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Constraints

reading of AtomPair failed in relax with constraint

Category: 
Constraints

Hello,

I am relaxing a protein with a chemically bound ligand (attach as C14_SPF). The ligand is composed of Phosphopantethine and acyl together which are bound to ALA (residue 36 of chain B) of my protein. Actually, the residue 36 was originally SER which is bound to Phosphopantethine and acyl, but for modeling I took the OG of SERin Phosphopantethine and converted SER to ALA.

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How to specify constraints during fold-and-dock?

Category: 
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

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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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