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Score function in protein-protein docking with constrains

Submitted by Zehui Zhou on Mon, 2023-02-06 03:31
Category: 
Scoring

Hi, everyone!

I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:

a. Whether the ref2015  or ref2015_cst function considers the ligand (with params file)?

b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?

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Rosetta 3 - General

No values for total score while running Rosetta score file.

Submitted by Shweata Maurya on Wed, 2023-02-01 02:05
Category: 
Scoring

I am running the Rosetta version - rosetta.source.release-334.tar.bz2 for designing two proteins but no values are generated for the total score. All the important files regarding this are attached. Please look at it and help me with this. 

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Rosetta 3 - General

Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi

Submitted by SamuelGong on Fri, 2023-01-27 06:20
Category: 
Scoring

Hi,

using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context

...................................

 

the flags and log file were attached.

Please help, thanks

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Rosetta 3 - General

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

Submitted by JW_24 on Tue, 2023-01-24 04:40
Category: 
Scoring

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

So far I thought the soft score function is supposed to feature lower repulsive terms.

ref2015_soft.wts:

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Rosetta 3 - General

What should I do to lower down the fa_sol scores?

Submitted by JasonIsaac on Mon, 2022-12-05 18:57
Category: 
Scoring

Greetings,

I ran a design protocol and I find my results score has high fa_sol scores like 250 around. What should I do to lower down the fa_sol scores? 

I used ResidueSelector to separate my alpha-helixs into three parts: buried, semi-buried and solvent exposure. And use resfiles to assign the amino acids, buried------hydrophobic, semi-buried------less hydrophobic, solvent exposure-------hydrophilic. 

And I am wondering if the fa_sol score of a model is too high, will it be insoluble in water after experimental expression?

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Rosetta 3 - General

Score.sc file showing total score 0 for all protein structures created

Submitted by aanshi on Wed, 2022-11-23 11:13
Category: 
Scoring

Hello, I am trying to use Rosetta to design the interface of my protein and would like to rank the predicted structures based on their scores however, after running the job, all the files show 0 for the total score. Could anyone take a look at my xml script and flags file (in the pdf file) to see if I'm missing something or how else to fix this issue? Thanks in advance!

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Rosetta 3 - Applications

Error with sequence_tolerance.R processing the checkpoint files, *.ga.entities and *.ga.generations.

Submitted by He Xiao on Mon, 2022-11-07 03:41
Category: 
Scoring

Hello,

the output files, *.ga.entities and *.ga.generations, were produced by sequence_tolerance application. 

When I tried to use sequence_tolerance.R processing the output files, I got the following error:

> source("/usr/local/rosetta_src_2021.16.61629_bundle/main/tools/analysis/apps/sequence_tolerance.R")

> process_seqtol("./2I0L_A_C_V2006_0001.ga.entities")

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Rosetta 3 - General

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