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Small Molecules

Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

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The question about ligand score function

Category: 
Small Molecules

Hello!

These are many .wts file in database\scoring\weights.
I  don't clearly know which weight is used in which occasions,
and  just use score function according to papers.


I  read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
 and its recommend references.

Post Situation: 

splitfile.py

Category: 
Docking
Small Molecules

I'm looking at the methods of the following paper:

Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.

and trying to follow along (to eventually adapt it for my own work).

I've hit a snag at one of the commands:

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Molecular oxygen

Category: 
Small Molecules

I am planning on docking a ligand in a cavity with a heme and a constrained oxygen. Whereas I can make params of ligands and non-canonical residues, I cannot for molecular oxygen (OXY). It is not in the database either. Molfile_to_params.py gives the following 

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PEPSPEC

Category: 
Small Molecules

Dear Readers,

I have been trying to use the pepspec application /main/source/bin/pepspec.linuxgccrelease @xyz.options with following as the contents of .options file

-in:file:s letssee.pdb
-pepspec:pep_anchor    90
-pepspec:pep_chain    A
-pepspec:n_prepend    0
-pepspec:n_append    0
-pepspec:n_peptides    100

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Altering substrate specificity

Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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relax - P6G molecule

Category: 
Small Molecules

I would like to relax some decoys with a small molecule, P6G, in a specific location, extracted from a homologous protein from PDB. For doing so, I have saved a PDB file with the protein as chain A and P6G as chain B. Rosetta does not recognize P6G as a residue, for obvious reasons.

Is there a straightforward way to run the relax protocol in this situation?

 

Best,

Post Situation: 

symmetric design in the presence of a nonsymmetric ligand

Category: 
Design
Symmetry
Small Molecules

Hello,

I am trying to design a C3 symmetrical protein with a ligand bound at the C3 interface. What is the best way around this in RosettaScripts? I was thinking to first symmetrize the pose with SetupForSymmetry and then add the ligand with AddChain mover. But it seams, SetupForSymmetry is not compatible with extra_res. As soon as the script arrives at SetupForSymmetry, it throws the following error:

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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".

 

Post Situation: 

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