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Meaning of Metalbinding_constraint

Category: 
Docking
Scoring

Dear Sir and Madam,

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).

Post Situation: 

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.

Post Situation: 

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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……………omit………………

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Post Situation: 

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,

Can you please advise me on how I should go about calculating atom-wise energy terms?

Should I simply sum pairwise energies for the nearest N-neighbours or is there a better way of doing this?

 

Thanks!

Post Situation: 

Individual Residue Energy

Category: 
Scoring

Hi everyone,

I'm trying to get the energies of individual residues in a pose and am encountering an error that I can't seem to find much information on. Here is a sample of my script:

from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.scoring import *

pyrosetta.init('-ignore_zero_occupancy false')

pose = pose_from_pdb(pdb_file)

sfxn = create_score_function('ref2015.wts')

score = pose.energies().residue_total_energy(1)

And here is the error I encounter:

Post Situation: 

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