# Scoring

## Hydrogen Bonding Distances and Atom identification

Category:
Scoring

We are using PyRosetta 2.83 to identify hydrogen bonds between atoms.  For example, take the following code:

pose = pose_from_pdb("/Users/kmolloy/Downloads/2ezk.pdb")
hbond_set = pose.get_hbonds()
hbond_set.show(pose, 5)
hbond_set.show(pose,7)

This results of running this code are shown below:

Post Situation:

## Error using ddg_monomer application (Assertion pose.residue(resnum).name1() == wt failed)

Category:
Scoring

Hi, I've unsuccessfully tried to run ddg_monomer app. I want to study the estability of a small protein after some mutations. I have used a pre-minimized pdb file as an input file, but I have the following error (last lines):

apps.public.ddg.ddg_monomer: wt is N resnum is 25 and mut is P
apps.public.ddg.ddg_monomer: wt is Y resnum is 60 and mut is H

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## Meaning of Metalbinding_constraint

Category:
Docking
Scoring

Would anyone here be kind to explain the following statement about metalbinding_constraint or send the relevant paper?:

1. The (bio)physical meaning of metalbinding_constraint. I would like to find out, the underlied forces and energies, including such thermodynamical parametres, as enthropy, enthalpy and so on and so forth. Hereby, the next question arises from this point.

2. How this 'metalbinding_constraint' is calculated (I mean the formula, but, nevertheless, I am open to any explanation).

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## hpatch commands and how to identify patches

Category:
Scoring

Hi everyone!

I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.

I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).

I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.

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## Clustering problem

Category:
Scoring

Hi guys.

I met a problem when I was doing the clustering. I excuted this command but it was unexpectedly ended killed and had no result. I've 200 pdb files in this folder.

I'll be really grateful if it can be solved.

\$ /home/suuo/Rosetta/main/source/bin/cluster.default.linuxgccrelease -database /home/suuo/Rosetta/main/database -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out in:file:s *.pdb

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## PDB Clustering

Category:
Scoring

Hello,

I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.

I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work.

I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.

I'm attaching the log files. Can you help me with these issues? Thank you in advance!

Post Situation:

## Show I be using beta_nov16 scorefxn?

Category:
Scoring

ref2015 is the default at least in pyrosetta and is beta_july15 without the need for the boolean option correction:beta_july15 to be set.

In the cartesian ddG paper, Park et al. 2016, beta_nov16 is made, which has several difference (below, code used here).

Post Situation:

## Atom-wise energy terms from nearest N-neighbors

Category:
Scoring

Hello PyRosetta users,