I want to do docking validation. I downloaded the protein from PDB and deleted the chains and cofactors and saved the co crystal in .pdb format from discovery studio visualizer. Subsequently, performed docking of cocrystal ligand. Then I had drawn the co crystal ligand in chem draw and energy minimized the ligand and the docked. When I open the docked conformer of both in discovery studio, the conformers merge into each other and while calculating rmsd, it shows an error - "Element types not matching the reference ligand". Kindly suggest am I going with the right method. What is the alternative?
You need to rename the atoms in one of the ligands to match the corresponding atom types in the other ligand.
@Rudy J Richardson sir, Thank you for your response. Could you please elaborate more...?
Chandni Pathak
Save your docking complex as a PDB file. Open the file in a text editor (not a word processor) such as gedit for linux or Notepad++ for Windows. Scroll down near the end of the file to the "HETATM" section and look at the atom names for the atoms in the ligand. Do the same with the PDB file of the X-ray structure of the complex. The names of the corresponding atoms in the ligand in the docking complex and the ligand in the X-ray structure need to be the same for doing an RMSD calculation. To help with recognizing the atoms in the ligand, you could open the docking ligand and the X-ray ligand in a molecular viewer. You can manually edit the ligand atoms in one of your PDB files using a text editor so that the corresponding ligand atoms have the same atom names. Then save the file as a PDB file. If all goes well, you can then align the two PDB structures in a molecular viewer and carry out the RMSD calculation. I hope this helps. Good luck!
-- RJR
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