interface
protocols.ligand_docking.ligand_options.MinimizeBackbone: (6) [ WARNING ] for backbone minimization to work properly, a stretch of at least 4 residues needs to be allowed to move. Stretch between 298 and 299 is too short. This should never happen after extending the interface

The program seems to get stucked in loop and continuously print this warning , never ending

I suspect the input might have a problem, but I can not figure out

Attached are my input file

Any kind of suggestion would be welcomed

Thanks

Attachment	Size
crystal_complex.pdb	212.69 KB

Category:

Docking

Post Situation:

Forums:

Chemically Modified Residues

Model GFP chromophore(cro) using NCAA or NC backbone method?

lei — Thu, 04 Apr 2024 13:23:06 +0000

Dear users,

Because GFP chromophore (CRO) comes from cyclization of three amino acids: S, Y, and G, I am not sure how to model it.

(1) In "Using NCAAs in Protein-Peptide Interface Design", Ornithine can be seen as a modified form of Lys: only one amino acid.

However, CRO includes three amino acids, so there are total three R groups. When preparing rotamer library, CHI angles from three R groups seems confusing.

(2) In "Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design", all five cases in this paper are non-peptidic oligomer scaffolds (noncanonical backbones): each oligomer has repeated unit (NC backbone unit). But there is only one CRO in GFP, it is not repeated unit.

If it is possible, could you please give me some hints, or any tutorial on modeling CRO using rosetta?

Many thanks!

Lei

Category:

Forums:

Post Situation: