HADDOCK run is getting failed repetedly

HADDOCK
1

Hi,

I’m trying to dock a newly synthesized small molecule with a DNA. I was following the ab initio docking protocol for that. Performed the first phase of docking run and analyzed the contacting residues. Using those residues I generated 2 restraint file (active and passive) for second phase of docking. However, the second phase is keep failing every time. Here is the link of the recent run: http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5771546473/1xav_dpnp_new/haddock.out

Please help me out here. I have finished few runs using the same protocol and they worked out well except this one.

Thank you.

2

The output tells you to check the FAILED file for error messages…

If you do so (https://milou.science.uu.nl/serviceresults/HADDOCK2.2/5771546473/1xav_dpnp_new/FAILED) you will read:

TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO! CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS
STRUCTURE NUMBER 460

So there is thus a problem with your restraint files. The restraints are not properly read or the atom selection does not return anything. Make sure to define the correct atom names / segids …

1 Like
3

PS: In case you define restraints to hydrogen atoms, you might want to keep all hydrogens in your structure by turning off the option to delete the non-polar hydrogens.

1 Like
4

I tried “turning off the option to delete the non-polar hydrogens”, yet it gave me same error.
Here’s my active.tbl file, please have a look:
! HADDOCK AIR restraints
! HADDOCK AIR restraints for 1st selection
!
assign ( resid 10 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 9 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 12 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 11 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 15 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 21 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 18 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 16 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 7 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 6 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 8 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 17 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 19 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 20 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 13 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 14 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 5 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 2 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 4 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

assign ( resid 3 and segid A)
(
( resid 1 and segid B)
) 2.0 2.0 0.0

! HADDOCK AIR restraints for 2nd selection
!
assign ( resid 1 and segid B)
(
( resid 10 and segid A)
or
( resid 9 and segid A)
or
( resid 12 and segid A)
or
( resid 11 and segid A)
or
( resid 15 and segid A)
or
( resid 21 and segid A)
or
( resid 18 and segid A)
or
( resid 16 and segid A)
or
( resid 7 and segid A)
or
( resid 6 and segid A)
or
( resid 8 and segid A)
or
( resid 17 and segid A)
or
( resid 19 and segid A)
or
( resid 20 and segid A)
or
( resid 13 and segid A)
or
( resid 14 and segid A)
or
( resid 5 and segid A)
or
( resid 2 and segid A)
or
( resid 4 and segid A)
or
( resid 3 and segid A)
) 2.0 2.0 0.0

! HADDOCK AIR restraints for 3rd selection
!

! HADDOCK AIR restraints for 4th selection
!

! HADDOCK AIR restraints for 5th selection
!

! HADDOCK AIR restraints for 6th selection
!

Please have a look.
I have been able to complete few docking runs but only this run is giving some issue.

5

Nothing wrong with your restraints.

Did you check that your are using the correct segIDs?

And that the residue numbers are correct? Is chain B a ligand? Does it have residue number 1?

6

I’m using correct segIDs.
I have tried docking twice and residue numbers come out same. So, I guess the numbers are correct.
Chain B is ligand with residue number 1. Does it conflicting with Chain A’s residue number ?

7

If you saved the haddockparam file returned by the server in the first submission step, please send it to me via email so that I can take a look.