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Enzyme Design

Convert Rotamer Vector to Chi Angles

Category: 
Enzyme Design

Dear PyRosetta Community,

I am attempting to find the closest rotamer to each residue in a protein and then obtain the chi angles for each of those closest rotamers. I have successfully used the core.pack.dunbrack.rotamer_from_chi function to obtain the rotamer vector, thanks to the topic "Rotamer information from pose." Is there a reverse function, essentially "chi_from_rotamer," that will return the chi angles that correspond to the rotamer vector that rotamer_from_chi yields?

Thank you.

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Files for Spatial Constraints

Category: 
Structure prediction
Enzyme Design
Constraints

Hi guys,

I am trying to locate the files to generate spatial constraints from homologous template structures for comparative modelling as given in the Thompson and Baker paper from 2011. I can't find them anywhere in the ROSETTA directories. Are they available anywhere?

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Running the Matcher on multiple PDBs

Category: 
Enzyme Design

I'm having issues getting the Matcher to run. My .flags file looks like this (file names changed):

-s PDB1.pdb

-s PDB2.pdb

-match:lig_name LIG

-match:scaffold_active_site_residues POS.pos

-match:geometric_constraint_file CST.cst

-extra_res_fa PARAM.params

-ex1

-ex2

-use_input_sc

Both PDBs are in the same directory, and the Matcher runs fine in that it will get a number of matches for PDB1.pdb, but then it just ends... see:

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rotamer library in coupled_moves

Category: 
Docking
Enzyme Design
Small Molecules

Hello, 

 

Recently, I had a chance to see a presentation about coupled_moves. There is hardly any information about it since the paper isn't published yet but I figured I would give it a try anyway. What I want to do is to redesign enzyme specificity for a new substrate . The problem is including rotamers library of my new substrate. 

 

I created ligand rotamers with Frog2 (no acces to MOE or OpenEye) and created params files with:

 

"molfile_2_params.py rotamers.mol2 --conformers-in-one-file".

 

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Issues running the Matcher in 3.4 and 3.5

Category: 
Enzyme Design

Hello,

I've run into an issue getting the Matcher to work correctly. I have attached a log file with the error I am receiving (In this particular case I ran 3.4, but the error is the same for 3.5). The specific error is below:

ERROR: olditer != target_restype_index_map_.end()
ERROR:: Exit from: src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc line: 677

Any help would be greatly appreciated and if additional information is needed I would be glad to provide it.

Thanks!

Post Situation: 

Enzdes constraint file not defined correctly

Category: 
Enzyme Design

Hi everyone,

I am doing enzyme design using a cst file and it seems that my constraint file is not properly defined.
I wish to define constraints such that the peptide N forms hydrogen bond with my ligand in the binding pocket. At the same time I would like this residue to be any other residue except proline. So i defined my cst as follows;

CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: O8 P1 O7
TEMPLATE:: ATOM_MAP: 1 residue3: EY1

TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 residue1: ACDEFGHIKLMNQRSTVWY

Post Situation: 

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