What kind of PDB files to use to initiate protein-ligand docking

User discussions
1

GROMACS version: GROMACS 2021.3
GROMACS modification: No

I have two PDB files (each corresponding to a ligand and a receptor).
Each downloaded separately from PDB.

I’d like to perform ligand to protein docking process with MD with GROMACS.

Using those two files directly, does GROMACS automatically perform the docking for us?
Or should we give the pre-docked PDB files?
These pre-docked PDB files may come from rigid-body docking tools like ClusPro.

2

GROMACS does not perform docking. You need to supply a suitable starting state for the system, produced by some other software that will do docking.

3

Hi Justin,

Thank you so much for your reply.
Should we give the result to GROMACS from rigid based docking or flexible docking?
What docking program you suggest to give us the initial state suitable for GROMACS?

sca

5

Whichever state makes sense. Sometimes a rigid docking approach is sufficient, sometimes it isn’t. That’s your decision based on the properties of the proteins involved.

6

Thanks Justin. I sincerely appreciate your help.