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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: 

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