You are here
Dear Friends and experts
I am trying to use "ddg_monomer.linuxgccrelease". First I want to pre-minimize the structure and get mincst.log file. I put all options in a flag file called pre_minimize
I run the following command:
1. To pre-minimize, the command from protocol is as following:
I found a structure of a binary protein complex and tried to use it as my template to predict the combined structure of another 2 proteins. In this case, should I use the protein-protein docking protocol or the comparative modeling protocol? If I should use the protein-protein docking protocol, is there anyway for me to utilize the PDB file of the template structure to save me some work? And if I should use comparative modeling, how can I build a structure by inputting 2 queries? I assumed that homology modeling only deals with one input query?
I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?
Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".
I included all the header files but still not working.
I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.
The tutorial at https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling says "You can build multiple loops in the same simulation by altering the blueprint file to indicate where these loops are".
I am exactly using the same files in the tutorial of https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling
In the "Extending the Termini" section, I use "3gbn_missing_cterm.pdb", "3gbn_missing_cterm.remodel" and "flag_missing_cterm" files as input, with a command
I'm trying to get started with comparative modeling for soluble proteins. I tried working through the demo/tutorial for membrane protein and adjusting for soluble, then also tried working with the RosettaCM workflow (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM). I'm having no trouble creating the input files, but seem to keep getting crashes at the step of calling rosetta_scripts.
When reading the source code, follow the function to find the class definition, but there is no way to know which class it inherits from or whether there is a defined subclass of the class. At the same time, I don't know which file the virtual function of the virtual base class is implemented in.So I would like to ask if there is a class diagram of the code