gnina
Overview
gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina.
The binary 1.3.1 version is installed on the CSF.
Restrictions on use
gnina is dual licensed under GPL and Apache. The GPL license is necessitated by the use of OpenBabel (which is GPL licensed). In order to use gnina under the Apache license only, all references to OpenBabel must be removed from the source code.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this.
Load one of the following modulefiles:
module load apps/binapps/gnina/1.3.1
Running the application
Please do not run gnina on the login node. gnina is intended to run using GPU/s.
GPU batch job submission
#!/bin/bash --login #SBATCH -p gpuA # A100 (80GB) GPUs ### Required flags #SBATCH -G N # (or --gpus=N) Number of GPUs #SBATCH -t 1-0 # Wallclock timelimit (1-0 is one day, 4-0 is max permitted) ### Optional flags #SBATCH -n 12 module purge module load apps/binapps/gnina/1.3.1 # See below for specific versions gnina args ... # See usage guidelines https://github.com/gnina/gnina?tab=readme-ov-file#usage
Submit the jobscript using:
sbatch scriptname