1. Quick start

1.1 Install Vina LC

Download the tarball of VinaLC. Unzip

tar -zxvf VinaLC.tar.gz

cd VinaLC 

In the VinaLC home directory, there is build script named "build". Inside the file you have to set your Boost and MPI path. For example

./makeit --build --boost=/path/to/boost/installation/directory --mpi=/path/to/mpi/installation/directory

This will configure the program and subsequently compile the executable. The executable, vinaBMPI, can be found under the apps subdirectory.

1.2 Run VinaLC

To run the program with slurm in debug mode:

srun -N4 -n4 -c12 -ppdebug ./vinaBMPI --recList recList.txt --ligList ligList.txt --geoList geoList.txt

-N4: 4 nodes will use -n4: 4 tasks will each task run on one node -c12: 12 threads will run on each node -ppdebug: use debug mode

1.2.2. Vina program option:

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./vinaBMPI --help

Input:
  --recList arg              receptor list file
  --fleList arg              flex part receptor list file
  --ligList arg              ligand list file
  --geoList arg              receptor geometry file
  --exhaustiveness arg (=8)  exhaustiveness (default value 8) of the global 
                             search (roughly proportional to time): 1+
  --granularity arg (=0.375) the granularity of grids (default value 0.375)
  --num_modes arg (=9)       maximum number (default value 9) of binding modes 
                             to generate
  --seed arg                 explicit random seed
  --randomize arg            Use different random seeds for complex
  --energy_range arg (=2)    maximum energy difference (default value 2.0) 
                             between the best binding mode and the worst one 
                             displayed (kcal/mol)
  --useScoreCF               Use score cutoff to save ligand with top score 
                             higher than certain critical value
  --scoreCF arg (=-8)        Score cutoff to save ligand with top score higher 
                             than certain value (default -8.0)

Information (optional):
  --help                display usage summary

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1.3. Run with different options

srun -N4 -n4 -c12 ./vinaBMPI --recList recList.txt --ligList ligList.txt
            --geoList geoList.txt --exhaustiveness 12 

srun -N4 -n4 -c12 ./vinaBMPI --recList recList.txt --ligList ligList.txt 
     
--geoList geoList.txt --exhaustiveness 12 --granularity 0.333 ...

Options, --recList --ligList --geoList are required to be specified.