I was trying to get the RMSD score of the protein having a ligand with the same protein after docking with that ligand. But getting zero score every time in Pymol. How to get rid of this problem? Can anyone please help me to figure out the problem?
Which software are you using for docking. If it is AutoDock then the. dlg file has all informations about the RMSD. just search for RMSD table and it will display the table and RMSD with respect to various conformations. You can view these conformations in pymol or even AutoDock tools GUI itself
You have to calculate RMSD between crystal ligand and docked pose of ligand. You can use Pymol to calculate RMSD between ligands. Use align command.
RMSD of a protein before and after docking can be obtained using pymol when you align them. It can be obtained with the help of MOE software.
Kiran Lokhande thank you for the suggestion... I have done this using pymol but getting a high rmsd value between two ligand (docked pose and crystal structure pose), can you suggest how to get low rmsd value (less than 3 A°)? Is there any special requirements are required for the ligand preparation?
Nayim Sepay thank you for the reply, actually I made a mistake in the question, talking about protein and ligand, actually I was trying to validate the docking procedure by alignment of both docked pose ligand and crystal structure ligand. If you have any advice for that it will be very helpful for me, as I am not able to get the rmsd value less than 3A° in pymol.
You can try to evaluate the docking results with our recently developed web server. It includes a tool for RMSD calculation (https://pegasus.lbic.unibo.it/pacdock/index.php).
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