# No Results of Local HADDOCK 2.4 for Antibody-Antigen Docking **URL:** \ **Category:** HADDOCK\ **Created:** [September 23, 2021, 1:05pm UTC](https://ask.bioexcel.eu/t/no-results-of-local-haddock-2-4-for-antibody-antigen-docking/3264 "2021-09-23T13:05:31Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![talipzengin](https://avatars.discourse-cdn.com/v4/letter/t/e99b99/32.png) [@talipzengin](https://ask.bioexcel.eu/u/talipzengin)\ **Post date:** [September 23, 2021, 1:05pm UTC](https://ask.bioexcel.eu/t/no-results-of-local-haddock-2-4-for-antibody-antigen-docking/3264/1 "2021-09-23T13:05:31Z")
Hi. I am using HADDOCK version: 2.4 - May 2021 release on the Ubuntu server. I am trying to run Ab-Ag HADDOCK tutorials locally. I used two different strategies from two tutorials ([Ambrosetti, et al BioRxiv, 2020](https://arxiv.org/abs/2005.03283) & [Tutorial describing the use of a local version of HADDOCK2.4](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/)) and tried docking with and without Unambiguous/Ambiguous Interaction Restraints, however, I did not get any results. HADDOCK runs without any errors, but its run takes \<1 second, creates the directories without docking results. I copied the commands and outputs below. I could not find any error messages. It looks as it runs normally. Is there any other option to find the errors? How can I solve this problem? Note: I have tried other Ab-Ag pairs with the same commands below and did not get results, however, HADDOCK server gave docking results including only 1 cluster with 4 models. Thanks in advance. **Following “Tutorial describing the use of a local version of HADDOCK2.4”:** > pdb\_fetch 4g6k \> 4g6k.pdb > pdb\_delhetatm 4g6k.pdb | pdb\_tidy \> 4g6k\_2.pdb > pdb\_selchain -H 4g6k\_2.pdb \> 4g6k\_H.pdb > echo TER \>\> 4g6k\_H.pdb > pdb\_selchain -L 4g6k\_2.pdb | pdb\_shiftres -500 \> 4g6k\_L.pdb > echo END \>\> 4g6k\_L.pdb > cat 4g6k\_H.pdb 4g6k\_L.pdb | pdb\_chain | pdb\_seg \> 4g6k-clean.pdb > freesasa 4g6k-clean.pdb --format=rsa \> 4g6k.rsa > awk ‘{if (NF==13 && ($7\>40 || $9\>40)) printf "%s ",$3; if (NF==14 && ($8\>40 || $10\>40)) printf "%s ",$4}’ 4g6k.rsa \> 4g6k-active.list > nano 4g6k-active\_2.list # Cross-referencing of solvent accessible against the predicted CDR residues gives a final list for HADDOCK. Save the two lines (with empty second line) below in the file. 27 28 30 32 33 35 37 56 57 58 59 61 101 102 103 527 528 531 532 550 552 553 554 556 592 593 594 ### > pdb\_fetch 4i1b | pdb\_delhetatm | pdb\_tidy \> 4i1b.pdb > freesasa 4i1b.pdb --format=rsa \> 4i1b.rsa > echo " " \> 4i1b-passive.list > awk ‘{if (NF==13 && ($7\>40 || $9\>40)) printf "%s ",$3; if (NF==14 && ($8\>40 || $10\>40)) printf "%s ",$4}’ 4i1b.rsa \>\> 4i1b-passive.list > python2.7 ../haddock-tools/active-passive-to-ambig.py 4g6k-active\_2.list 4i1b-passive.list | sed s/segid/name\ CA\ and\ segid/g | sed s/2.0/3.0/g \> antibody-antigen-ambig.tbl > nano antibody-antigen-unambig.tbl # saved the lines below in it ! antibody inter-chain restraints assign (segid A and resi 189 and name CA) (segid A and resi 693 and name CA) 21.023 0.0 0.0 assign (segid A and resi 116 and name CA) (segid A and resi 702 and name CA) 44.487 0.0 0.0 ! cross-link assign (segid A and resid 66 and name CB) (segid B and resid 99 and name CB) 23 23 0 > nano run.param # saved the parameters below in it. AMBIG\_TBL=antibody-antigen-ambig.tbl HADDOCK\_DIR=/HADDOCK/haddock2.4-2021-05 N\_COMP=2 PDB\_FILE1=4g6k-clean.pdb PDB\_FILE2=4i1b.pdb PROJECT\_DIR=./ PROT\_SEGID\_1=A PROT\_SEGID\_2=B RUN\_NUMBER=1 UNAMBIG\_TBL=antibody-antigen-unambig.tbl > source ../haddock2.4-2021-05/haddock\_configure.sh > haddock2.4 &\> haddock.out & ############################################################################## Starting HADDOCK on: 2021-09-23 15:43:12 HADDOCK version: 2.4 - May 2021 release Python version: 2.7.18 (default, Mar 8 2021, 13:02:45) [GCC 9.3.0] reading parameters from the file ./run.param setting some variables: N\_COMP set to: 2 RUN\_NUMBER set to: 1 HADDOCK\_DIR set to: /HADDOCK/haddock2.4-2021-05 UNAMBIG\_TBL set to: antibody-antigen-unambig.tbl PROT\_SEGID\_2 set to: B PROT\_SEGID\_1 set to: A PDB\_FILE1 set to: 4g6k-clean.pdb AMBIG\_TBL set to: antibody-antigen-ambig.tbl PROJECT\_DIR set to: . PDB\_FILE2 set to: 4i1b.pdb runDir= ./run1 project . exists, run 1 does not exist create the new run 1 4g6k-clean.pdb copied to ./run1/data/sequence after removing the chain and segIDs 4i1b.pdb copied to ./run1/data/sequence after removing the chain and segIDs editing run.cns: setting the default values copying run.param to ./run1/data/run.param created new run1 for the project . copying distance restraints data to ./run1/data/distances/unambig.tbl copying distance restraints data to ./run1/structures/it0/unambig.tbl copying distance restraints data to ./run1/structures/it1/unambig.tbl copying distance restraints data to ./run1/structures/it1/water/unambig.tbl copying AIR restraint data to ./run1/data/distances/ambig.tbl copying AIR restraint data to ./run1/structures/it0/ambig.tbl copying AIR restraint data to ./run1/structures/it1/ambig.tbl copying AIR restraint data to ./run1/structures/it1/water/ambig.tbl new project . has been set up. Now you have to edit run.cns in ./run1 Finishing HADDOCK on: 2021-09-23 15:43:12 ############################################################################## **Following “Ambrosetti, et al BioRxiv, 2020 & Tutorial describing the use of a local version of HADDOCK2.4”:** > pdb\_fetch 4g6k \> 4g6k.pdb > python2.7 ../HADDOCK-antibody-antigen/ImmunoPDB.py -i 4g6k.pdb -o 4g6k\_ch.pdb --scheme c --rename > python2.7 ../HADDOCK-antibody-antigen/ab\_haddock\_format.py 4g6k\_ch.pdb 4g6k-HADDOCK.pdb A \> 4g6k-active.txt > pdb\_tidy 4g6k-HADDOCK.pdb \> oo; mv oo 4g6k-HADDOCK.pdb ### > pdb\_fetch 4i1b | pdb\_delhetatm | pdb\_tidy \> 4i1b.pdb > pdb\_rplchain -A:B 4i1b.pdb \> oo; mv oo 4i1b.pdb # Replaces chain A for chain B > freesasa 4i1b.pdb --format=rsa \> 4i1b.rsa > echo " " \> 4i1b-passive.list > awk ‘{if (NF==13 && ($7\>40 || $9\>40)) printf "%s ",$3; if (NF==14 && ($8\>40 || $10\>40)) printf "%s ",$4}’ 4i1b.rsa \>\> 4i1b-passive.list > python2.7 ../haddock-tools/active-passive-to-ambig.py 4g6k-active\_2.list 4i1b-passive.list | sed s/segid/name\ CA\ and\ segid/g | sed s/2.0/3.0/g \> antibody-antigen-ambig.tbl > nano antibody-antigen-unambig.tbl # saved the lines below in it ! antibody inter-chain restraints assign (segid A and resi 189 and name CA) (segid A and resi 413 and name CA) 21.023 0.0 0.0 assign (segid A and resi 116 and name CA) (segid A and resi 422 and name CA) 44.487 0.0 0.0 ! cross-link assign (segid A and resid 66 and name CB) (segid B and resid 99 and name CB) 23 23 0 > nano run.param