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enzyme design and scoring function

Category: 
Enzyme Design

Hello,

In enzyme design, the scoring function is enzdes.wts. Do we need to change it to the most recent scoring function (ref2015)?

Also, is SR_*_interf_E_1_2 the binding energy? can we say this score is related to specificity of an enzyme?

 

any suggestion is appreciated.

Post Situation: 

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:

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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: 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

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How to provide multiple templates for Robetta with RosettaCM option?

Category: 
Structure prediction

The FAQ of robetta said "You can load multiple templates, modify the alignments, add constraints, and more before submitting.“ However, I cannot find the option for loading multiple templates on the Robetta webserver. Is that possible?

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RosettaCM: threading okay, but hybridize loses many secondary structure

Category: 
Structure prediction

I use two templates to run the RosettaCM, each template representing different parts of the target. The threading step can retain most of the secondary structure. However, when doing the hybridize step, one part in the target loses half of its beta-sheets. Is this a common issue?

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RosettaCM: "Ligands must be added to all templates"

Category: 
Structure prediction

The RosettaCM requires Ligands must be added to all templates with a non-zero weight in the XML file!

In my case, the templates represent different parts of the target, so some template includes the ligand while some template does not. Do I really need to add the ligand to the template that does not have the ligand?

If it is necessary, how to do it? It is not likely to use some alignment to "estimate" the ligand location in the template.

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Add a ligand with only one atom (i.e. Zn) to the RosettaCM

Category: 
Structure prediction

My understanding for adding the ligand is to use the molfile_to_params script to generate XXX.cen.params, XXX.fa.params, XXX.tors files. 

My ligand is just a one atom Zn. When molfile_to_params script is used, I got this error

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How to Perform point mutations with NCAA

Category: 
Structure prediction

Hello Everyone,

I am trying to mutate multiple residues of a peptide with NCAA to determine their structure and ΔΔG of mutation on Rosetta. 

I would be grateful if anyone could share any research article, material or guidance to proceed on this matter.

 

P.S. - I am a beginner at Rosetta without any bacl ground in coding or bioinformatics. Any help and advice is appreciated.

 

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Flex-pep-docking (ab-initio mode)

Category: 
Docking

Hello all,

To perform the Flex-pep-docking protocol (ab-initio mode), I need to create fragment files for the target peptide (with 8 residues). I have tried to do this with the make-fragment.pl script . However, I get the attached error. I have already installed the last version of Blast tools. please let me know what is the problem and how it can be solved?

Post Situation: 

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