Trouble Configuring HADDOCK2.5

HADDOCK
1

Hi!
I’ve been able to complete CNS setup, but the final steps of the HADDOCK setup (for Haddock2.4 from the instruction manual webpage) don’t seem to be working for me:

Edit then a configuration file specific to your system.

This configuration file should contain the following information:

CNSTMP defining the location of your CNS executable
QUEUETMP defining the submission command for running the jobs (e.g. either via csh or through a specific command submitting to your local batch system)
NUMJOBs defining the number of concurrent jobs executed (or submitted).
QUEUESUB defining the HADDOCK python script used to run the jobs (the default QueueSubmit_concat.py should do in most cases).

And example configuration file for running on local resources assuming a 4 core system would be:

set CNSTMP=/home/software/cns/cns_solve-1.31-UU-Linux64bits.exe set QUEUETMP=/bin/csh set NUMJOB=4 set QUEUESUB=QueueSubmit_concat.py

For submitting to a batch system instead you might want to use a wrapper script. An example for torque can be found here.

In order to configure HADDOCK, call the install.csh script with as argument the configuration script you just created:

./install.csh my-config-file

I also tried using a wrapper script for running on slurm instead but this also didn’t seem to work for me.

This is my current configuration file:
cat haddock_config.ini
[HADDOCK]
CNS_EXE=/scratch/dkarunat/software/haddock2.5-2024-12/bin/cns
QUEUE_CMD=/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/csh
NUM_JOBS=20
SUBMIT_SCRIPT=ssub_slurm

This is my current SLURM wrapper script:
#!/bin/csh -f
if ($#argv < 1) then
** echo “Usage : ssub_slurm jobname”**
** exit 1**
endif

# check if job exists + make it executable
set jobname=$1
if (! -e $1) then
** echo “job file does not exist”**
** exit 1**
endif
if (! -x $jobname) chmod +x $jobname

# write temporary slurm script
set slurmjob=$jobname.slurmjob.$$
if (! -e $slurmjob) then
** touch $slurmjob**
else
** \rm $slurmjob**
** touch $slurmjob**
endif
set PWD=pwd

echo “#!/bin/csh” >> $slurmjob
echo “#SBATCH --job-name=$jobname” >> $slurmjob
echo “#SBATCH --output=$PWD/$jobname.out.%j” >> $slurmjob
echo “#SBATCH --error=$PWD/$jobname.err.%j” >> $slurmjob
echo “#SBATCH --ntasks=1” >> $slurmjob
echo “#SBATCH --cpus-per-task=1” >> $slurmjob
echo “cd $PWD” >> $slurmjob
echo “./$jobname” >> $slurmjob

chmod +x $slurmjob
sbatch $slurmjob
rm -f $slurmjob
exit

2

QUEUE_CMD should point to your slurm submission script

3

Oh okay, so it should look like this?

[HADDOCK]
CNS_EXE=/scratch/dkarunat/software/haddock2.5-2024-12/bin/cns
QUEUE_CMD=ssub_slurm
NUM_JOBS=20
SUBMIT_SCRIPT=ssub_slurm

4

You don’t need the SUBMIT_SCRIPT entry
and best to give the full path to your script

5

Thank you! I believe that it worked:

This was the content of my final configuration file:

cat haddock_config.ini
[HADDOCK]
CNS_EXE=/scratch/dkarunat/software/haddock2.5-2024-12/bin/cns
QUEUE_CMD=/scratch/dkarunat/software/haddock2.5-2024-12/ssub_slurm
NUM_JOBS=20
[THIRD_PARTY]
PRODIGY=
WHISCY=
DISVIS=

python3 install.py haddock_config.ini
[2025/07/17 13:02:15] Reading configuration file
[2025/07/17 13:02:15] success!
[2025/07/17 13:02:15] Editing run.cns
[2025/07/17 13:02:16] success!
[2025/07/17 13:02:16] Configuring queue submission scripts
[2025/07/17 13:02:16] success!
[2025/07/17 13:02:16] Configuring results processing scripts
[2025/07/17 13:02:16] success!
[2025/07/17 13:02:16] Compiling C/C++ tools
[2025/07/17 13:02:21] success!
[2025/07/17 13:02:21] Writing source files
[2025/07/17 13:02:21] success!

6

Are you actually following the installation instructions of haddock2.5?

Check the INSTALLATION.md file in the haddock2.5 directory

7

I’ve tried to follow the instructions in that file and also the instructions in the manual on the haddock2.4 webpage, but I keep getting stuck.

The INSTALLATION.md file mentioned to install the third party software and I’ve downloaded the auxillary software mentioned on the webpage: CNS, Python 3.11, FreeSASA, reduce (MolProbity), HADDOCK-tools, PDB-tools.

But I’m not sure where to find the links mentioned for:
third-party executable not found in PATH: NACCESS
third-party executable not found in PATH: PALES
third-party executable not found in PATH: PROFIT
third-party executable not found in PATH: TENSOR2

I’ve followed the instructions for CNS and then tried to run haddock. I got the following output:

[dkarunat@gra-login2 haddock2.5-2024-12]$ python install.py configs/config.local
[2025/07/19 18:52:36] Reading configuration file
[2025/07/19 18:52:36] success!
[2025/07/19 18:52:36] Editing run.cns
[2025/07/19 18:52:36] success!
[2025/07/19 18:52:36] Configuring queue submission scripts
[2025/07/19 18:52:36] success!
[2025/07/19 18:52:36] Configuring results processing scripts
[2025/07/19 18:52:36] success!
[2025/07/19 18:52:36] Compiling C/C++ tools
[2025/07/19 18:52:41] success!
[2025/07/19 18:52:41] Writing source files
[2025/07/19 18:52:41] third-party executable not found in PATH: NACCESS
[2025/07/19 18:52:41] third-party executable not found in PATH: PALES
[2025/07/19 18:52:41] third-party executable not found in PATH: PROFIT
[2025/07/19 18:52:41] third-party executable not found in PATH: TENSOR2
[2025/07/19 18:52:41] success!

But I still am unable to run haddock on the example files:

[dkarunat@gra-login2 run1]$ haddock2.5
[2025-07-19 19:00:37]
##############################################################################

Starting HADDOCK2.5 #
#
N-components version of HADDOCK (current maximum is 20) #
#
Copyright 2003-2024 Alexandre Bonvin, Utrecht University. #
Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. #
All rights reserved. #
This code is part of the HADDOCK software and governed by its #
license. Please see the LICENSE file that should have been included #
as part of this package. #

##############################################################################

[2025-07-19 19:00:37] Starting HADDOCK
[2025-07-19 19:00:37] HADDOCK version: 2.5 - December 2024
[2025-07-19 19:00:37] Parsing run.cns file
[2025-07-19 19:00:37] Parsing run.param in /scratch/dkarunat/software/haddock2.5-2024-12/examples/protein-ligand/run1/data
[2025-07-19 19:00:37] Reading parameters from the file /scratch/dkarunat/software/haddock2.5-2024-12/examples/protein-ligand/run1/data/run.param
[2025-07-19 19:00:37] setting some variables:
[2025-07-19 19:00:37] AMBIG_TBL set to: ./ambig-active-it0.tbl
[2025-07-19 19:00:37] HADDOCK_DIR set to: ../..
[2025-07-19 19:00:37] N_COMP set to: 2
[2025-07-19 19:00:37] PDB_FILE1 set to: ./neuraminidase-2BAT.pdb
[2025-07-19 19:00:37] PDB_FILE2 set to: ./oseltamivir_zwitterion.pdb
[2025-07-19 19:00:37] PROJECT_DIR set to: .
[2025-07-19 19:00:37] PROT_SEGID_1 set to: A
[2025-07-19 19:00:37] PROT_SEGID_2 set to: B
[2025-07-19 19:00:37] RUN_NUMBER set to: 1
[2025-07-19 19:00:37] UNAMBIG_TBL set to: ./ambig-passive-it1.tbl
[2025-07-19 19:00:37] AMBIG_TBL ./ambig-active-it0.tbl
[2025-07-19 19:00:37] HADDOCK_DIR ../..
[2025-07-19 19:00:37] N_COMP 2
[2025-07-19 19:00:37] PDB_FILE1 ./neuraminidase-2BAT.pdb
[2025-07-19 19:00:37] PDB_FILE2 ./oseltamivir_zwitterion.pdb
[2025-07-19 19:00:37] PROJECT_DIR .
[2025-07-19 19:00:37] PROT_SEGID_1 A
[2025-07-19 19:00:37] PROT_SEGID_2 B
[2025-07-19 19:00:37] RUN_NUMBER 1
[2025-07-19 19:00:37] UNAMBIG_TBL ./ambig-passive-it1.tbl
[2025-07-19 19:00:37] Looking for existing files
[2025-07-19 19:00:38] waterdock false
[2025-07-19 19:00:38] Generating PSF and PDB file of molecule 1
[2025-07-19 19:00:38] Generating PSF and PDB file of molecule 2
[2025-07-19 19:00:38] waiting for the psf files…
[2025-07-19 19:00:38] waiting for the psf files…
[2025-07-19 19:00:49] waiting for the psf files…
[2025-07-19 19:00:49] waiting for the psf files…
[2025-07-19 19:01:01] waiting for the psf files…
[2025-07-19 19:01:01] waiting for the psf files…
[2025-07-19 19:01:11] waiting for the psf files…
[2025-07-19 19:01:11] waiting for the psf files…
[2025-07-19 19:01:23] waiting for the psf files…
[2025-07-19 19:01:23] waiting for the psf files…
[2025-07-19 19:01:33] waiting for the psf files…
[2025-07-19 19:01:33] waiting for the psf files…
[2025-07-19 19:01:44] waiting for the psf files…
[2025-07-19 19:01:44] waiting for the psf files…
[2025-07-19 19:01:57] waiting for the psf files…
[2025-07-19 19:01:57] Error in the topology generation: prot_psf_mol2 could not be created
[2025-07-19 19:01:57] HADDOCK stopped
[2025-07-19 19:01:57] ##############################################################################
[2025-07-19 19:01:57] Finishing HADDOCK
[2025-07-19 19:01:57] Au revoir. Tot ziens. Bye bye.

8

third-party executable not found in PATH: NACCESS
third-party executable not found in PATH: PALES
third-party executable not found in PATH: PROFIT
third-party executable not found in PATH: TENSOR2

Not an issue. But installing profit could be nice to run the analysis. This is the software used in some scripts to calculate RMSDs.

Is the CNS executable working?
The one you defined in the config file.
For some troubleshooting instructions see: https://github.com/haddocking/haddock3/blob/main/docs/CNS.md

Try calling it from the command line.

Also if you are trying the protein-ligand example, you should follow the commands defined in run-example.csh as it does require copying the ligand param/topo files into the HADDOCK run directory.

Try first the protein-protein example

9

[dkarunat@gra-login2 haddock2.5-2024-12]$ cat /scratch/dkarunat/software/haddock2.5-2024-12/haddock_config.ini
[HADDOCK]
CNS_EXE=/scratch/dkarunat/software/haddock2.5-2024-12/bin/cns
QUEUE_CMD=/scratch/dkarunat/software/haddock2.5-2024-12/ssub_slurm
NUM_JOBS=20
[THIRD_PARTY]
PRODIGY=
WHISCY=
DISVIS=

[dkarunat@gra-login2 haddock2.5-2024-12]$ /scratch/dkarunat/software/haddock2.5-2024-12/bin/cns
============================================================
** | |**
** | Crystallography & NMR System (CNS) |**
** | CNSsolve |**
** | |**
** ============================================================**
** Version: 1.3 at patch level U**
** Status: Special UU release with Rg, paramagnetic**
** and Z-restraints (A. Bonvin, UU 2013)**
** ============================================================**
** Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,**
** P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,**
** J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,**
** L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.**
** Copyright (c) 1997-2010 Yale University**
** ============================================================**
** Running on machine: hostname unknown (x86_64/Linux,64-bit)**
** Program started by: dkarunat**
** Program started at: 12:19:05 on 20-Jul-2025**
** ============================================================**

** FFT3C: Using FFTPACK4.1**

CNSsolve>^C
[dkarunat@gra-login2 haddock2.5-2024-12]$

I ran the protein-protein example using:
cd /scratch/dkarunat/software/haddock2.5-2024-12/examples/protein-protein
source /scratch/dkarunat/software/haddock2.5-2024-12/haddock_configure.sh
csh run-example.csh

[dkarunat@gra-login2 protein-protein]$ csh run-example.csh

==========================================================

RUNNING NOW E2A-HPR PROTEIN-PROTEIN DOCKING EXAMPLE

==========================================================

######################################################

HADDOCK scoring water

=========== run1 =============

===> Cluster stats water <====

===> Cluster stats it1 <====

===> water single structure i-RMSD stats <====
water first medium <2A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
water first acceptable <4A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
water best acceptable or higher : Rank 78 i-RMSD: 0.00 Fnat: 0.00

