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%time results = list(xml_obj(pose_obj)) error

Submitted by TENY BAEK on Wed, 2022-11-02 23:31
Category: 
PyRosetta

08.02-Ligand-Docking-pyrosetta.distributed.ipynb

When I ran the following syntax in this file, an error came out and it did not proceed.

if not os.getenv("DEBUG"):

    %time results = list(xml_obj(pose_obj))

I also set up Conda on Google Collabor
There is an error, do you know how to solve it?

The results of the implementation were as follows

 

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PyRosetta - Scripts

Issues compiling Rosetta on stampede2

Submitted by Ajlukasiewicz on Wed, 2022-11-02 13:54
Category: 
Compilation

Hi everyone,

I am trying to compile rosetta3.13 on stampede2 using the SCons assistant as described in the documentation. 

I am using the command:  

./scons.py -j1 bin mode=release bin extras=mpi

which has repeatedly given the error

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Rosetta 3 - Build/Install

Failure to produce a cst file

Submitted by biotech on Wed, 2022-10-26 11:17
Category: 
Constraints

Hi, I generated a mincst.log using the below command:

minimize_with_cst.default.linuxgccrelease -s fe.pdb  -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/protein-institute/ROSETTA/rosetta_bin_linux_2020.08.61146_bundle/main/database -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false > mincst.log

then produced mincst.log file was employed for generating a cst file as input for the high-resolution protocol of ddg_monomer using the below command:

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Rosetta 3 - General

Ligand Rotamer Control in Macther

Submitted by Hirbond on Tue, 2022-10-25 13:01
Category: 
Docking

I am trying to run matcher with several residue constraints, and have already benchmarked the constraints individually and combined. Problem is that my ligand has several rotamers and once I enable the rotamers consideration in the matcher, the match enumeration makes the run impractical. I could solve this by removing the ligand rotamer consideration for the constraints that don't need it. Is there a way to do this for individual constraints?

 

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Rosetta 3 - Applications

Setting pivots points for GenKIC

Submitted by almeida85 on Tue, 2022-10-25 02:32
Category: 
Non-Canonical Peptides

Hi all,

I want to use GenKIC to generate macrocycles of a peptide bound to a receptor with the anchor design approach. Previously, I used simple_cycpep_predict, from the command line, to generate the candidates, but not bound to the receptor.

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Forums: 
Rosetta 3 - Applications

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