Failure to write antibody-antigen-ambig.tbl

HADDOCK
,
1

Dear Developer,

I am using a local version of Haddock2.4 and following the ab-antigen tutorial where the paratope is known and the epitope is not.(Tutorial describing the use of a local version of HADDOCK2.4 – Bonvin Lab)

I will share some of the code for the HADDOCK setup:

pdb_reres -1 ${val1}_paragraph.pdb > ${val1}_haddock.pdb

mv ${val1}_haddock.pdb ../4_Haddock1

cd ../4_Haddock1

pdb_selchain -A ${antigen}.pdb | pdb_shiftres -500 > ${antigen}_ren.pdb

rm ${antigen}.pdb

mv ${antigen}_ren.pdb ${antigen}.pdb

sed -i ‘s/ENDMDL/END/g’ ${val1}_haddock.pdb

pdb_validate ${val1}_haddock.pdb

pdb_validate ${antigen}.pdb

restrain_bodies.py ${val1}_haddock.pdb > ${val1}_unambig.tbl

freesasa ${antigen}.pdb --format=rsa >${antigen}_haddock.rsa

echo " " >${antigen}_haddock_passive.list

awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’ ${antigen}_haddock.rsa >>${antigen}_haddock_passive.list

freesasa ${val1}_haddock.pdb --format=rsa >${val1}_haddock.rsa

echo " " >${val1}_haddock_active.list

awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’ ${val1}_haddock.rsa >>${val1}_haddock_active.list

active-passive-to-ambig.py ${val1}_haddock_active.list ${antigen}_haddock_passive.list | sed s/segid/name\ CA\ and\ segid/g | sed s/2.0/3.0/g >antibody-antigen-ambig.tbl

in the last command, I am supposed to produce the antibody-antigen-ambig.tbl file, which I do, except that is empty.

Could you help me identifying what I must have done wrong?

Thank you so much

Valerio

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

2

May-be for generating restraints in this case you could look at another tool we have to generate HADDOCK restraints:

[

Home - haddock-restraints
bonvinlab.org

favicon.png
](https://www.bonvinlab.org/haddock-restraints/home.html)

Debugging such scripts is typically a step by step process to figure out which step fails.

3

Dear developer,

Thanks, it worked!! I managed to write the .tbl file and run haddock.

I have another issue tough. I have decided to select my docking solution as follows:

run ana_cluster best 4
read the cluster with best haddock score from cluster_haddock-score.txt_best4
search the same cluster in cluster.out (which strangely only has two structures per cluster) and select the lowest number x after the “>”
look for the structure at line x in file.list.

By examining the resulting structure I realized that the Ab residues I have selected in the Ab_active_list.txt and included in the antibody-antigen_unambig.tbl are not involved in the interaction at all. here is a picture (residues from ab_active.list in yellow):

image
image872×503 147 KB

Then went to see if there are any AIR violations relative to this structure or its cluster and found none, which seems strange.

this is from the PBD:

REMARK FILENAME=“4_Haddock1_371w.pdb0”
REMARK ===============================================================
REMARK HADDOCK run for 4_Haddock1
REMARK initial structure: 4_Haddock1_371.pdb
REMARK ===============================================================
REMARK total,bonds,angles,improper,dihe,vdw,elec,air,cdih,coup,rdcs,vean,dani,xpcs,rg
REMARK energies: -371.633, 0, 0, 0, 0, -62.9218, -308.711, 0, 0, 0, 0, 0, 0, 0, 0
REMARK ===============================================================
REMARK bonds,angles,impropers,dihe,air,cdih,coup,rdcs,vean,dani,xpcs
REMARK rms-dev.: 0,0,0,0,0,0,0, 0, 0, 0, 0
REMARK ===============================================================
REMARK air,cdih,coup,rdcs,vean,dani,xpcs
REMARK >0.3,>5,>1,>0,>5,>0.2,>0.2
REMARK violations.: 0, 0, 0, 0, 0, 0, 0
REMARK ===============================================================
REMARK CVpartition#,violations,rms
REMARK AIRs cross-validation: 0, 0, 0
REMARK ===============================================================
REMARK NCS energy: 0
REMARK ===============================================================
REMARK Symmetry energy: 0
REMARK ===============================================================
REMARK Membrane restraining energy: 0
REMARK ===============================================================
REMARK Local cross-correlation: 0.0000
REMARK ===============================================================
REMARK Desolvation energy: 9.66111
REMARK Internal energy free molecules: -30951
REMARK Internal energy complex: -30811.4
REMARK Binding energy: -222.377
REMARK ===============================================================
REMARK buried surface area: 2116.55
REMARK ===============================================================
REMARK water - chain_1: 0 0 0
REMARK water - chain_2: 0 0 0
REMARK ===============================================================
REMARK water - water: 0 0 0
REMARK ===============================================================

and this from the cluster_haddock-sorted.stat

#Cluster haddock-score sd rmsd sd rmsd-Emin sd Nstruc Einter sd Enb sd Evdw+0.1Eelec sd Evdw sd Eelec sd Eair sd Ecdih sd Ecoup sd Esani sd Evean sd Edani sd #AIRviol sd #dihedviol sd #Coupviol sd #Saniviol sd #Veanviol sd #Daniviol sd BSA sd #dH sd #Edesolv sd
file.nam_clust16 -109.536 5.467 0.178 0.178 39.235 0.031 2 -365.91 5.72 -365.91 5.72 -88.22 5.57 -57.37 5.55 -308.54 0.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.000 2023.675 92.875 -201.199 21.178 9.540 0.121

Why is a structure with m
issing restraints claims to have zero restraint violations? And, if my restraints have been correctly passed, why such structure would rank so high? What am I missing/doing wrong?

I am running 10000 structures for it0, 400 for it1 and itw.

Here attached are the run.cns that I have used, as well as ab_active_list, antigen_passive_list

, ab-antigen.tbl and the cluster.out

Thanks for your help

Valerio Chiarini

run.txt (150.6 KB)
antibody-antigen-ambig.tbl (199.7 KB)
antigen_haddock_passive.list.txt (1.3 KB)
Ab_haddock_active.list.txt (45 Bytes)
cluster.out.txt (341 Bytes)

1 Like
4

The run.cns does not look like the one you used as it contain example PDB file from the HADDOCK examples…

No restraint energy might mean there is an error in your restraints definition (e.g. mismatch in chain IDs or numbering).

Did you try running this on the server?

If it works you can then check the generated restraint files and the run.cns file.

5

Yes, you’re right. I uploaded the wrong one. here the one I used:

run.cns.txt (150.7 KB)

sorry for the mis-upload

6

Could you share the full run directory via some download link?

7

Yes sure!!! here it is:

and here is the bash code I use to automatize the preparation and the submission of the run:

HADDOCK.txt (14.2 KB)

8

The problem comes from turning on random AIRs (the ranair=true parameter in run.cns).

This causes any restraint in ambig.tbl to be ignored.

9

Ok thanks!! I will risubmit right away. This might also be the cause for lack of cluster population? As I said, from cluster.out each cluster seems to be only two-structures big…