In Patchdock server refinement is recommended for protein-protein docking mainly. But in your case its Metal ion-protein docking so minimization is not compulsory. For additional validation of your complex you can subjects obtained model to Firedock or Can do MD simulations study to get stable results.

Thank you Sir Vikas Kumar

Sir actually I tried with the refinement after getting the patchdock solution. but here again i faced one issue. the structure that I obtained after firedock refinement showed same ligand binding twice in the same receptor in each individual solution.

Help me to clear this query.

Thanks in advance.

That should not happen but if you are getting then you can try other docking servers HDOCK, HADDDOCK, ClusPro and many more are there and based on consensus you can select final model. Further if you the facility for MD simulation then you can refine the model. Find out some papers which are similar with your Aim and Objective then you can decide but to do next.

Ok thank you sir.

I tried with the HADDOCK and Cluspro this morning but the server was not responding. I shall try it once again. If I face any other issue I will get back to you sir.

Hello miss. Will you be kind to explain please how did you performed the docking of protein-ion metal?

Thanks in advance