Protein - dsDNA specificity

HADDOCK
2

Hi! In this scenario in which you are inspecting aminoacid-nucbase interactions, the best course would be to define your protein motif as active and the bases as passive, excluding all phosphate backbone atoms

However there is no automatic way of defining such specific restraints, you need to define the atoms manually in a code editor (do not use Word/OpenOffice).

First input your active and passive residues using this tool: http://milou.science.uu.nl/services/GenTBL and then define the atoms:

Chain A Protein active residues: 1, 2
Chain B DNA (sequence: ATCGA) passive residues: 1, 2, 3, 4, 5

assign ( resid 1  and segid A)
       (
        ( resid 1  and segid B and (name N9 or name C4 or name C2 or name N3 or name C6 or name N6 or name N1 or name C8 or name N7 or name C5))
     or
        ( resid 2  and segid B and (name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name O4 or name C7))
    or
        ( resid 3  and segid B and (name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name N4))
    or
        ( resid 4  and segid B and (name C3' or name C2' or name O2' or name C1' or name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name O4))
    or
        ( resid 5  and segid B and (name N9 or name C4 or name C2 or name N3 or name C6 or name N6 or name N1 or name C8 or name N7 or name C5))
        ) 2.0 2.0 0.0

assign ( resid 2  and segid A)
       (
        ( resid 1  and segid B and (name N9 or name C4 or name C2 or name N3 or name C6 or name N6 or name N1 or name C8 or name N7 or name C5))
     or
        ( resid 2  and segid B and (name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name O4 or name C7))
    or
        ( resid 3  and segid B and (name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name N4))
    or
        ( resid 4  and segid B and (name C3' or name C2' or name O2' or name C1' or name N1 or name C6 or name N3 or name C2 or name O2 or name C5 or name C4 or name O4))
    or
        ( resid 5  and segid B and (name N9 or name C4 or name C2 or name N3 or name C6 or name N6 or name N1 or name C8 or name N7 or name C5))
        ) 2.0 2.0 0.0

Keep in mind that if the syntax is wrong the run will fail! Save this file as ambig.tbl and upload it as ambiguous restraints, you might need Guru access for that.

Good luck!