You are here

Home

Scoring

Hydrogen Bonding Distances and Atom identification

Submitted by kmolloy717 on Fri, 2021-06-25 08:15
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: 
Unsolved
Forums: 
PyRosetta - General

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

Submitted by sgaray on Thu, 2021-06-24 14:47
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: reading in mutfile
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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Meaning of Metalbinding_constraint

Submitted by Corvin on Wed, 2021-05-19 07:54
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: 
Unsolved
Forums: 
Rosetta 3 - General

hpatch commands and how to identify patches

Submitted by Bianca Oliva on Thu, 2021-04-29 04:02
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: 
Unsolved
Forums: 
Rosetta 3 - Applications

Clustering problem

Submitted by Suuo on Tue, 2021-04-20 01:40
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

………………………………

……………omit………………

………………………………

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

PDB Clustering

Submitted by code_Monkey on Mon, 2021-04-05 10:40
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: 
Unsolved
Forums: 
Rosetta 3 - Applications

Show I be using beta_nov16 scorefxn?

Submitted by matteoferla on Thu, 2021-04-01 04:06
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: 
Unsolved
Forums: 
Rosetta 3 - General

Atom-wise energy terms from nearest N-neighbors

Submitted by jasiozaucha on Thu, 2021-03-25 14:49
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: 
Unsolved
Forums: 
PyRosetta - General

Pages

Subscribe to RSS - Scoring