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Scoring

hbond_sr_bb and hbond_lr_bb for different chains

Category: 
Scoring

In the rosetta scoring function, what energy term describes backbone-backbone hydrogen bonding between residues on different protein chains

hbond_sr_bb                                Backbone-backbone hbonds close in primary sequence.  All hydrogen bonding terms support canonical and noncanonical types.
hbond_lr_bb                                Backbone-backbone hbonds distant in primary sequence.

 

Post Situation: 

Score function: unable to open input_files/1qys.pdb

Category: 
Scoring

Hello all, 

I am new to rosetta trying to follow the tutorials on line. I am currently working on with the mac binaries on MacOS mojave

Seems I cannot generate a score file in the working directory.

the following input is being done within source directory

INPUT: $ROSETTA3/bin/score_jd2.default.macosclangrelease -in:file:s input_files/1qys.pdb

 

Error:

ERROR: Cannot open file "input_files/1qys.pdb"

ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 362

Post Situation: 

Scoring functions: talaris2013 incompatible versions

Category: 
Scoring

 I'm tryintg to sort the generated sequences from the .spec output with the following command and I use the flag to activate talaris:

~/tools/analysis/apps/gen_pepspec_pwm.py 1cka_spec.spec 3 0.1 binding-prot_score pepspec_background.binding-prot-0.1.pwm -corrections::restore_talaris_behavior

But I get error:

Post Situation: 

'standard.wts' does not exist

Category: 
Scoring

Hi all,

I am trying to run the Pepsec demo and I got the following error:

ERROR: Unable to open weights/patch file. None of (./)standard.wts or (./)standard.wts.wts or /mnt/d/Softwares/Rosetta/rosetta_src_2020.08.61146_bundle/main/database/scoring/weights/standard.wts or /mnt/d/Softwares/Rosetta/rosetta_src_2020.08.61146_bundle/main/database/scoring/weights/standard.wts.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 3461

Post Situation: 

density scoring

Category: 
Scoring

Hi,

I have some questions about setting for scoring and weights. That would be really helpful if someone could answer the questions.

1.

I looked into the folder>   Rosetta/main/database/scoring,  there are loads of score files.I'm wondering  How to choose the right one.

Should I just use one for all applications? For example, If I use Rosetta3.12, should I use  ref2015.wts for relax, loopmodel,etc?

Could someone please kindly explain to me what's the difference between these score files?

Post Situation: 

what factors determine the lowest (best) LigInterfaceEnergy score?

Category: 
Docking
Scoring
Small Molecules

Hi everyone.

We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.

Post Situation: 

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