This program generates input decks for miniBUDE from a set of mol2 and bhff files.
Sample mol2 and bhff files can be found in raw/*.
The program uses CMake and requires a C++17-conformant compiler with OpenMP support and the appropriate C++17 standard library. For GCC, the first version supported is 9.3.0.
First, generate a build:
cmake -Bbuild -H. -DCMAKE_BUILD_TYPE=Release
And then proceed with compilation:
cmake --build build --target makedeck --config Release
The binary will be located at build/makedeck.
To generate an input deck, simply specify all the required parameters as described in --help:
This program generates input decks for the bude benchmark program.
Usage: ./makedeck [OPTIONS]
Options:
-h --help Print this message
-f --forcefield Path to a forcefield bhff file
-p --protein Path to a protein mol2 file
-l --ligand Path to a ligand mol2 file
-s --pose-seed The random seed used to generate pose combinations (default: 42)
-n --pose-length The amount of poses to generate (default: 65536)
-o --out The output directory (containing {protein,ligand,forcefield,poses}.dat,{input,energies}.txt) name of the decks
--force If specified, any file/directory that matches the output dir name will be deleted/overwritten
For example:
./makedeck -f heavy_by-residue_2016-v1.bhff -p scan_receptorSurfPoint00000099.mol2 -l scan_receptorSurfPoint00000099.mol2 -o output --force
The deck will be created in a directory named output.
It should contain the following files:
forcefield.in
ligand.in
poses.in
protein.in
params.txt # contains original program arguments used to generate this deck
ref_energies.out # contains reference energies used for verification
The input deck directory can then be specified in all miniBUDE implementations:
./bude --deck output
This project contains unit tests. First, create a debug build:
cmake -Bbuild -H. -DCMAKE_BUILD_TYPE=Debug
And then proceed with compilation:
cmake --build build --target tests --config Debug
And then run the test binary build/tests.