Hi,
i am trying to display an interaction between a drug and its active site on pymol. i have saved the coordinate file for the most favourable confirmation from Autodock. i then go into pymol and open the macromolecule first. i then go ahead and open the coordinate file for the drug which should allow the drug to be positioned correctly according to what the most favourable confirmation is. however instead of showing the drug and the macromolecule as a complex. pymol shows them seperately and far apart from each other, I don't understand what is causing this. can someone help please ?
Dear Wares Hamidi,
It sounds like there may be an issue with the alignment of the drug coordinate file and the macromolecule structure in Pymol. One possible solution is to use the "align" command in Pymol to superimpose the two structures so that they are in the same orientation. Here are the steps you can try:
This should create a new object called "complex" that contains both the drug and macromolecule in the correct orientation. You can then use the usual Pymol commands to visualize the interaction between the drug and the active site of the macromolecule.
If this doesn't work out, a possible issue could be that the grid size is too large or blind docking was done. So, make sure that the grid size is properly defined.
Best,
Satyendra
You can write the best complex from autodock and save it as pdbqt. You can then directly open it by just clicking on it. Sorry, if I am sounding foolish, I am a newbie in computational modelling. Just trying to help you.
After running Autodock, you should extract the docked ligand conformations from the .pdbqt file. In the following paper, at slide 22 (pag 852) it is explained how to do it. Hope it helps.
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