The problem hasn't been solved
Hi, sorry to bother you I am using the following function to create a packer:
Hello,
the output files, *.ga.entities and *.ga.generations, were produced by sequence_tolerance application.
When I tried to use sequence_tolerance.R processing the output files, I got the following error:
> source("/usr/local/rosetta_src_2021.16.61629_bundle/main/tools/analysis/apps/sequence_tolerance.R")
> process_seqtol("./2I0L_A_C_V2006_0001.ga.entities")
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
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
Hi there, I would also like to ask for an email address confirmation. My user name is bozturk (bas18@dsmz.de), and my affiliation is Leibniz Institute DSMZ, which is an academic institution. Thank you!
Hi all,
Does anyone know how best to optimize compiling rosetta to take advantage of AMD Epyc (zen3/zen4) and Ryzen archatectures?
For example:
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
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:
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?
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.