The problem hasn't been solved
The terms "residue packing", "repacking", "pack", etc. appear all over rosetta documentation. What is their meaning?
I have two .pdb structures of the same protein. What is the rosetta command to get the RMSD between them?
Hello,
I would like to use checkpoints in order to restart a job if it ends because of a wall-time before he finishes.
I tried the flags:
-in:file:checkpoint true
-run:checkpoint true
But no file is generated, it doesn't look to work.
Anyone knows how I can use checkpoint in the docking protocol?
Thanks
Amélie
I have the .pdb structure of a complex of two chains.
I want to try the effect of a mutation in one of the interfaces on the binding energy. I am new to Rosetta. Can someone explain step by step how to compute this delta-delta-G?
Thanks.
I am getting a lot of "unitialized" warnings during compilation of rosetta 3.5. See examples below (there is a lot more). I am using Ubuntu 14.04 amd64. I have gcc 4.8 and 4.7 installed. I am compiling with ./scons.py -j1 mode=release cxx_ver=4.7 bin.
When looking at the graphical docking output (Interface score I_sc / RMSD) the values shown when hovering over the dot do not match the values on the graph itself (see screenshot, ScoreGraph.png). The lowest scoring decoy has a I_sc of ~-6 while the value shown is -4.5. The numbers of the decoy do not match either, the lowest scoring decoy from the result list is 0927 and has a I_sc of -6.228 (which would fit the graph), but on the graph the number is 0836. In another run the values and numbers matched.
Hi,
I would like to know whether the enzyme design protocol of Rosetta Suite can be used for increasing the catalytic activity of the enzyme. Here, I don't have to design the active site from scratch, but I need to design the active site in such a way so that the catalytic activity of the enzyme is increased. Also, the enzyme I am dealing with does not have data for transition state modeling for the substrate that I am dealing with.
Please provide you comments and suggestions
Thanks
--
BH
Hi, novice Rosetta user here (so apologies in advance for simple / silly questions).
I have small peptide ligands that I am using in standard grafting / design. This has been relatively straightforward. However, one monkey wrench I'd like to throw into the works would be for the design scripts to use a noncanonical amino acid instead of the corresponding canonical one. For example, instead of tyrosine, design interfaces assuming all tyrosines are phosphorylated, or alternatively, impose acetylation or methylation on certain residues.
Hi everyone,
I'm trying to run Rosetta kinematic loop on my computer but I got an error message after few seconds:
ERROR: Cannot open PDB file "input_pdb"
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 184
The comand that I have used and the screenshot of the error page is shown below:
Hello,
I have problems using the RNA Denovo protocol on the web server. I try to get a structure for a duplex RNA, with a bulge, and the calculations fail, giving the error message: Protocol failed to produce any results! (File output/protein-0.out not found!)