# Docking of 2000 protein-antibody pairs using HADDOCK **URL:** \ **Category:** HADDOCK\ **Created:** [February 2, 2021, 7:08am UTC](https://ask.bioexcel.eu/t/docking-of-2000-protein-antibody-pairs-using-haddock/2809 "2021-02-02T07:08:25Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Gayatri1](https://avatars.discourse-cdn.com/v4/letter/g/f1d935/32.png) [@Gayatri1](https://ask.bioexcel.eu/u/Gayatri1)\ **Post date:** [February 2, 2021, 7:08am UTC](https://ask.bioexcel.eu/t/docking-of-2000-protein-antibody-pairs-using-haddock/2809/1 "2021-02-02T07:08:25Z")
I was using local version of haddock for performing protein-antibody docking. I had three datasets comprising of positive(71 pairs), negative( 288 pairs) and complete dataset(2000 pairs). The haddock process was automated using a python code and it ran successfully for positive and negative dataset. But, while running for 2000 antigen-antibody pairs, it crashed multiple times. For several cases it went like: Starting HADDOCK on: 2021-02-01 18:56:35 HADDOCK version: 2.4 - September 2020 release Python version: 2.7.17 (default, Sep 30 2020, 13:38:04) [GCC 7.5.0] parsing run.cns file parsing run.param in /home/iiitd/gayatri/antibodies\_pdbs/120-updated-variants/2b04\_ab/run2b04\_ab\_min\_3007k8x\_V445A/data reading parameters from the file /home/iiitd/gayatri/antibodies\_pdbs/120-updated-variants/2b04\_ab/run2b04\_ab\_min\_3007k8x\_V445A/data/run.param setting some variables: N\_COMP set to: 2 RUN\_NUMBER set to: 2b04\_ab\_min\_3007k8x\_V445A HADDOCK\_DIR set to: /home/iiitd/gayatri/haddock2.4-2020-09 UNAMBIG\_TBL set to: 2b04\_ab\_renum-unambig.tbl PROT\_SEGID\_2 set to: B PROT\_SEGID\_1 set to: A PDB\_FILE1 set to: 2b04\_ab\_renum.pdb AMBIG\_TBL set to: 2b04-7k8x-ambig.tbl PROJECT\_DIR set to: . PDB\_FILE2 set to: …/min\_3007k8x\_V445A.pdb N\_COMP 2 RUN\_NUMBER 2b04\_ab\_min\_3007k8x\_V445A HADDOCK\_DIR /home/iiitd/gayatri/haddock2.4-2020-09 UNAMBIG\_TBL 2b04\_ab\_renum-unambig.tbl PROT\_SEGID\_2 B PROT\_SEGID\_1 A PDB\_FILE1 2b04\_ab\_renum.pdb AMBIG\_TBL 2b04-7k8x-ambig.tbl PROJECT\_DIR . PDB\_FILE2 …/min\_3007k8x\_V445A.pdb looking for existing files waterdock false waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… waiting for the psf files… and no docking was performed. The generate\_2.out in begin directory gave this. ( SER 803 N ) 6644.0 EVALUATE: symbol $ID2 set to 6644.00 (real) SELRPN: 1 atoms have been selected out of 9649 ( SER 803 N ) EVALUATE: symbol $SEGID2 set to “” (string) SELRPN: 1 atoms have been selected out of 9649 ( SER 803 N ) 803 EVALUATE: symbol $RESID2 set to “803” (string) SELRPN: 1 atoms have been selected out of 9649 ( SER 803 N ) SER EVALUATE: symbol $RESN2 set to “SER” (string) SELRPN: 1 atoms have been selected out of 9649 SHOW: sum over selected elements = 1.000000 NEXTCD: condition evaluated as false SELRPN: 1 atoms have been selected out of 9649 SELRPN: 1 atoms have been selected out of 9649 GEOM= 1.335219 NEXTCD: condition evaluated as false FOR ID LOOP: symbol ID1 set to 6650.00 (real) SELRPN: 1 atoms have been selected out of 9649 ( SER 803 C ) It kept all the cores of system 100% occupied giving no results at the end. Also, I observed that for a single haddock run it runs around 680 tasks in background keeping all cores busy. Is it something related to 100% CPU utilisation ? For few other cases, it seemed as if it worked but gave no complexes with generete\_2.out showing this --------------- cycle= 100 ------ stepsize= 0.0003 ----------------------- | Etotal =154.401 grad(E)=3.037 E(BOND)=0.166 E(ANGL)=126.590 | | E(DIHE)=17.506 E(IMPR)=0.254 E(VDW )=9.884 | | --- | NBONDS: found 154320 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0002 ----------------------- | Etotal =143.248 grad(E)=3.036 E(BOND)=0.172 E(ANGL)=126.550 | | E(DIHE)=6.030 E(IMPR)=0.285 E(VDW )=10.212 | | --- | --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =139.753 grad(E)=3.033 E(BOND)=0.175 E(ANGL)=126.620 | | E(DIHE)=2.488 E(IMPR)=0.189 E(VDW )=10.282 | | --- | --------------- cycle= 250 ------ stepsize= -0.0002 ----------------------- | Etotal =138.643 grad(E)=3.029 E(BOND)=0.171 E(ANGL)=126.444 | | E(DIHE)=1.733 E(IMPR)=0.167 E(VDW )=10.127 | | --- | --------------- cycle= 300 ------ stepsize= -0.0002 ----------------------- | Etotal =138.396 grad(E)=3.028 E(BOND)=0.169 E(ANGL)=126.400 | | E(DIHE)=1.488 E(IMPR)=0.161 E(VDW )=10.178 | | --- | --------------- cycle= 350 ------ stepsize= -0.0002 ----------------------- | Etotal =138.392 grad(E)=3.028 E(BOND)=0.169 E(ANGL)=126.399 | | E(DIHE)=1.488 E(IMPR)=0.161 E(VDW )=10.176 | | --- | --------------- cycle= 400 ------ stepsize= -0.0005 ----------------------- Could you please guide how can I run docking for such a large dataset or where am I going wrong here? ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [February 2, 2021, 10:00am UTC](https://ask.bioexcel.eu/t/docking-of-2000-protein-antibody-pairs-using-haddock/2809/2 "2021-02-02T10:00:19Z")
