protein-DNA docking problem

HADDOCK
1

Hi all,

I am trying to dock 1 protein molecule to a DNA molecule in HADDOCK2.4. I am facing the following issues:

  1. Haddock is not taking the both the strands of DNA as a single input and I had to specify both DNA chains as two different molecules. Is it normal? or I am making a mistake.

  2. In total I have 3 molecules now to dock to each other. In the Input parameter tab, for each molecule, 2 windows are being shown to input active and passive residues. So I filled the parameters as:
    -For Protein (molecule 1): I selected the active residues to bind to DNA strand (A) and set the partner selection as 2. The I selected the same residues for strand DNA strand (B) in the second window and set the partner selection as 3.

  • For DNA strand A (molecule 2): I selected the active bases that bind to Protein 1 and set the partner selection as 1. Then I selected the whole DNA Strand as active residues that bind the molecule 3 (DNA strand B) and set the partner selection as 3.

For DNA strand B (molecule 3): I selected the active bases that bind to Protein 1 and set the partner selection as 1. Then I selected the whole DNA Strand as active residues for the molecule 2 (DNA strand A) and set the partner selection as 2.

But after this, I am still stuck at this page without any error message. I guess I am missing to input some information but don’t know where.
Please help!!

2

I am trying to dock 1 protein molecule to a DNA molecule in HADDOCK2.4. I am facing the following issues:

  1. Haddock is not taking the both the strands of DNA as a single input and I had to specify both DNA chains as two different molecules. Is it normal? or I am making a mistake

Renumber the second strand such as there is not overlap in residue numbering.
E.g. by shifting the number by a fixed amount using for example our pub-tools web server
Then submit it as a single molecule

Which should make you next questions unnecessary :slight_smile:

3

Thank you so much. It worked. :slight_smile: