Unsolved

The problem hasn't been solved

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

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

Post Situation:

Issues compiling Rosetta on stampede2

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

Post Situation:

Optimizing rosetta builds for AMD Epyc/Ryzen processors

Category:
Compilation

Hi all,

Does anyone know how best to optimize compiling rosetta to take advantage of AMD Epyc (zen3/zen4) and Ryzen archatectures?

For example:

Post Situation:

total_score changes when decomposing bb hbonds ref2015

Category:
Scoring

Hi. Really sorry to disturb you but I don't understand some behaviour regarding scoring.
I will first describe the issue and paste the code.  Originally I was using

Post Situation:

Failure to produce a cst file

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:

Post Situation:

Ligand Rotamer Control in Macther

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?

Post Situation:

Setting pivots points for GenKIC

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.

Post Situation:

Category:
ROSIE

Hi there,

These two days the ROSIE server seems to be offline, and I always get "502 Bad Gateway". I am wondering if the server is working now or it is just my problem.

Thanks,

Jun

Post Situation:

Category:
ROSIE

Hi there,

I tried to log in to Rosie server with my github credentials but it I got the following error message:

Post Situation: