Magnesium ion in a post-docking adjustment

Question

[Rodolfo Adrián]

Hi, I was wondering if a post-docking adjustment of my Protein-Ligand (RNA) Model is validated: I performed a docking simulation with Autodock Vina v. 1.2.0, and then I used AlphaFill in the same protein I used for the docking (without the ligand, obviously), and then I used the tool MatchMaker in Chimera to get an alignment, and a single PDB of the protein-ligand-ion complex. My question is if this approach is validated, or how should I address this issue (because I have not yet used a software which can handle Mg ions correctly), because I will then perform a MD simulation with GROMACS and I was also wondering which FF to use that can handle the Mg ion.

>>THANKS A BUNCH FOR ANY HELP AND/OR ORIENTATION ON THIS TOPIC<<

[dthorbur]

AlphaFold3 (assuming you're not at conflict with their terms of use) can handle both ligands and ions. And what do you mean by validated? Generally with in silico work like this, each case has a high error rate and needs wet lab validation anyway. At least my knowledge of false-positive rates in PPI research indicates we're not quite there, but it's a step up from older methods.

Your logic sounds reasonable in terms of the methodology, but you are also omitting the single most powerful tool in your field.