Order of input molecules

1

Dear Haddock team,
Is there any order for giving the input molecules. I am docking protein and DNA. I usually give protein as the first molecule. But when I gave DNA as the first molecule (keeping all the parameters same) I find that I have more protein residues interacting with DNA. Why is this so?
During docking should DNA be always given as the first molecule as proteins dock onto DNA.

Thanks in advance
K Sindhu

2

This reflects the chaotic nature of such computations. You will be randomising differently the starting orientations, adding numbers in a different order…

In general I would put the largest molecule as first, but this is not a hard rule.

Are you getting a single cluster?
Are you looking at more than one cluster?

Also when analysing results, don’t look only at one model.