How to use Vina

https://github.com/mokarrom/mpi-vina
http://vina.scripps.edu/download.html for vina binary file

MPI-vina is an MPI program that should be used with parallel.q queue here is an example of SGE script according to the one found in Src folder. Edit according to your needs.

#!/bin/bash
 
#$ -q parallel.q
#$ -pe mpi 16   ## change me
 
module load vina
 
#Compile the application.
ls > ligandlist ./Ligand
mkdir -p Output
mkdir -p ProcessedLigand
make
 
#Run the application.
echo "MPI-Vina is running..."
mpirun mpiVINA > Output/MpiVina.log
echo "Processing has finished"
echo "See the MpiVina.log file."
 
#Result analysis.
echo "Analysizing the results..."
cd Output
grep "  1 " *.txt | cut -c1-12,35-42 > result
#grep "  1 " *.txt | cut -c1-7,30-35 > result
echo "See the 'result' file in 'Output' directory."
#cat result
 
echo "Sorting the results..."
sort -n +1 -2 result -o SortedResult
echo "See the 'SortedResult' file in 'Output' directory."
#cat SortedResult

vina seems to be sequential program ( or even parallel multicore) used for post-processing. It should be used in mesoshared node.

within a terminal in mesoshared:

$ module load vina
$ vina