Scoring

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Problems with Cterm_amidation.txt

Submitted by helenah on Thu, 2020-10-08 04:52

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Scoring

Hi everyone,

I am trying to use Cterm_amidation.txt. I would like to replace -OH in the C-terminal end with -NH2. However, I get the following error

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'standard.wts' does not exist

Submitted by almeida85 on Mon, 2020-09-14 02:26

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

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Scoring docking error

Submitted by almeida85 on Wed, 2020-09-02 01:32

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Scoring

Hello,

I want to do a simple scoring of some docking solutions. My flags are:

-in:file:l list.txt
-score:weights docking
-out:file:scorefile scoring/score_docking.sc

... but I get this error:

[ ERROR ]: Caught exception:

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density scoring

Submitted by Tianyang89 on Sat, 2020-08-29 04:54

Category:

Scoring

Hi,

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?

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what factors determine the lowest (best) LigInterfaceEnergy score?

Submitted by jmaly on Wed, 2020-08-26 13:07

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.

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Generating Atom Pair Constraints

Submitted by Peik on Wed, 2020-08-05 15:39

Category:

Scoring

Hi,

I'm trying to mutate and minimize a complex with atom pair constraints applied to the residues around the mutated position, but the constraints do not seem to be getting applied to my pose. This is what I have:

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Solved

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PyRosetta - General

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Controlling Input in the Tutorial

Submitted by Smbat on Wed, 2020-07-29 22:41

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Scoring

Hi All,

I am trying tor learn Rosetta basics using the tutorial https://www.rosettacommons.org/demos/latest/tutorials/input_and_output/input_and_output

However, when I try like it is instructed in the tutorial following error happens:

Infinity4s-iMac-2:main smbatgevorgyan$ cd demos/tutorials/input_and_output/

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Quick mysql output question

Submitted by pedro.guillem on Thu, 2020-07-23 03:45

Category:

Scoring

Hello everyone,

I have compiled rosetta with OpenMPI and MySQL. It works.

I'm using relax to pack+score a few thousand poses but the output will create lots of tables with A LOT of info. I just need to output the pose name and the total score of the pose.

I was wondering which flags should I use (@relax.flags) to output only the SCORE table to MySQL, not the atom coordinates and the rest of the info.

By this I mean the same info as the default.sc file, but sent to a single table in mysql.

Thanks in advance.

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Segfault when loading scorefxn() and load_from_pdb()

Submitted by mm on Wed, 2020-07-22 03:00

Category:

Scoring

PyRosetta

Hi,

I am trying to load a structure from PDB and then calculate pairwise residue energies between residues in the structure. For this, I want to first load the scorefxn and then the structure (or viceversa), but whenever I try, either of them gives me a segfault, i.e. if I do scorefxn = get_fa_scorefxn(); pose_from_pdb() the latter crashes and if I do the opposite, get_fa_scorefxn() crashes.

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