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Scoring

Energy scores of D-amino acids

Category: 
Scoring

I used PyMOL and Maestro to invert the chirality of single L-amino acids into D-amino acids, as well as all L-residue polypeptide to all D-residue polypeptides. Even though they are mutually mirror images, but D-amino acids and D-polypeptides all have remarkably higher energy scores than their counterparts by using PyRosetta scoring protocol. May I ask what are some possible reasons for this difference? I am wondering whether it is caused by computational error or more delicate design, such as strong and weak nuclear forces, in Rosetta tool.

Post Situation: 

optimisation of a protein-protein interface

Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

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Docking Prepack protocol working or not ?

Category: 
Docking
Scoring

Hi Rosetta community, 

I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning : 

[ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

and my score_sc file contains 0.000 for the total score for every generated structure.

Here the command I used to run prepack:

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score_jd2 errors out with: ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'

Category: 
Scoring

I am trying to calculate rmsd using a template pdb structure using score_jd2. When I try to run the following command,

$ROSETTA3/bin/score_jd2.macosclangrelease -in:file:silent decoys_alp_tcn.out -evaluation:rmsd 2alp.pdb `cat pdb_list` FULL -out:file:silent rescored_decoys.out

it errors out saying ERROR: Unrecognized residue: SO4. Then I rerun the same with -ignore_unrecognized_res

Then I get the following error:

ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'

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[dev] not seeing energy in pose row for new energy term in design

Category: 
Scoring

Hi all,

I made an EnergyMethod to add a few new energy terms and am trying to use them in fixbb. However, for two of these terms, the 'pose' row shows only 0, even though the individual position rows show non-zero values that sum to non-zero. This is how I set my terms in the emap:

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[dev] Using h-bonding values in new energy term

Category: 
Scoring

Hi all,

I'm implementing a new energy term and need to weight it based on the bb h-bonding energy of this residue and the two residues it is bonded to. It is a ContextDependentOneBodyEnergy and I have everything working except this weight. Obviously rosetta already has methods that calculate hbond_lr_bb and hbond_sr_bb. My question is - what is the best way to get the hbond energys of the residues in my energy method?

Thanks!

-Igor

Post Situation: 

Interface Analyzer Segmentation Fault

Category: 
Scoring

Hello,

I relaxed the homodimeric biological assembly of PDB 1ISA, and am trying to use Interface Analyzer to calculate the interfacial energy between the subunits. I have cleaned the strucutre to removed all the water, metals, et.c and leave only the protein residues. Below are the command line flags I am using:

Post Situation: 

Different weights in the constraints for each stage of AbinitioRelax

Category: 
Scoring

As each stage of AbInitio protocol call a different function (score0, score1, score2, score5 e score3), it appears to me that use a single cst_weight in my command line doesn't make sense (a single weight for every single stage). For that reason, I would like to test different weights for cst in each stage of Abinitio.

Post Situation: 

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