You are here

Docking

Creation of crystal_complex.pdb for docking

Category: 
Docking

Hello all,

I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.

Post Situation: 

Stub Libraries for DockWithHotspotMover

Category: 
Docking

Hello!

I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?

Thank you so much.

Post Situation: 

Filters saying atom type does not exist on residue

Category: 
Docking

Hi,

I'm currently try to dock a ligand into a dimeric structure using Rosettascripts. When I do normal docking everything goes okay but once I add filters it no longer functions, getting the warning  [ WARNING ] Residue 477 of type CHA does not have atom with type H4. The run will continue then fail at the end. This is the name for the atom in the PDB itself so I'm unsure what exactly is happening. I've attached the xml I'm using below, any help would be greatly appreciated! (Unfortunately the pdb was too large to attach.)

Post Situation: 

setting timeout option in MPI run

Category: 
Docking

Hi

I'm now trying to set timout option in my rosetta MPI run

which means that after certain period of time, whole process are automatically stopped

I run with following commands

mpirun -np 10 rosetta_scripts.mpi.linuxgccrelease @options

where options is

Post Situation: 

Rigidifying ligand

Category: 
Docking

I have a ligand with which I am trying to design a pocket in a synthetic protein.

Now the ligand doesn't have any rotatble bonds, because it's carbon chain is full of conjugated bonds,

However it keeps isomerizing some of the bonds,

is there any way I could completly fix the carbon chain?

Post Situation: 

Pages

Subscribe to RSS - Docking