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Docking

RosettaDock 4.0 ambiguous ERROR

Category: 
Docking

Hi all,

I'm running a protein-protein docking (both partners are ~240 res. monomers) and I get the following error:

---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

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Rosetta-foldtree and docking

Category: 
Docking

Hello everyone,

I'm using Rosetta's docking_ Protocol does the docking of two proteins (one protein is double chain and the other protein is single chain), but when I run the command:

$ROSETTA/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking

It explains that "Cannot compute center of mass of zero residues! ". How to solve this problem?

My parameter settings are as follows:

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small ligand docking in Ubuntu 20.04, please help

Category: 
Docking

    Hi, sorry for disturbing you but  I have problems about samll ligand docking in Ubuntu 20.04. It occurs errors when I followed jens Meiler's toturial about small ligand docking.

command line:

$ ~/Desktop/rosetta_workshop/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @options.txt -nstruct 5 -database ~/Desktop/rosetta_workshop/rosetta/main/database/

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Docking mover

Category: 
Docking

Hello, I have been reviewing the docking movers to perform both types, global and local. I have been testing them for a while now and with the active options to perform the global docking first, very little movement and exploration of the protein is observed in the output, the disturbances are practically local instead of global, this occurs both for DockingProtocol Mover and for Docking Mover. Would I have to first use DockingInitialPerturbation Mover or else use global docking flags and then use DockingProtocol or Docking for local?

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ligand dock into HEM containg pdb

Category: 
Docking

 Hi all

 I would like to dock  unknown chemical into PDB which have HEM as a cofactor

 But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>
                        <ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
                </RESIDUE_SELECTORS>
.

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charge grid in rosetta ligand docking using rosetta script

Category: 
Docking

 

 Ho all

 Recently I'm trying to do protein-ligand docking with rosetta scripting interface

 what I want to do is to incorporate charge grid in rosetta script xml file as shown below

                 <SCORINGGRIDS ligand_chain="X" width="25" name="charge">
                        <ChargeGrid grid_name="charge" weight="1.0"/>
                </SCORINGGRIDS>
.

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