RosettaCommons - Docking

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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

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How do I implement more CPU cores in the execution of FlexPepDock?

ChoripanSalado — Thu, 02 May 2024 15:55:45 +0000

Hello all. I am a university student currently doing my thesis, and I really don't know if this topic has been adressed before, but I couldn't find anything like my question.

For my thesis I need to use the FlexPepDock program of Rosetta in a local Linux machine. As the subject says, I want to implement more cores in the processing of my samples, because one job is generally taking a very long time while it uses only one core of the CPU. The lab provided me with a machine that has 8 cores dedicated for my analisis (without crashing the system), and I'd like to know if I can speed up things a bit with more processing power in one docking.

I am aware that I'm capable to run multiple FlexPepDock jobs locally using these cores, but as I said, I want to dedicate more cores to a single job.

I am no Linux pro or anything like that, so if anyone has an idea and can make me a step by step list of how to make this possible (if it is), I would be very grateful :)

Thanks in advance for all your answers.

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clustering PDBs from docking

jbujons — Wed, 24 Apr 2024 15:34:14 +0000

Hi,

I performed a protein-protein docking within rosetta by using a single receptor structure and several conformations of the same ligand protein. Now I am trying to cluster the results (aprox 1000 structures) using the cluster application included in rosetta by running:

cluster.linuxgccrelease -in:file:l pdblist -in::file::fullatom

I found that the result of this is a relatively small number of clusters, but the disparity of RMSDs inside each cluster is quite large: there are structures that differ by up to 50 A in RMSD relative to the best scored structure in the cluster, which is non-sense. I read some posts saying that rosetta does a previous superposition of structures before doing the clustering, so I guess that this is the reason for what I am seeing: once supeposed, all the structures are very similar and all of them exhibit low RMSD values, therefore the clustering application groups all of them in a few clusters.

Therefore, what I need is to perform the clustering without a previous superposition, which I read is possible but cannot find any info in the documentation pages about how to do that. I would very much appreciate if somebody can point where this info can be found or what would be the right commands to achieve that.

Regards,

Jordi

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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

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Canceling jobs - RosettaDock5.0

katie — Tue, 09 Apr 2024 19:30:08 +0000

On April 3, I submitted three identical jobs listed below:
21428
21427
21425

I want to cancel the jobs but when I hit “Cancel” nothing happens. How can I kill these jobs?

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Hamiltonian Exchange

JSK — Mon, 18 Mar 2024 19:48:32 +0000

I ran the below command for docking ;

$PATH_dir/bin/rosetta_scripts.mpi.linuxiccrelease -run:n_replica 1 -out:level 300 -mute all_high_mpi_rank_filebuf -out:nstruct 4 -in:file:s top1.pdb -in:file:native native.pdb -parser:protocol dock.xml -evaluation:DockMetrics -DockMetrics true -score:weights muds_2021 ~~ -partners AB_C -out::file::output_pose_cache_data false -out:path:all output -out:file:silent decoys.out -out:file:scorefile scores.fsc -run:intermediate_structures -jd2:mpi_timeout_factor 0 -ignore_zero_occupancy 0 -multiple_processes_writing_to_one_directory -database $PATH_dir/database

Then, they showed "ERROR: For HamiltonianExchange the number of exchange cells 3 has to be consistent with the option -run:n_replica 1".

but I already input "-run:n_replica 1" in the above command...

Please let me know how I can solve this problem...

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Hamiltonian Exchange

JSK — Mon, 18 Mar 2024 19:44:27 +0000

I ran the below command for docking ;

Then, they showed "ERROR: For HamiltonianExchange the number of exchange cells 3 has to be consistent with the option -run:n_replica 1".

but I already input "-run:n_replica 1" in the above command...

Please let me know how I can solve this problem...

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Error in score funtion "hack_elec 0.42"

intomybioverse — Sun, 17 Mar 2024 13:33:15 +0000

Hello everyone!

I am getting this following error when I am trying to run a rosettaDNA application program in which i want to change the specificity of a protein so that it binds to a target DNA. In most published articles, I have seen "hack_elec 0.42 " or similar values. However, it's not working in my case. Can you help me with this?

core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: optimizedenergyfxn.wts
score_typeextract failed: hack_elec

ERROR: bad line in file optimizedenergyfxn.wts:hack_elec 0.42
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 455

Attachment	Size
This is the book I am referring to.	413.9 KB

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several question in mpensemble dock

lluoto — Tue, 12 Mar 2024 14:54:28 +0000

Hey guys, I counterpart with problems as topic saying:

First, I want to use others computational results as reference to optimized docking option, so I have to relax them into same scorefunction, meanwhile relax the inputs which generate from different methods for better results and avoid disulfide bonds error due to different scorefunction, right?

however, as I run rosetta_scripts.linuxgccrelease for mpfastrelax on my identical subunits multi-chain, error occurs as mpfastrelax_log.txt describe, seems the beginning mover cause the problem(flag as mpfastrelax file),but when I use mprelax for ensemble (flag relax_for_ensemble), it complete the work. I avoid use relaxed model to generate initiate model and failed during prepack (flag prepack_ensemble) as log in prepack_log.txt

Second, as look at in rigid dock us franklin2019 scorefunction, it seems only output the interface residues score about i_sc etc. but still little terms without explain in reference or tutoria, like dock_ens_conf and st_rmsd, and does single protein with relax in franklin2019 will output score terms correctly? could I relax all the inputs in same scorefunction? And what about the I_sc terms range in the membrane environment? Besides mpframework_docking_fa_2015 output terms CAPRI_rank value to 1.84467e+19, does it refer to CAPRI competition scoring criteria and correct?

Third is the docking ligand restrict,mpdocksetup method will split a subunit of multi chain complex and dock partner in the place, so I generate initiate model manually and I have already point out the partner as ABCD_EFGH (flag MPdock),but finally the chain B still disperse from multi-chain complex and act as docking ligand, move around as picture(only unexcepted ligand chain b show in different color ,other partner did not move, attached initiate model and several results), seems I have to convert multi-chain into single chian? But the gap convert into super long loop must be extraordinary.

and suggest might be helpful, thanks.

lluoto

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