RosettaCommons - Loop Modeling

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Error Run Blueprint File

ileanexis — Thu, 07 Mar 2024 18:28:20 +0000

This error appear when I try run the Blueprint file for a missing loops.

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I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi

Edward — Sat, 25 Nov 2023 12:58:53 +0000

Take 6A5E for example,it has multiple breaks. i try to feed a blueprint file with all loops,however it turn out only the first loop was remodel .guess what when i view it in pymol i still got the same number of break .

here is my command$> mpiexec -np 18 remodel.cxx11threadmpiserialization.linuxgccrelease @missing_resi_loop

and my flag file

-loops
-in:file:s FER-LLG2.pdb
-remodel:blueprint ferllgb.remodel

-run:chain B
-remodel:num_trajectory 1
-remodel:quick_and_dirty

-out:path:all output_files
-out:file:scorefile all_missing_loops.sc

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error in loop remodeling

syntekabio2019 — Wed, 05 Apr 2023 08:00:15 +0000

Hi I'm trying to fill the missing loop with remodel.linuxgccrelease in rosetta

for some pdb, there's no problem in filling missing loop

but I got following error with certain PDB

core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLL | aa = .......
core.fragment.picking_old.vall.eval.ABEGOEval: abego = LLLLLLL
core.sequence.ABEGOManager: [ ERROR ] Unrecognized abego index: L

ERROR: Unrecognized abego
ERROR:: Exit from: src/core/sequence/ABEGOManager.cc line: 408
protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job PTPRB_2i5xB_UA5_0001

I searched a lot in google , but I couldn't figure out what 'Unrecognized abego index: L' means

Does anybody know how to figure out this problem?

Attached files are:

input PDB : PTPRB_2i5xB_UA5.pdb

blueprint file : PTPRB_2i5xB_UA5.remodel

flag file for remodel run : flags

log file : log_PTPRB_2i5x

command line : remodel.linuxgccrelease @flags

flags file look like following

-in:file:s PTPRB_2i5xB_UA5.pdb
-remodel:blueprint PTPRB_2i5xB_UA5.remodel

-run:chain A
-remodel:num_trajectory 1

-out:path:all output_files
-out:file:scorefile PTPRB_2i5xB_UA5.sc

Attachment	Size
blue print file	2.27 KB
input pdb	178.21 KB
log file	19.84 KB

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Protein Protein Docking with Linker

mrinal — Mon, 20 Mar 2023 22:58:06 +0000

I am trying to dock to two proteins where the ends should be connected by a polyglycine linker. Is there a tutorial on protein protein docking constrained by a polyglycine linker. I would want to vary the linker and see the effect on the protein protein docking.

Mrinal

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Segmentation fault with nstruct > 1

Brian Wiley — Mon, 13 Feb 2023 04:46:41 +0000

I am running loop model with the remodel protocol (remodel.static.linuxgccrelease). It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault. Anyone experience this before?

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Loop modeling

Robertofg — Tue, 22 Nov 2022 08:34:52 +0000

Hello,

I have a basic question about loop modelling. Can I use the edges as cutpoint or they should be excluded?

For instance, if my loop goes from residues 100 to 109, can residue 100 to be a cutpoint?

Thank you in advance,

Roberto

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GeneralizedKIC disulfide closure

Ken — Tue, 16 Aug 2022 20:32:10 +0000

Hi all,

I have been banging my head against the wall on this for a while now, and I think it's time to get help. Here is my problem. I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me.

Here is what I have done. I have a 7mer peptide and I am able to use GenKIC to close via head-to-tail, but when I try to close the loop via disulfide linkage, it errors out with the message "Mover make_disulfide not found in map".

Here is what I have run that works:

rosetta_scripts.static.linuxgccrelease -nstruct 10 -in:file:s input/CAAWAAC.pdb -in:file:fullatom -write_all_connect_info -parser:protocol xml/closeH2T.xml -jd2:failed_job_exception false -mute protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter core.chemical.AtomICoor core.conformation.Residue

This is the one that errors out:

rosetta_scripts.static.linuxgccrelease -nstruct 10 -in:file:s input/CAAWAAC.pdb -in:file:fullatom -write_all_connect_info -parser:protocol xml/closeDS.xml -jd2:failed_job_exception false -mute protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter core.chemical.AtomICoor core.conformation.Residue

Does anybody know what the error message is complaining about?

Best,

Ken

Attachment	Size
Head to tail xml that works	3.58 KB
disulfide xml that does not work	3.27 KB
toy structure	7.83 KB

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Designing Feasible Backbones

csvajda — Sat, 13 Aug 2022 15:08:13 +0000

Hi there!

In the process of trying to learn protein design for the last year and a half I have been focusing on using the newest and best tools for designing sequences. And the tools for designing a sequence to match a conformation seem to be reaching a level, such as with the protein MPNN release, that they're almost plug and play.
But I've come to realize that just because a backbone looks realistic doesn't mean it is. As a proxy to check this, when designing a sequence with either trRosetta or MPNN and then running it through a program like AlphaFold or RoseTTAfold I can see pretty quickly if the structure/sequence are in the ballpark or are totally unfoldable.
My question is this: how does one avoid the process or blind trial and error when trying to get a backbone that fits the needs of a project but is also in realistic conformation space? Is it truly a numbers game of eyeballing realistic structures and repeating? Or are there tools and metrics to do the grunt work prior to sequence design?

any answers would be greatly appreciated!

-Cooper Svajda

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Antigen-antibody modeling

aastha.pal — Mon, 27 Jun 2022 16:34:56 +0000

I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."

Not sure what is going wrong. I checked the numbering but it looks correct. Please advise on this. Thanks!

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