Installing pre-compiled APBS for electrostatic surface and PDB2PQR for protonation state calculations on Ubuntu/MacOsX

How to get APBS and PDB2PQR running

Source: ABPS & PDB2PQR

ABPS can be downloaded from the Github or Sourceforge repositories as pre-compiled binaries. However, after downloading the packages some additional things such as PATHs have to be adjusted to get the executable running. This article should give some hints and a solution how it worked out to get it running on Ubuntu_20.04 LTS and MacOsX_Catalina.

Before you start please register as it is mentioned on the Webpage!

ABPS (Adaptive Poisson-Boltzmann Solver) version 3.0.0

Should also work on WSL for Windows10

• Download abps from Github or Sourceforge for your system.
• Unzip and add the executables and libraries into your PATHs
• Copy the apbs into a directory you like, such as ~/programs.

Ubuntu

• Hence, the PATH of abps is not in your local path of programs you have to add it in your ~/.bashrc file.
• Therefore, add this somewhere in your ~/.bashrc file:

export PATH=~/programs/APBS-3.0.0.Linux/bin:$PATH

• APBS also requires different libraries which are included in the downloaded package, however as the executables, these are not in the local library paths.
• Add this somewhere in your ~/.bashrc file:

export LD_LIBRARY_PATH=~/programs/APBS-3.0.0.Linux/lib:$LD_LIBRARY_PATH

• Finally, source the ~/.bashrc file and you are able to execute it from the command-line.
• Additionally, apbs also requires the library package libreadline7_7.0,which can be installed via adding the package server to the /etc/apt/sources.listas it can be found here.

e.g. deb http://cz.archive.ubuntu.com/ubuntu bionic main

• With the apt package manager libreadline7_7.0 can be installed

sudo apt-get update

sudo apt-get upgrade

sudo apt-get install libreadline7

• Now apbs should run…

It is not recommended to download the .deb package and to add it manually via the Ubuntu Software Center, therefore use the way via the package server and apt

• Finally, source the ~/.bashrcfile or restart the terminal and you are able to execute it from the command-line.

Mac

• Add this somewhere in your ~/.bash_profile file

export PATH=~/programs/APBS-3.0.0.Darwin/bin:$PATH

• Again we have also to add the libs into the environmental paths.
• Add this somewhere in your ~/.bash_profile file:

export DYLD_FALLBACK_LIBRARY_PATH=~/programs/APBS-3.0.0.Darwin/lib:$DYLD_FALLBACK_LIBRARY_PATH

• Additionally, apbs also requires a library, which is installed by gcc, therefore you have to install gcc, however apbs is linked to gcc_9, hence there is a newer version of gcc you have to add a link from the folder with 10 to 9.

brew install gcc

ln -s /usr/local/opt/gcc/lib/gcc/10 /usr/local/opt/gcc/lib/gcc/9

• Finally, source the ~/.bash_profilefile or restart the terminal and you are able to execute it from the command-line.

PDB2PQR version 2.1.1

• Download the latest release of pdb2pqr from the Github repository.
• Extract it and copy the folder into a directory you like, such as ~/programs.
• If your folder ~/programs is in your PATH you can make a symbolic link to it

Ubuntu

ln -s ~/programs/pdb2pqr-linux-bin64-2.1.1/pdb2pqr ~/programs

• or you can make the link to a standard path such as /usr/local/bin

sudo ln -s ~/programs/pdb2pqr-linux-bin64-2.1.1/pdb2pqr /usr/local/bin

Mac

ln -s ~/programs/pdb2pqr-osx-bin64-2.1.1/pdb2pqr ~/programs

• or you can make the link to a standard path such as /usr/local/bin

sudo ln -s ~/programs/pdb2pqr-osx-bin64-2.1.1/pdb2pqr /usr/local/bin