Hi everyone,
I would like to create some double mutations in my protein and thought to get a prediction of the ddG change using Rosetta's ddg_monomer application. I tried running the preminimization using:
Hello,
I have been trying to use the Cterm_amidation patch, but everytime I use it in FastDesign or scoring it turns it back into a regular C terminus.
I've read the posts from other users, but I still can't make it work... What am I doing wrong?
Things I've tried so far:
I added "-include_patches Cterm_amidation" flag, both with the input file having a regular C terminus and with a neutral terminus - in this case I made sure the names of the atoms matched these in the patch:
Hello,
I'm a new user wants to run a RosettaScripts with disulfize mover, but right after I start the scripts, I got the following crash report. Any comments or suggestions on how to solve the issues? Thanks a million.
I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.
I am using Remodel in Pyrosetta 4 2020.49 release (a stable) for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.
Hello,
I am using pepspec to design a peptide inhibitor of a serine protease. I am using a structure of the enzyme, with a docked Arg, obtained from a crystal structure (so no Anchor Docking is needed). I want to design a peptide by adding residues to the N-terminal side of the anchored Arg. Previous pepspec, I repacked the structure with fixbb with:
Heya,
I am new to Pyrosetta and attempting to implement the Cartesian delta detla G paper, however i am struggling a bit with it. There is already a tutorial on delta deltaG in the official tutorials, and from my understanding the differences to the Cartesian version are simply an initial relax with a different score function (ref2015_cart) and then backbone relaxes around the mutation site. This is kinda what i am struggling with.
How can i relax only a certain site + 2-5 sites around it?
Hello everyone!!
I am trying to work on the protein-protein interface design using rosetta scripts. I am new to running rosetta scripts. So, I kindly need help on that.
I ran the configure file given in the first step which threw me an error of Nobsub in path. I tried installing bsub and adding paths to the bash file but still wasn't able to proceed further.
Kindly help me out if there are any mistakes or details i may have missed in setting up the run.
Thanks in advance
HI All,
I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.
When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes.
Dear fellows,
