Docking

Hi All,

How do you generate parameters for a stapled helix peptide? The residues that are "stapled" are alanines at positions 1 and 5, inclusive. The "staple" is a 8-carbon linker. The flanking residues are all natural amino acids.

Thanks!

Hello,

I have been trying to dock a ligand into my protein but I am getting two different errors. The first time I ran sbatch launch_design.sh and it would time out and give the files pocket-183006.err and .out, but the out file was empty. I tried running multiple jobs by creating a new file RosettaDesign.sh but it would fail, and I got the files pocket2-198770.err and .out. The error I received is residue outside res_map range. I have uploaded the files in text form and was wondering what is causing it to fail.

Hi

I've been wondering why docking protocol moves protein which i dont want to be moved

so in my case, I have a complex PDB file with chain A, B, and C. 

A is a small protein, and B and C is neighboured together, and C is the receptor

What i want to do is docking A to C, while B and C is not moved or designed.

so i made a xml script like below:

Hi everyone,

I want to dock a transition state model at the zinc site of human carbonic anhydrase II and redesign the protein. According to the paper (Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777.), I use ~/rosetta/tools/zinc_site_redesign module to do my job. Cleaning of PDB was successful, but when I tried to align the protein PDB with my transition state model, error occured: