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Constraints

Using logic in resfile, Rosetta Scripts

Category: 
Constraints

Hi,

I am designing a protein-protien interface using Rosetta Scripts, and would like to use logic in the resfile. 

For example, if one amino acid at a given position is re-designed to be [list of aa], then the redesign at this other defined position should be limited to [list of aa]

Is this possible?

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Remodel with residue constraints

Category: 
Constraints

Hi,

I am trying to remodel a given structure where I want to replace a chain say B with same residues say alanines. How can I use remodel with constraints? To be more specific, how to write constraint files. I did look up the remodel documentation for the cst file. But, they describe atom level information. Is there a way to just do it at the residue level? (I mean, just give the residues I want to replace in the new structure?)

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Perform MPI relax with movemap files

Category: 
Constraints

Hi,

I want to relax around 3K structures. Also, I have a movemap file for each of these structures. How do I trigger mpi runs for relax with movemap files?

Earlier, when I did not need the movemaps, I used the following command:

mpiexec -np 32 $ROSETTA/bin/relax.mpi.macosclangrelease -in:file:l <pdb list file> -nstruct 20

But, now I want to perform relax with move map associated with each of the pdb file in the pdb list file. How do I do it?

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Design with limited number of aminoacids at given position

Category: 
Design
Constraints

Hi!

What is the easiest way to allow only a single residue type (e.g. Trp) at a given position during the design?

I use FastDesign Mover with symmetry. I thought about ReadResfile and PIKAA command, but perhaps it could be done directly from the Rosetta Script? Via task_operations=... ?

Best wishes,

Staszek

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lysine-aspartate isopeptide bond

Category: 
Constraints

Hello,
I am working with protein which have isopeptide bonds in them and I am not sure how to handle them.

An isopeptide bond is when a lysine residue forms an amide bond with an aspartate or asparagine (same result). Isopeptide bonds —in bacteria at least— have an O or N atom missing from the Asp, Asn or Lys and a CONECT at the end of the file and to the best of my knowledge there is no special HETATOM O-lysylaspartyl double residue.

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How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

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DomainAssembly Mover with constraints (using RosettaScripts)

Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

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dock & design

Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

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Enzyme Design with additional covalent backbone bonds

Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

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