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Molecular oxygen

Submitted by matteoferla on Sat, 2018-02-24 06:05
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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Rosetta 3 - General

PEPSPEC

Submitted by Neeraj on Wed, 2018-01-03 02:24
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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Rosetta 3 - Applications

Altering substrate specificity

Submitted by bp on Thu, 2016-12-22 02:45
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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Rosetta 3 - Applications

relax - P6G molecule

Submitted by allan.ferrari on Wed, 2016-11-30 05:01
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,

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Rosetta 3 - General

symmetric design in the presence of a nonsymmetric ligand

Submitted by msardejani on Fri, 2016-09-30 15:17
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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Rosetta 3 - Applications

rotamer library in coupled_moves

Submitted by mtyras on Fri, 2015-05-29 07:46
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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Rosetta 3 - Applications

ligand docking with rosetta_scripts.linuxgccrelease

Submitted by xpzhang on Thu, 2015-02-26 10:57
Category: 
Small Molecules

I installed the latest rosetta common (rosetta_src_2015.05.57576_bundle.tgz) and tried the following demo with error:
/demos/protocol_capture/2012/ligand_water_docking

setting ligand_soft_rep weight hack_elec to 0.42

ERROR: unrecognized score_type type hack_elec
ERROR:: Exit from: src/core/scoring/ScoreTypeManager.cc line: 477

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '1HXW_input_0001'
Error:

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Rosetta 3 - General

metal_ions formal charge question

Submitted by lah435 on Tue, 2015-02-03 09:35
Category: 
Small Molecules

Quick question: I've noticed that some of the .params files in residue_types/metal_ions have a "formal charge entry" such as for Zn: CHARGE ZN FORMAL +2, but some other divalent cations like Co lack this entry.

Is this entry even used by Rosetta?
Could some of these entries be incorrect?
Should the formal charge entry be added if I want to use that metal ion?

Thanks!

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Rosetta 3 - General

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Rosetta 3 - General

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