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Constraints

Correct way to force a specific histidine tautomer

Category: 
Constraints

 

I need protonation on the epsilon 2 nitrogen (HIE, HSE) and not on the (HID, HSD). The reason for this is that HID is mechanistically wrong and plays havok with my ligand.

Even though MutateResidue in pyrosetta does not accept the `mutate_self` argument it appears it calls HID HIS_D and HIE HIS and the mover thinks of them as not self of each other, so this works with switching and the heavy atoms are kept in place.

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Limit on backbone movement in relax?

Category: 
Constraints

Hi, I am using Rosetta 3.7 and the following flags for relax:

relax.linuxgccrelease -s complex.pdb -out:suffix _relax -nstruct 5 -relax:default_repeats 5 -out:path:pdb ./ -out:path:score ./ -ignore_unrecognized_res

I was wondering if there are any default restraints on backbone displacement in this, I believe in principle unconstrained, procedure.

With thanks and best regards,

Szymon

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Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

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Error Implementing Match Style Constraints

Category: 
Constraints

Hello,

I'm docking a small molecule into an enzyme utilizing using match style constraints and the EnzRepackMinimize Mover.   The constraint is between my small molecule and a cofactor in the enzyme.

I've generated the params file for both my small molecule and the cofactor.  When I run my script with the following distance constraint, everything works fine.

CONSTRAINT:: distanceAB:  1.2 0.1     1000  0    2

When I run my protocol trying to turn on the covalency term as in the following line

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Ligand question - aromatic bonds not being enforced?

Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

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Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo

Category: 
Constraints

I'm running into some issues applying the DRRAFTER instructions to model RNA loops between several distinct rigid-body helices, and am asking for advice here on how to proceed.

My goal is to rebuild the loop structures between two base-paired regions opf a stem loop. A fake secondary structure is like so:

>...5'-strand-of-pieceA...stemloop...3'-strand-of-pieceA

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Relax with constraints

Category: 
Constraints

Hi everyone,

I am a newbee in Pyrosetta, and I am trying to learn how to relax with constraints. I wanted to do distance constraints, but I am not sure if I am doing it right or wrong at all.  The score came out to be almost the same for with and without the constraint. Can anyone give me any advise? 

#------------------------Set up Score Function-----------------------

scorefxn = get_fa_scorefxn() 
score_before = scorefxn(pose)

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problems with implementing NOE constraints

Category: 
Constraints

Hi I'm running csRosettaCM with POMONA alignments and I would like to include NOE constraints in my models. Some of my constraints are on the side chains, therefore I cannot implement them in centroid mode, and would like to implement them in the full atom mode. However, it seemed like csRosetta has ignored my cst_fa_file and did not take in the constraints on the side chain. Any suggestion on how to fix this? And if it is possible to run csRosetta in full atom mode directly?

I have the following in my flags file:

-cst_fa_file noe_fa.cst

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