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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.
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: Cannot open file "input_files/1qys.pdb"
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 362
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:
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
I have some questions about setting for scoring and weights. That would be really helpful if someone could answer the questions.
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?
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.