The problem hasn't been solved
heya, i am wondering how rosetta deals with hydrogens. should i make them all explicit? or only the polar ones? I am trying to relax and dock something, and its something i am not really sure with. thanks!
I want to evaluate the ddg between WT and disulfide bond mutants
1. I try to use ddg_monomer and fond it does not suport it
2. Then I build disulfide bond mutants with moddler, and then try to use ddg_monomer to evaluate the ddg ( mutant CYS recovery to the amino acid of WT), and it does not work , too.
3. Just as 2. I try to use another APP, cartesian_ddg ， and disulfide bond mutants as the star model，and ddgs seem is similar(just try three mutant)
Hi,
I am trying to generate a ncAA. My current workflow is using a program called iQmol which has a connection to a QChem server, to produce an appropriate mol file. I then use mol_file_to_params.py to get the params files. It creates a params file with all the atoms quite close together. Running mol_file_to_params gives me this output with the attached files:
edanhabel@Edans-MacBook-Pro-2 molfile2params % python molfile_to_params.py iqmol_pymol_aromatic.mol2 -n f5p --clobber --amino-acid PHE
Hello,
I have a pdb with crystallographic waters which appear to be important for the protein structure, and perhaps function. I am generating mutations using pyrosetta and evaluting their relative scores, and exporting structures to be simulated with MD.
Hello,
i am trying to do a relax of a certain area of my protein, however, it seems as though the entire backbone moves (and the free energy of the entire system drops dramatically, an other indication the entire thing is beeing relaxed). My code is as follows:
working_pose = pose.clone()
sfxn = create_score_function("ref2015_cart")
Hi,
I've currently installed rosetta3 on aws cloud vm under ubuntu OS (Ubuntu 20.04.2 LTS).
I try to use a protocol from Khersonsky et al. 2018 (PMID: 30270109).
In order to do so, a rosetta_scripts_jd3.default.linuxgccrelease file is needed.
However, I did not find such file under $ROSETTA/main/source/bin/
My rosetta version is: rosetta_src_2021.16.61629_bundle
I've compiled it with: ./scons.py -j8 mode=release bin
Hi,
I am new to rosetta and I want to perform protein-lignad docking using rosetta3.13, I used my own PDB files and the option.txt, dock.xml under the folder rosetta/main/demos/tutorials/ligand_docking to perform docking. I found the ligand was still outside the protein after docking. Therefore, I tried to add the start coordinates for the ligand in the dock.xml but didn't find a right way. Could you help me with this? I attached the PDB file I used for docking.
Thanks,
Huanhuan
Dear Sir/Madam, in my .xml script, I wish to use a if_X_scoreterm, from InterfaceScoreCalculator mover, such as interface_delta_X as GenericMonteCarlo criterion but this term cannot recognized by Rosetta. There is no such kind of score_type. I wonder if there is way to do so?
Thanks
Best Regards
Rico
I'm following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I'm in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault.
Hello,
I am using FARFAR to get the possible structures for a A-bulge RNA duplex with the following specifications:
Input sequence: CCGGCAGUGUG+CACACGUCGG
Input secstruct (((((.(((((+))))))))))
I need to keep the structure in the duplex form and not the hairpin. All output files I got with the mentioned specifications are RNA hairpins. Is there a way I can keep the structure in the duplex form.
thanks for yoyr help.
Best,
Amir