The problem hasn't been solved
Good evening,
I am experiencing an odd behaviour with the cartesian_ddg application (Rosetta version 3.11) when trying to specify multiple simultaneous mutations to non-canonical residues in the mut_file.
Dear all,
I am trying to compile ROSETTA 3.12 on Red Hat Enterprise Linux Server release 6.5. I install the gcc (GCC) 10.1.0, and run the follow command
./scons.py bin mode=release -j 60
I get some error information like:
Dear all,
I am using the "antibody_H3" command to model the H3 loop of antibodies according to the guide at https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol.
Can everyone tell me why my ligand FMN is twisted after using molfile_to_params.py script to prepare param file? It still looks normal when I open with pymol. But it looks twisted after I open with Maestro.
Does anyone have similar experiences?
Dear contributors,
I'd like to change the rosetta scoring function in remodel to favour models that have less hydrophobic area. Main reason is low computing power for the task at hand.
Changing fa_sol is definitely the option? Should i change the lk_ball_wtd as well?
Can anyone suggest to me how to relax a protein with a non-covalent ligand? I want to make sure the ligand-binding site does not change dramatically. In the following scenarios, which one looks reasonable:
1) relax protein with ligand; use movemap to exclude the rotamer of ligand residue
Hi all,
I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:
Hello folks,
I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix.
Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH.
So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like
Hello folks,
I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix.
Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH.
So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like