CNS Installation

The computational engine for most of HADDOCK3’s modules is the Crystallography and NMR System (CNS). Once you have cloned the HADDOCK3 repository, please follow these instructions to compile a CNS executable that can be used to run HADDOCK.

Before starting, make sure you download the system requirements, they are gcc, gfortran and csh. Luckily they are easily available from the package manager, so if you are using Ubuntu (for example):

sudo apt-get install gcc gfortran csh

Make sure gfortran is in your $PATH, check it with which gfortran.

1. Downloading CNS

Downloading CNS requires a license, which academic users can request for free.

To Download CNS, go to their website and click on the Download menu and fill the form. You will be sent a password for the download via e-mail - keep in mind only education e-mails are allowed for this.

You will receive a login/password in the e-mail, once you have those go to the download page and use the provided login/password to download the CNS package - the archive you need is: cns_solve_1.3_all.tar.gz.

The CNS website is not currently using SSL certificates, this mean your download might be blocked or it might give you a warning, double check in your browser.

Once the archive cns_solve_1.3_all.tar.gz has been downloaded, move it to a $HOME/software directory (or any other directory of your choice) and decompress it:

mkdir ~/software
mv ~/Downloads/cns_solve_1.3_all.tar.gz ~/software/
tar -zxvf cns_solve_1.3_all.tar.gz

The command above will have create a cns_solve_1.3 directory in the ~/software directory, containing the CNS source code.

2. Configuring CNS

Go to the CNS directory:

cd cns_solve_1.3

Inside this directory there will be a cns_solve_env file.

You need to edit this file to point to the current directory.

You will need to change line 18 of this file to point to the current directory.

You can do that either by opening this file in a code editor such as VScode or vim, or by running the command below:

sed -i 's@_CNSsolve_location_@'"$PWD"'@' cns_solve_env

Note: On a Mac, the default sed version will give an error with the above command. Install instead gnu-sed using brew, and then replace sed by gsed in the above command.

Check if the substitution worked:

sed -n 18p cns_solve_env

The expected output will be (with the path to your CNS installation directory):

        setenv CNS_SOLVE '/Absolute/path/where/cns_solve/is/cns_solve_1.3'

3. Patch CNS with HADDOCK custom files

For HADDOCK to use CNS, some modifications were made to the CNS source code. We provide those modifications together with the haddock3 source files.

❗ You cannot use CNS in HADDOCK without these patched files❗

Copy the CNS files distributed with HADDOCK3 to the CNS directory:

\cp -r ~/software/haddock3/varia/cns1.3/[bis]*  ~/software/cns_solve_1.3/

Note: Make sure to use the correct path to your haddock3 location in the above command.

4. Compiling CNS

Before installing CNS, you need to check wether your operating system is supported by CNS.

The list of supported architectures can be seen with the following command:

ls ~/software/cns_solve_1.3/instlib/machine/supported
arm-aarch64-linux  intel-x86_64bit-linux  linux  mac-arm-darwin  mac-intel-darwin

To check what is your architecture, type the following command:


You might get something like unknown-..., in that case installation is still possible, however it means the compiler options might not be properly defined - check the Troubleshooting section

Several Makefile headers are already provided - here we will use on the one that uses gfortran as the compiler.

Now it is time to compile CNS, you can do that with the following command:

make install compiler=gfortran

You should see the progress of the compilation, followed by a confirmation that an executable has been created.

The executable will be located in a new architecture-specific directory.

For example under Linux (Intel or AMD processors) it will be under ~software/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-XXXXXXX.exe And on a Mac with arm processors (M1/2/3) is will be under ~software/cns_solve_1.3/mac-arm64-darwin/source/cns_solve-XXXXXXX.exe

The XXXXXXX will be a number specific to your compilation.

Check if it is working by executing it:


If you see the CNS prompt, the compilation was successful! 🎉

|                                                          |
|            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)

The command to exit CNS is stop!

If this does not work, check the troubleshooting section below.

Note: If you want to use CNS as standalone application, you should first source the cns_solve_env file (csh) or .cns_solve_env_sh file (bash). CNS will then be defined in you path and can be simply started using cns as command. If using bash, make sure to first edit the cns_solve_env variable in the .cns_solve_env_sh file to define the installation directory as described above.

5. Installing the created CNS executable into haddock3

You can find the freshly compiled CNS executable a newly created directory in the CNS installation directory named after the architecture of your system. E.g. for a M1/2/3/ Mac Arm processor it will be mac-arm64-darwin. In the source directory in that directory you can find the compiled CNS executable.

ls mac-arm64-darwin/source/*exe
> mac-arm64-darwin/source/cns_solve-2405221019.exe

You can then copy this executable into the haddock3/bin directory, renaming it simply to cns.


1. System not recognized

If the installation fails because your OS/hardware are not recognized, most likely the bin/getarch script needs to be updated.

From within your CNS installation directory type the following command to check if your system is recognized:


For an unknown system you might see as output:

~/software/cns_solve_1.31-UU> ./bin/getarch

If your OS/hardware is unknown, this is not per se a problem, but it means the compiler options might not be properly defined. For example, the default CNS package will not recognize the Mac M1/2/3/ processors (but after copying the CNS files distributed with haddock3 it should!). To solve that edit the ./bin/get_arch script and add lines such as your system be recognized (e.g. after line 179 - this should be added after a line containing exit 0). Here is an example to add support for the Mac M1/2/3 processors:

    echo mac-arm64-darwin
    exit 0 ;;

You should then create a directory under instlib/machine/supported with the same name as the one you defined in getarch. Copy then and edit if needed the files from another supported system into the directory you created.

2. Compiler

If no suitable compiler is found, you will get an error message:

Error: no suitable compiler (ifort, pgf95, ifort_i4, ifort_mp or pgf95_mp) found

In this case, you will have to install a compiler. For more information, check the CNS Installation page. One Fortran compiler that is easy (and free) to install is gfortran. It is part of the GNU Compiler Collection (GCC), which can be installed with one command if you have homebrew:

brew install gcc

Alternatively, gfortran can be downloaded as a separate binary.

3. Makefile

If a suitable compiler is installed but no corresponding Makefile.header is found, make install will give an error as well. For example (with gfortran):

Error: Makefile template for compiler gfortran is not available

Makefile headers for each supported system-compiler combination are provided in instlib/machine/supported/ (for unsupported systems, see instlib/machine/unsupported/). If you already tried make install, the appropriate directory for your system (eg. mac-intel-darwin) will have been copied to the main cns_solve_1.3 directory. If this directory does not contain the desired file (eg. Makefile.header.2.gfortran), you can create one manually.

For example, for gfortran, create a new file named Makefile.header.6.gfortran inside the directory containing Makefile headers for your system. Save the following lines in this file:

# fortran options
F77 = gfortran
F77STD = -fdefault-integer-8 -w -fallow-argument-mismatch
F77OPT = -O3 $(CNS_MALIGN_I86) -funroll-loops -ffast-math -march=native -mtune=native
F77FLAGS = $(F77STD) $(F77OPT) $(EXT_F77FLAGS) $(F77BUG)

# C options
CC = gcc
CPP = g++

# link options
LD = gfortran
LDFLAGS = -w $(EXT_LDFLAGS) -static-libgfortran

Note the -fallow-argument-mismatch flag. From gfortran version 10 onward, type mismatches by default give an error rather than a warning. This flag returns warnings instead, so that CNS compilation can successfully complete. If a Makefile.header.x.gfortran is provided for your system but compilation fails with (many) Error: Type mismatch, you may need to add this flag to the provided file.