- OpenCL-accelerated version of AutoDock4.2.6. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.
- Besides the legacy Solis-Wets local search method, AutoDock-GPU adds newly implemented local-search methods based on gradients of the scoring function. One of these methods, ADADELTA, has proven to increase significantly the docking quality in terms of RMSDs and scores.
- It targets platforms based on GPU as well as multicore CPU accelerators.
- Observed speedups of up to 4x (quad-core CPU) and 56x (GPU) over the original serial AutoDock 4.2 (Solis-Wets) on CPU.
| Operating system | CPU | GPU |
|---|---|---|
| CentOS 6.7 & 6.8 / Ubuntu 14.04 & 16.04 | Intel SDK for OpenCL 2017 | AMD APP SDK v3.0 / CUDA v8.0 & v9.0 |
| macOS Catalina 10.15.1 | Apple / Intel | Apple / Intel Iris, Radeon Vega 64 |
Other environments or configurations likely work as well, but are untested.
make DEVICE=<TYPE> NUMWI=<NWI>| Parameters | Description | Values |
|---|---|---|
<TYPE> |
Accelerator chosen | CPU, GPU |
<NWI> |
OpenCL work-group size | 1, 2, 4, 8, 16, 32, 64, 128, 256 |
Hints: The best work-group size depends on the GPU and workload. Try NUMWI=128 or NUMWI=64 for modern cards with the example workloads. On macOS, use NUMWI=1 for CPUs.
After successful compilation, the host binary autodock_<type>_<N>wi is placed under bin.
| Binary-name portion | Description | Values |
|---|---|---|
| <type> | Accelerator chosen | cpu, gpu |
| <N> | OpenCL work-group size | 1, 2, 4, 8,16, 32, 64, 128, 256 |
./bin/autodock_<type>_<N>wi \
-ffile <protein>.maps.fld \
-lfile <ligand>.pdbqt \
-nrun <nruns>| Mandatory options | Description | Value |
|---|---|---|
| -ffile | Protein file | <protein>.maps.fld |
| -lfile | Ligand file | <ligand>.pdbqt |
./bin/autodock_gpu_64wi \
-ffile ./input/1stp/derived/1stp_protein.maps.fld \
-lfile ./input/1stp/derived/1stp_ligand.pdbqt \
-nrun 10By default the output log file is written in the current working folder. Examples of output logs can be found under examples/output.
| Argument | Description | Default value |
|---|---|---|
| -nrun | # LGA runs | 1 |
| -nev | # Score evaluations (max.) per LGA run | 2500000 |
| -ngen | # Generations (max.) per LGA run | 27000 |
| -lsmet | Local-search method | sw (Solis-Wets) |
| -lsit | # Local-search iterations (max.) | 300 |
| -psize | Population size | 150 |
| -mrat | Mutation rate | 2 (%) |
| -crat | Crossover rate | 80 (%) |
| -lsrat | Local-search rate | 80 (%) |
| -trat | Tournament (selection) rate | 60 (%) |
| -resnam | Name for docking output log | "docking" |
| -hsym | Handle symmetry in RMSD calc. | 1 |
| -devnum | OpenCL device number | 1 |
| -cgmaps | Use individual maps for CG-G0 instead of the same one | 0 (use same map) |
For a complete list of available arguments and their default values, check getparameters.cpp.
Visit the project Wiki.