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DDG_monomer application

Category: 
Design

Hello,

I am new in Rosetta. I would like to compare stability of the wild-type and mutated proteins using DDG_monomer. Since my protein is quite big I use the low resolution protocol for now. The results that I obtained look weird to me. Could you please tell me if they are supposed to be like this or I do something wrong?

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Icouldnot find DDMI protocol for design protein

Category: 
Design

Hello

I want to design my protein by Rossetta according to DDMI protocol that is used in article"computational design of PAK1 binding protein".In this article designing of protein PAK1 done by protocol DDMI in Rossetta version 2.1. but i could not find this protocol in Rossetta 3.0. Do this protocol exist in Rossetta 3.0 with different name or this protocol removed in Rossetta3.0?the command line of this protocol according to the article mentions below:

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Rosetta Script for ddg_monomer protocol 16

Category: 
Design

Hi all. 

I want to predict the effect of a point mutation in a protein stability. I have the .pdb crystal structure of the wild type.

After a literature search, I think this paper presents the most comprehensive study of different methods for this analysis DOI:10.1002/prot.22921. So I want to do the prediction using their protocol 16. I also found python code for this protocol here: https://github.com/Kortemme-Lab/ddg/tree/master/protocols/ddg_monomer_16.

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cyclization_type flag in simple_cycpep_predict

Category: 
Structure prediction
Design
Constraints

Dear Rosetta users or developers,

 

I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).

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EnergyMethodCreator error when writing custom energy method

Category: 
Design

Hi,

I have been trying to write a custom energy method class  following the workshop #11 from the Gray lab and this tutorial http://graylab.jhu.edu/pyrosetta/downloads/scripts/test/T850_SubClassing.py . Here is what I have:

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side chain repacking error

Category: 
Design

Hello!

- I tried fix_bb script and used a resfile > 1 A NATAA, 2 A NATAA and so on as per sample resfile but it shows an error "core.pack.task.ResfileReader: On line 2, the chain identifier 'NATAA' must be just a single character in [_A-Za-z] (note the chain identifier is case sensitive)." I could not understand it.

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output file in ddg calcualtion

Category: 
Design

Hello!

While using ddg_monomer script, I tried flag --ggd:dump_pdbs 'false' and 'true' both, but it is not producing any output pdb file?  any suggestion?

 

"-ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration"

 

Thanks!

Malkeet

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