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Scoring function for disordered peptide ddG calculations?

Submitted by austin.weigle.usda on Tue, 2024-05-28 14:52
Category: 
PyRosetta

I am looking to do a ddG analysis on some peptide structures that I have developed through simulation. Previously, I have used pyrosetta for performing ddG analyses on membrane proteins. In that case, I was able to use the franklin_2019 weights as my scoring function.

Poking around, I have seen that there are a good number of weights files listed as:
/PATH/pyrosetta/lib/python3.9/site-packages/pyrosetta/database/scoring/weights/*.wts

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PyRosetta - Applications

Error in snugdock application

Submitted by syntekabio2019 on Tue, 2024-05-28 00:59
Category: 
Docking

 

 Hi all

 Recently  I;m involved in antibody related project

 While I'm running snugdock application with my antibody( H chain: Lchain) and antigen complex

 I got following error :

 Can't find residue type 'VRT' in type set of mode fa_standard

 In my PDB , only standard amino acid residues are there.

 and I think VRT means something like virtual related object.

 I don't know why this kind of error occur

 Attached file is my pdb file with this error

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Rosetta 3 - Applications

Question about blueprint file generation

Submitted by ng98 on Fri, 2024-05-24 03:02
Category: 
Design

Hi, I am trying to use Rosetta to design an immunoglobulin structure based on the existing antibody structure. I read the paper :Chidyausiku,Tamuka M.,et al."De novo design of immunoglobulin-like domains".Nature Communications,vol.13,2022,https://doi.org/10.1038/s41467-022-33004-6. And I found in the paper that the backbone generation was made by Rosetta Monte Carlo fragment assembly using blueprints specifying secondary structures and ABEGO tor-

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Rosetta 3 - General

Unable to get non-commercial license to get username/password

Submitted by David123 on Fri, 2024-05-17 15:39
Category: 
PyRosetta

Hi team,

As noted in the steps to get non commercial license, there is a license form people can fill up to register for username/password to use Pyrosetta. Seems the form is unable to find.

Thanks for assistance.

 

david

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PyRosetta - Build/Install

PDB file showing error - missing heavyatom: OXT on residue LYS:CtermProteinFull 59

Submitted by intomybioverse on Wed, 2024-05-15 23:38
Category: 
Design

Hello everyone!

I am redesigning the specificity of a protein and make it interact with a DNA sequence. I am trying to run the RosettaDNA application program based on the demos. However, I am getting this error.

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 89 in file myfile.pdb. Best match rsd_type:  ADE:UpperDNA
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LYS:CtermProteinFull 59

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Rosetta 3 - Applications

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