AMBIG\_TBL=antibody-antigen-ambig.tbl HADDOCK\_DIR=/HADDOCK/haddock2.4-2021-05 N\_COMP=2 PDB\_FILE1=4g6k-HADDOCK.pdb PDB\_FILE2=4i1b.pdb PROJECT\_DIR=./ PROT\_SEGID\_1=A PROT\_SEGID\_2=B RUN\_NUMBER=1 UNAMBIG\_TBL=antibody-antigen-unambig.tbl > source ../haddock2.4-2021-05/haddock\_configure.sh > haddock2.4 &\> haddock.out & ############################################################################## Starting HADDOCK on: 2021-09-23 15:12:41 HADDOCK version: 2.4 - May 2021 release Python version: 2.7.18 (default, Mar 8 2021, 13:02:45) [GCC 9.3.0] reading parameters from the file ./run.param setting some variables: N\_COMP set to: 2 RUN\_NUMBER set to: 1 HADDOCK\_DIR set to: /HADDOCK/haddock2.4-2021-05 UNAMBIG\_TBL set to: antibody-antigen-unambig.tbl PROT\_SEGID\_2 set to: B PROT\_SEGID\_1 set to: A PDB\_FILE1 set to: 4g6k-HADDOCK.pdb AMBIG\_TBL set to: antibody-antigen-ambig.tbl PROJECT\_DIR set to: . PDB\_FILE2 set to: 4i1b.pdb runDir= ./run1 project . exists, run 1 does not exist create the new run 1 4g6k-HADDOCK.pdb copied to ./run1/data/sequence after removing the chain and segIDs 4i1b.pdb copied to ./run1/data/sequence after removing the chain and segIDs editing run.cns: setting the default values copying run.param to ./run1/data/run.param created new run1 for the project . copying distance restraints data to ./run1/data/distances/unambig.tbl copying distance restraints data to ./run1/structures/it0/unambig.tbl copying distance restraints data to ./run1/structures/it1/unambig.tbl copying distance restraints data to ./run1/structures/it1/water/unambig.tbl copying AIR restraint data to ./run1/data/distances/ambig.tbl copying AIR restraint data to ./run1/structures/it0/ambig.tbl copying AIR restraint data to ./run1/structures/it1/ambig.tbl copying AIR restraint data to ./run1/structures/it1/water/ambig.tbl new project . has been set up. Now you have to edit run.cns in ./run1 Finishing HADDOCK on: 2021-09-23 15:12:41 ############################################################################## ---
**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 23, 2021, 1:20pm UTC](https://ask.bioexcel.eu/t/no-results-of-local-haddock-2-4-for-antibody-antigen-docking/3264/2 "2021-09-23T13:20:01Z")
The first call to haddock creates and populates the directory structure. You need then to edit the run.cns file and then call again haddock. I.e. perform the next step as described in: > **[Tutorial describing the use of a local version of HADDOCK2.4](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#customizing-the-docking-parameters)** > > A tutorial describing the use a local version HADDOCK2.4 ---
**Author:** ![talipzengin](https://avatars.discourse-cdn.com/v4/letter/t/e99b99/32.png) [@talipzengin](https://ask.bioexcel.eu/u/talipzengin)\ **Post date:** [September 23, 2021, 5:28pm UTC](https://ask.bioexcel.eu/t/no-results-of-local-haddock-2-4-for-antibody-antigen-docking/3264/3 "2021-09-23T17:28:26Z")
Oh, I see. I thought that it would run with default parameters without customizing them. Thanks very much 🙏 ---
**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 23, 2021, 7:46pm UTC](https://ask.bioexcel.eu/t/no-results-of-local-haddock-2-4-for-antibody-antigen-docking/3264/4 "2021-09-23T19:46:01Z")
I will run with default parameters, but you will still need to call haddock a second time from within the run dir.