# HADDOCK run is getting failed repetedly **URL:** \ **Category:** HADDOCK\ **Created:** [August 17, 2017, 1:06pm UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451 "2017-08-17T13:06:20Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [August 17, 2017, 1:06pm UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/1 "2017-08-17T13:06:20Z")
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](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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [August 17, 2017, 1:41pm UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/2 "2017-08-17T13:41:58Z")
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](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 … ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [August 17, 2017, 1:54pm UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/3 "2017-08-17T13:54:01Z")
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. ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [September 5, 2017, 5:34am UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/4 "2017-09-05T05:34:11Z")
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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 5, 2017, 5:49am UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/5 "2017-09-05T05:49:09Z")
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? ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [September 5, 2017, 5:56am UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/6 "2017-09-05T05:56:40Z")
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 ? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 5, 2017, 7:02am UTC](https://ask.bioexcel.eu/t/haddock-run-is-getting-failed-repetedly/451/7 "2017-09-05T07:02:43Z")
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.