ADL: How to dock mulitple ligands to one receptor/protein

Van Dam, Hubertus hvandam at
Fri Oct 30 19:19:27 PDT 2020

Hi Fatahiya,

Autodock only docks one ligand at a time. To dock two ligands simultaneously you want to run two instances of Autodock at the same time each docking one ligand. To automate doing that within a single node you could use something like GNU parallel (see: Just be careful to make sure that you use unique filenames in each docking calculation.

Best wishes,


Hubertus van Dam, 631-344-6020, hvandam at
Brookhaven National Laboratory

On 10/30/20, 20:26, "autodock-bounces at on behalf of fatahiya mohamed tap" <autodock-bounces at on behalf of fatahiyamohamedtap at> wrote:


    May I know how to dock two ligands to one protein at the same time or

    Thank you in advance for your kind help.

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