Sequentially dock two molecules vs multi-ligand docking

[andrew0901]

Hi,

I want to dock a cofactor-substrate pair into several designed enzyme pocket (no metal). What I found was that the cofactor usually get a good pose while the substrate not. So I'm wondering:

1. Is it at all possible to do sequential docking in one-line command, i.e. cofactor first then the substrate with the cofactor held in place?
2. If the above option not supported, can I combine the docked cofactor pose and the enzyme into one .pdb and perform another round of docking? Do I prepare the receptor as usual and is ADFRsuite able to handle it?
3. Conceptually are sequential docking and docking two molecules at the same time different? Or are they gonna yield the same result?

I'd appreciate your help! Thanks in advance.

[diogomart]

Hello,

1. no
2. this is the way to do it
3. yes they are different, no guarantees of getting the same result

[andrew0901]

Thanks for your reply. Then my question is how to prepare a receptor with small molecule in it? ADFRsuite gives me the message:

' ' apparently composed of not std residues. Deleting

And the prepared .pdbqt has no small molecule that I want to have there.

[rwxayheee]

Hi @andrew0901
The default behavior of ADFRSuite's prepare receptor is to delete chains that are entirely made up of nonstandard residues or ligands. With that, to keep a small molecule you could change the small molecule's chain ID to the same chain ID as the protein receptor

[rwxayheee]

Closing as resolved.