How to prepare protein receptor for docking and what are the tools to be used for this.
For docking using Vina, first I used ligand and receptor from the tutorial and I was able to get the expected results. But when I used the receptor from RCSB PDB after removing ligand, hetatm and water and same ligand from tutorial, I was not able to reproduce the results. This means that receptor has to be prepared differently before converting PDB into PDBQT.
Thank you
Thank you Martin. I found where it was going wrong. I compared the PDB file provided in the tutorial and my PDB file. The order of the atoms, seems to be culprit. I changed the order of atoms in my file and to my surprise I got the expected results. I will adopt these to other receptors and see what happens. Any way thank you again for extending the help. I will definitely seek you help in my further assignments. Attached, please find the results.
Yes I did. I followed all the steps while preparing the receptor as shown in the tutorial (http://vina.scripps.edu/tutorial.html). I removed water, hetatm and ligand from PDB. Then I added polar H and converted PDB into PDBQT using ADT. But no help. The docked ligand confirmation was red one as shown in the post of May 2. After thoroughly studing the PDB tutorial file I found that sequence of some atoms was different (CE2 CE3 NE1; NE2 OE1; NE2 OD1; NE2 OG1). I incorporated these changes in my PDB file and after docking, the ligand pose was yellow one. I adopted these changes to other receptors but it did not work for all the proteins. For some receptors RMSD was >2.
You can try this server https://sibiolead.com/. It performs PLIP analysis too
- Badges
- Science topic
- Similar topics
- Filing