> [@Gayatri1](#): > > while running for 2000 antigen-antibody pairs, it crashed multiple times This looks like a problem with your input data, hence no topology. Check if there is something wrong with these 2000 models, either in numbering, chain, molecule composition, heteroatoms and etc. The logs you posted here do not have any relevant information about the errors, please check the last lines of `begin/generate_x.out` to see why the topology could not be generated for each particular case. Good luck! ---
**Author:** ![Gayatri1](https://avatars.discourse-cdn.com/v4/letter/g/f1d935/32.png) [@Gayatri1](https://ask.bioexcel.eu/u/Gayatri1)\ **Post date:** [February 2, 2021, 12:00pm UTC](https://ask.bioexcel.eu/t/docking-of-2000-protein-antibody-pairs-using-haddock/2809/3 "2021-02-02T12:00:25Z")
Thanks for this quick response. So I have 18 antibodies that were docked with 120 antigen protein structures. There were in total ~2000 pairs for docking. One case in which the docking terminated had this in begin/generate\_x.out file. HEAP: maximum use = 20827112 current use = 96000 bytes HEAP: maximum overhead = 3008 current overhead = 752 bytes VCLOSE: Display file reset to OUTPUT. ============================================================ Maximum dynamic memory allocation: 20827112 bytes Maximum dynamic memory overhead: 3008 bytes Program started at: 14:40:33 on 31-Jan-2021 Program stopped at: 15:17:03 on 31-Jan-2021 CPU time used: 24.0398 seconds ============================================================ Regarding something wrong with the structures, I want to add that there were few cases for which same antigen model properly docked with an antibody while failed with another antibody. Also, the antibody structures were properly modelled since all the 18 antibodies worked well with negative and positive datasets. An example of same antigen with different antibody giving successful results for one case and failed for other case. generate\_2.out for successful run case. EVALUATE: symbol $OUTSTRING set to ““BEGIN:min\_3007k8x\_N440Y\_1.pdb”” (string) EVALUATE: symbol $NUM set to 2.00000 (real) NEXTCD: condition evaluated as false SELRPN: 9538 atoms have been selected out of 9538 ASSFIL: file min\_3007k8x\_N440Y.psf opened. ASSFIL: file min\_3007k8x\_N440Y.psf opened. HEAP: maximum use = 20768648 current use = 96000 bytes HEAP: maximum overhead = 3008 current overhead = 752 bytes VCLOSE: Display file reset to OUTPUT. ============================================================ Maximum dynamic memory allocation: 20768648 bytes Maximum dynamic memory overhead: 3008 bytes Program started at: 13:31:36 on 31-Jan-2021 Program stopped at: 13:43:13 on 31-Jan-2021 CPU time used: 23.6038 seconds generate\_2.out for a failed run case. EVALUATE: symbol $OUTSTRING set to ““BEGIN:min\_3007k8x\_N440Y\_1.pdb”” (string) EVALUATE: symbol $NUM set to 2.00000 (real) NEXTCD: condition evaluated as false SELRPN: 9538 atoms have been selected out of 9538 ASSFIL: file min\_3007k8x\_N440Y.psf opened. ASSFIL: file min\_3007k8x\_N440Y.psf opened. HEAP: maximum use = 20768648 current use = 96000 bytes HEAP: maximum overhead = 3008 current overhead = 752 bytes VCLOSE: Display file reset to OUTPUT. ============================================================ Maximum dynamic memory allocation: 20768648 bytes Maximum dynamic memory overhead: 3008 bytes Program started at: 13:58:57 on 31-Jan-2021 Program stopped at: 14:25:59 on 31-Jan-2021 CPU time used: 23.5330 seconds ============================================================ ---
**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:** [February 2, 2021, 12:54pm UTC](https://ask.bioexcel.eu/t/docking-of-2000-protein-antibody-pairs-using-haddock/2809/4 "2021-02-02T12:54:14Z")
Look for error messages in the generate\_X.out file in case of failures - start from the bottom of the file. If the psf files are not generated the docking can not proceed