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non-zero ddG of binding even without mutations

Category: 
Design

Hello,

I was trying to work with the "calculate protein-protein ddG" tutorial. The tutorial comes with a resfile for mutating an Alanine with Tryptophan at residue 98. Following the steps gives, I get a ddG value of -6.6533 REU.

However, when I replace the line "98 D PIKAA W" with "98 D PIKAA A" (i.e. esentially replacing the alanine with alanine), I'm still getting a ddG value of 6.6643 REU. Can anyone point out why I might be getting a non-zero ddG even though I'm not even 'mutating' the proteins.

Regards,

top-gun98

Post Situation: 

Scoring correlation with electron density map

Category: 
Structure prediction

I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:

"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb  -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"

Post Situation: 

Changing amino acid profile while keeping the backbone conformation between 2 protein structures (need help)

Category: 
Design

Hello, i am a masters student trying to play around with rosetta. And i have a project in mind. I have two protein structures: nanocages. each with 60 monomers but the chains are a little bit different with different aa profiles. Now what I want to do is to make a structure with the backbone conformation profile of one of the nanocages but with the amino acid profile of the other one. How do i go about doing this? I'm sorry if I wasn't clear english is not my native language. 

Thanks for your help in advance. 

Post Situation: 

Intel MPI: early exit due to job process stopped.

Category: 
Docking

Hello, I am using rosetta docking_protocol compiled with Intel MPI (from Intel® oneAPI Toolkits 2020), and I have some problems / bug reports.

I requested 3 output poses with '-nstruct 3' and I ran 'mpirun -n 3 docking_protocol.mpi.linuxiccrelease ...' to start one master rank and two slave ranks. However, when one slave (rank 2) finished its jobs and master will send spin down signal:

Post Situation: 

Calculating SAP score using RosettaScripts

Category: 
Scoring

Hello,

I am trying to calculate the per residue SAP scores of a protein structure using Rosetta scripts. The .xml script I am using is shown below.

<ROSETTASCRIPTS>

    <SCOREFXNS>

    </SCOREFXNS>

    <RESIDUE_SELECTORS>

    </RESIDUE_SELECTORS>

    <FILTERS>

    </FILTERS>

    <SIMPLE_METRICS>

        <PerResidueSapScoreMetric name="sapscore"/>

    </SIMPLE_METRICS>

Post Situation: 

Set torsions for atoms in different residues

Category: 
Non-Canonical Peptides

I am working with a polymer with a non-aminoacidic backbone comprising two subunits, each defined as individual residues. I have already defined the params file for both subunits; however, I am experiencing issues exploring torsions between these connected residues. I am setting the angle movement using pose.conformation().set_torsion_angle(). This function has worked for angles between atoms inside the same subunit. However, when trying to set_torsion_angle() for atoms residing in different residues, I get the following error:

Post Situation: 

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