===> it1 single structure i-RMSD stats <====
it1 first medium <2A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
it1 first acceptable <4A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
it1 best acceptable or higher : Rank 147 i-RMSD: 0.00 Fnat: 0.00

===> it0 single structure i-RMSD stats <====
it0 first medium <2A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
it0 first acceptable <4A : Rank 1 i-RMSD: 0.00 Fnat: 0.00
it0 best acceptable or higher : Rank 391 i-RMSD: 0.00 Fnat: 0.00

===> Overall number of acceptable or better models <===

it0: structures with i-RMSD<4A: 1000

it0: structures within best200 with i-RMSD<4A: 200

it0: structures within best200 with i-RMSD<2A: 200

it0: structures within best200 with i-RMSD<1A: 200

it1: structures with i-RMSD<4A: 200

it1: structures with i-RMSD<2A: 200

it1: structures with i-RMSD<21: 200

water: structures with i-RMSD<4A: 200

water: structures with i-RMSD<2A: 200

water: structures with i-RMSD<1A: 200

==========================================================

E2A-HPR PROTEIN-PROTEIN DOCKING EXAMPLE COMPLETED

==========================================================

[dkarunat@gra-login2 protein-protein]$

I still have to download PROFIT, but I think that it worked otherwise, as the following outputs were created:
[dkarunat@gra-login1 run1]$ ls -l
total 757
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:25 begin
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 begin-aa
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 data
-rw-r----- 1 dkarunat dkarunat 196 Jul 20 12:46 haddock.log
-rw-r----- 1 dkarunat dkarunat 17261 Jul 20 13:01 haddock.out
drwxrwx— 2 dkarunat dkarunat 4096 Jul 20 12:24 packages
-rw-r----- 1 dkarunat dkarunat 24319 Jul 20 12:43 protein-protein_run1_1w.inp
-rwxr-x— 1 dkarunat dkarunat 584 Jul 20 12:43 protein-protein_run1_1w.job
-rw-r----- 1 dkarunat dkarunat 100719 Jul 20 12:44 protein-protein_run1_1w.out.gz
-rwxr-x— 1 dkarunat dkarunat 669 Jul 20 12:43 protein-protein_run1_fcc_matrix.job
-rwxr-x— 1 dkarunat dkarunat 675 Jul 20 13:00 protein-protein_run1_fcc_matrix-water.job
-rw-r----- 1 dkarunat dkarunat 27032 Jul 20 12:24 protein-protein_run1_generate_1.inp
-rwxr-x— 1 dkarunat dkarunat 349 Jul 20 12:24 protein-protein_run1_generate_1.job
-rw-r----- 1 dkarunat dkarunat 27032 Jul 20 12:24 protein-protein_run1_generate_2.inp
-rwxr-x— 1 dkarunat dkarunat 349 Jul 20 12:24 protein-protein_run1_generate_2.job
-rwxr-x— 1 dkarunat dkarunat 349 Jul 20 12:25 protein-protein_run1_generate_complex.job
-rwxr-x— 1 dkarunat dkarunat 318 Jul 20 13:00 protein-protein_run1_get_average.job
-rw-r----- 1 dkarunat dkarunat 53367 Jul 20 12:25 protein-protein_run1_it0_refine_1.inp
-rwxr-x— 1 dkarunat dkarunat 623 Jul 20 12:25 protein-protein_run1_it0_refine_1.job
-rw-r----- 1 dkarunat dkarunat 53369 Jul 20 12:32 protein-protein_run1_it1_refine_1.inp
-rwxr-x— 1 dkarunat dkarunat 630 Jul 20 12:32 protein-protein_run1_it1_refine_1.job
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 protocols
-rw-r----- 1 dkarunat dkarunat 153984 Jul 20 12:24 run.cns
-rw-r----- 1 dkarunat dkarunat 153981 Jul 20 12:24 run.cns.orig
-rw-r----- 1 dkarunat dkarunat 153986 Jul 20 12:28 run_newseed.cns
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 structures
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 tools
drwxr-x— 2 dkarunat dkarunat 4096 Jul 20 12:24 toppar