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Minimising space exploration during docking

Category: 
Docking

Hello,

I am trying to dock a single helix onto a specific region of a protein. When running a docking simulation using Pyrosetta the helix moves to another site on the protein. Is it possible to only allow the helix to explore a certain region of the target protein?

Many thanks in advance,

Alexander

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Snugdock+ensembledock usage

Category: 
Docking

Hi all,

I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.

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Help for a Beginner Needed! Installation on Win 8 Computer

Category: 
Compilation

Hi- Being very new to this, I've only had a chance to skim through the forums. I did have a few questions, though. As I'm new to using python and RC, I want to thank whomever for answering for their patience in helping me understand this.

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Questions for "modeling_instructions.pdf" in "Homology or Loop Modelling"

Category: 
Structure prediction

Dear Sir or Madam,
I am trying to following "modeling_instructions.pdf" in "Homology or Loop Modelling".

http://www.meilerlab.org/index.php/jobs/resources

The first thing I need help is
Section "2. Run ROSETTA Comparative Model protocol".
After typing the COMMAND FOR COMPARATIVE MODELING PROTOCOL (attached) into terminal, I got "Exit 255" in the prompt and "ERROR" in the comparative_model.log (attached). The options file is also attached.

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flexpepdock_score_only

Category: 
Scoring

Hi,
I used flexpepdock_score_only find the rmsca between 2 complexes. I also caculated the rmsca between the 2 complexes ((deltax^2+deltay^2+deltaz^2)^0.5) but the rmsCA score I got was different than the one I got using flexpepdock_score_only. Why is that happening?

Note - both complexes have the same sequence of aa.

Thanks!

Post Situation: 

Viewing and modifying hydrogen bond detection criteria

Category: 
Scoring

Hello! I have been working with PyRosetta for a while to model protein-ligand interactions. I was getting hydrogen-bond information from other software, but wanted to use PyRosetta's Hbond set for my pose. Rosetta did not find all the expected hydrogen bonds, so I wanted to check what criteria was used by Rosetta to find the HBs, and also see whether I could tweak these criteria in any way (things like maximum distance, or maximum angles, etc.).

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Rosetta membrane blastpgp/psiblast database problem for lips4 generation

Category: 
Membrane

I have run Rosetta membrane successful in the past, but it seems that now the blastpgp database necessary to run the run_lips.pl script is obsolete.
In the lastest BLAST release, blastpgp has been dropped entirely in favor of psiblast.
I am then blocked and I cannot generate the lips4 file using:
run_lips.pl <fasta file> <span file> <path to blastpgp> <path to nr database> <path to alignblast.pl script>

Is there a way of the run_lips.pl connecting the psiblast, or does it need to be modified?

Post Situation: 

Atom_.cc line 304

Category: 
Structure prediction

Hi list,
I'm running the minirosetta.mpi threading protocol and everything seems to be working fine.
The query silent is been regularly updated and I can extra pdbs from it.
However, from time to time get the following error message on screen.

ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 304

Any ideas?
Best.
Fred

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