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Segmentation Fault during prepacking

Submitted by Sunyp_IM on Fri, 2020-06-12 11:24
Category: 
Docking

Dear all,

   When I do prepack of a antibody-antigen complex with the following command,

mpirun -np 6 docking_prepack_protocol.mpi.linuxgccrelease\
  -in:file:s nb0-ag-start.pdb\
  -ex1\
  -ex2\
  -partners H_A\
  -ensemble1 nb_ensemble.list\
  -ensemble2 ag_ensemble.list\
  -docking:dock_rtmin\
  -out:path:all prepacking
 

I always get a "segmentation Fault" like the following: 

[END_BACKTRACE]

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Rosetta 3 - Applications

reading of AtomPair failed in relax with constraint

Submitted by hajar on Wed, 2020-06-10 10:02
Category: 
Constraints

Hello,

I am relaxing a protein with a chemically bound ligand (attach as C14_SPF). The ligand is composed of Phosphopantethine and acyl together which are bound to ALA (residue 36 of chain B) of my protein. Actually, the residue 36 was originally SER which is bound to Phosphopantethine and acyl, but for modeling I took the OG of SERin Phosphopantethine and converted SER to ALA.

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Rosetta 3 - General

Interface Analyzer with Glycans

Submitted by drewaight on Tue, 2020-06-09 20:06
Category: 
Scoring

Hello all, 

            Is it possible to run InterfaceAnalyzer with a structure with Glycans? Everytime I apply the InterfaceAnalyzerMover on my structure I get a segmentation fault. If I just delete the carbohydrates it works just fine. The pose has been processed with all of the usual flags(below). Is there some trick to using glycans and InterfaceAnalyzerMover or can someone point me in the right direction? Thanks so much.

                                                                                                        Drew

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PyRosetta - General

Difference between interface_delta_X and dG_separated?

Submitted by Nicole Deng on Sat, 2020-06-06 06:31
Category: 
Design

Hi, everyone!

I am using RosettaLigand design protocol to design some mutants, in order to improve binding affinity to a small molecule. When I was using InterfaceAnalyzer, there were 2 values representing binding affinity, interface_delta_X and dG_separated. I want to know the difference between these 2 values and which one I can use during the filter process.

Any suggestion will be appreciated!

Nicole

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Rosetta 3 - General

Error in building fragment_picker with boost_thread

Submitted by Ken on Thu, 2020-06-04 09:33
Category: 
Compilation

Hi all,

I am new to the whole Rosetta community and am asking for some help in compiling Rosetta3.  I have downloaded build Rosetta3.12 build 2020.08.61146 and tried to compile the thread boost version of fragment pick by using

./scons.py mode=release extras=boost_thread bin/fragment_picker.boost_thread.linuxgccrelease -j 20

The error message that I get is:

**************************************************

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Rosetta 3 - Build/Install

"Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease

Submitted by Sunyp_IM on Thu, 2020-06-04 05:53
Category: 
Structure prediction

Dear all,

I am trying to modeling a camelid antibody with the sequence (nb.fasta) as following:

$cat nb.fasta

>heavy
QVQLQESGGGLVQAGGSLRLSCAASGTIFETEGMGWYRQAPGKEREFVATIGGGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVIAFTEHKYSYWGQGTQVTVSSLE

 

I use antibody.linuxgccrelease to model it:

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Rosetta 3 - Applications

adding greek_alphabets in non-canonical AA parameter generation

Submitted by hajar on Wed, 2020-06-03 14:00
Category: 
Non-Canonical Peptides

Hello

I am running molfile_to_params_polymer.py to get the .params file for my non-canonical aa. But I got the error below. I think it might be due to the long chain of my non-canonical amino acid. I tried to increase the greek letters list in line 1655 of the script, but it did not work. Maybe it needs to modiy several lines of code.

Also, I got large numbers (as you see the error below).Can someone help to modify the code for my non-canonical  amino acid to resolve the error?

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PyRosetta - Scripts

Colab Install Help

Submitted by installhelp on Wed, 2020-06-03 07:26
Category: 
Compilation

I'm trying to install Pyrosetta using Colab with the workshop notebooks but I keep getting errors. The main error is locating the tar file in My Drive. The code I'm running is: 

#sys.path.insert(0, google_drive_packages_path)

 

# installing PyRosetta

if sys.version_info.major != 3 or sys.version_info.minor != 6:

    print('Need Python-3.6 to run!')

    sys.exit(1)

 

import_start_time = time.time()

 

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PyRosetta - Build/Install

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