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Docking

Ligand Docking with Rosetta Scripts memory problem

Category: 
Docking

Hi,

I am trying to dock a small molecule with holo dimer protein (153 aa, 1 Cu and 1 Zn per chain). I followed the Ligand Docking Tutorial and it all works fine until I try to generate more than ~50 output structures. Using both MPI and default builds, all 8 GB of RAM and 5 GB of Swap are slowly filled up until my linux system kills the program. Below I have listed different commands and how many strucures it generated before swamping memory. The basic options file and xml file is attached is attached.

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Ligand params file proton_chi parameters

Category: 
Docking

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

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Protein Docking Error

Category: 
Docking

Dear All,

 

I am learning how to do protein-ligand docking and I am following the Rosetta built-in tutorial: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

 

I did not change anything whatsoever. I used the same tutorial files (as is) and attempted to run the calculation as such:

{PATH_TO_ROSETTA}/main/source/bin/rosetta_scripts.linuxgccrelease @options

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Produces a set of rotamers from a given residue

Category: 
Docking

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:

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Issues with residues and structure changing with FlexPepDock; is this normal?

Category: 
Docking

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.

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SNUGDOCK

Category: 
Docking

Hello,

I am trying to run SnugDock locally, and I follow the well explained demo. I noticed that makefab.pl script is missing. It should be in the demo / rosettascripts directory but its not there. Also, there is a link in the README.md file but its blocked by a usename and password....

Can anyone help?

 

Thanks,

Adva

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