Docking

Hi,

I am getting the following error message when I try to extract pdb files from a silent file (output from ligand docking using RosettaScripts). 

Hi,

I am using RosettaLigand application to dock a small molecule into the active site of an apo-protein structure of my interest. Instead of using a pre-generated conformers, I am using the "dummy" method of specifying proton_chi sampling for all freely rotating bonds. (So even for C-C or C-O bonds, I would add another proton_chi line below to add sampling for those chi angles)

My question is simple, but it seems pretty hard to google anywhere to find documentation for the parameters following PROTON_CHI

Dear Rosettaers

I would like to dock Individual residues against the target surface on my protein. In this way, I have to produce a set of individual hydrophobic rotamers which can bind to a hydrophobic pocket on my protein. 

I used this RosettaScript to generate inverse rotamers:

This is probably a silly question so I apologize if so, but recently lab has been investigating some novel interaction sites between a protein and peptide based off of recent crosslinking and IP data. I created some pdb files of the protein and the peptide aligned at the various novel and established crosslinking sites and submitted them to FlexPepDock to see if the models were reasonable.