Retrieve water mediated contacts on solvated docking

1

DEar Haddock support team,
I am performing a protein - DNA docking by choosing solvated docking option in Haddock.The docking results from Haddock show no water molecules. Does this men that no water molecules are involved in making any contacts or one should use other softwares (NUCPLOT) to find about the participation of water and retrieve the information.

Thanks in advane
K Sindhu

2

You need to download the full run archive to find the PDB files containing the water.
Those will be in structures/it1/water

3

Thank You. I got it.
But the file contains 200 complexes, how to find the complex coming under the first cluster with the best haddock score.
Further I also don’t find any water molecules in the clusters. Does this mean that there are no water molecules involved in the interactions.

4

Dear Haddock team’
Regarding my previous query, I got the files for clusters with haddock scores for the water refinement stage.
I want to know why no water molecules are present in the complex.

Thanks in advance
K Sindhu

5

Can you share the link to your run?

6

Dear Haddock team,
I am very sorry my earlier question was incorrect. Actually the run was performed with water refinement in the third step and not with solvated docking. But even in that case shouldn’t I get water molecules in the complex.
The link for the file is https://alcazar.science.uu.nl/serviceresults/HADDOCK2.2/2431298518/IDR22GKUfull-flexi

Thank you
K Sindhu

7

Unlikely

And the waters are not saved unless you turn on the keep water option

8

Ok…
Thank you.