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protein ligand docking

Submitted by patrickchirdon on Sun, 2018-12-30 15:07
Category: 
Docking

Hello!

I'm not able to generate a score.sc file because something is not allowing me to dock my ligands to my protein.  I get the error

 Cannot normalize xyzVector of length() zero
Error: [ ERROR ] 
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

Here's an example of my params file.  I've attached a copy of my ligand/receptor .pdb and my dock.xml as well:

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Rosetta 3 - General

Pyrosetta doesn't recognize the correct docking partners

Submitted by hamedkhakzad on Sun, 2018-12-23 11:54
Category: 
Docking

Hi all,

I can run rosetta docking protocol on my pdb file and there is no problem when I define partners as "MN_A". However, the same doesn't work on pyrosetta demo code of docking. I tried to solve this in several different ways by changing the docking jump value or etc but nothing acheived! Output models are still wrong in the format of M_NA. How can I fix this?

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PyRosetta - Scripts

Error when using RabD with a nanobody.

Submitted by zhangying1990 on Mon, 2018-12-17 04:40
Category: 
Design

Hi Everyone,

Recently, I am using RabD to design my nanobodies, But I can not perform it smoothly:

 

>>>Error returns:

ERROR] Exception caught by JobDistributor for job complex.1_0001

 

File: src/protocols/antibody/AntibodyInfo.cc:1117

 

L1 start resnum not found in pose: 24 L

Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB.

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Rosetta 3 - General

Add hemes to cytochrome structures

Submitted by BuddySphinx on Sun, 2018-12-16 13:46
Category: 
Structure prediction

Dear all,

I am using abintio protocol to predict a cytochrome structure. After I generated the model, it did not give HEME locations. The pdb output only contains the regular protein residues, but missing the location of hemes. I am wondering is there anyway to tell Rosetta also predict the hemes? 

Thank you

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Rosetta 3 - General

reporting bugs? (erraser in rosetta 3.10)

Submitted by meyer on Fri, 2018-12-14 09:40
Category: 
Compilation

Hi,

Is this the right place to report bugs that have appeared in erraser?  If not, could someone point me to the correct location?

These appear to be occuring in the rosetta 3.10 release (some in python code, others appearing to be in c++ code); and do not appear in erraser from rosetta 3.7; and occur when using the demo example from https://www.rosettacommons.org/demos/latest/public/erraser/README.

 

Best,

Pete

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Rosetta 3 - Applications

Model truncated proteins

Submitted by BuddySphinx on Wed, 2018-12-12 10:32
Category: 
Structure prediction

Dear all,

I just started to use Rosetta and I am trying to model my protein with truncated sequence (First ~200 aa). I have pdb file of the full sequence and I would like to know the structure will look with first ~200 aa. Which protocol is better for me to use? Comparative modeling or Ab initio modeling? I am also curious about what that input native proteins is doing? Should I just provide my full sequence pdb file?

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Rosetta 3 - Applications

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