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Errors in Interface_design_demo

Category: 
Design

Hello there,

When I try to run the minpac_optE-premin under interface_design_demo, I got the following error message:

File: src/utility/options/OptionCollection.cc:239
ERROR:

File: src/utility/options/OptionCollection.cc:1324
Option matching -corrections:score:hb_sp2_peak_heigh_above_trough not found in command line top-level context

[ WARNING ] Tried to calculate the visibility of Tracer 'Error' before init() was called!
[ WARNING ] This tracer will not obey commandline options.

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Chemically bound ligand connection error

Category: 
Chemically Modified Residues

I am following the protocol for Relax Around A Chemically Bound Ligand

/path/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -s AcpP-TesA-C8.pdb -in:file:fullatom -extra_res_fa ./LG.params -cst_fa_file chemical_bond.cst -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -overwrite 

and I get the error 

Post Situation: 

protein ligand docking

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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Pyrosetta doesn't recognize the correct docking partners

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?

Post Situation: 

Error when using RabD with a nanobody.

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.

Post Situation: 

Add hemes to cytochrome structures

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

Post Situation: 

reporting bugs? (erraser in rosetta 3.10)

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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