ADAPT download and installation

You will need to register to download the software.

ADAPT requires FoldX, Rosetta, SCWRL, AmberTools, sietraj, brimin to be installed independently. Before running ADAPT, please make sure that the environment (e.g. LD_LIBRARY_PATH variable) is properly set for these programs.

The current version was tested on CentOS 8.2 with FoldX 5, Rosetta 3.5 fixbb, Rosetta 3.9 rosetta_scripts and Scwrl 4.0.

1. Unpack the archive
2. Edit the adapt.sh, adapt.csh, modulefiles/adapt source files to reflect the location of the ADAPT directory, the Biopython directory, the AmberTools directory (AMBERHOME), the FoldX executable, the rosetta_scripts and fixbb executables, the SCWRL executable, and the sietraj and brimin executables.
   One of these files (depending on your environment) will need to be sourced to prepare your environment before running any of the provided scripts (see Linux Environment below). The Module file must also be moved to the appropriate location (please ask your system administrator if necessary).
3. Run the install_biopython.sh script to install a custom version of Biopython (required in the FoldX and Rosetta protocols). This requires that python3 as well as gcc, patch and possibly other packages are already installed on the machine.

Before running any of the provided scripts, it is required to source one of the environment files:

   Bash users:          source path/to/adapt.sh
   Csh/Tcsh users:      source path/to/adapt.csh
   Module users:        module load adapt

The following environment variables must also be set:

   AB_CHAINS :: comma separated list of the PDB chain identifiers of the antibody, for example H,L
   ACIDIC    :: set to 'yes' for a low-pH treatment of HIS and GLU residues (empty otherwise).

Please refer to the README.txt file inside the archive for additional information on Structure Preparation and Mutant identification.nt identification.

Send feedback, suggestions or queries to mm-admin@nrc-cnrc.gc.ca.