Downloads

Create Ligands folder and put all pdbqt files in it.
prepare protein and place as it is in pdbqt format.

ls Ligands/*.pdbqt | time parallel -j+0 --eta 'vina --config conf.txt --receptor epi_isl_1589734.pdbqt --cpu 20 --exhaustiveness 34 --ligand {} --out {.}_complex.pdbqt --log {.}_log.txt'

change receptor file name
change cpu numbers

config file

num_modes = 9
center_x = 213.275
center_y = 186.807549799
center_z = 214.792652602
size_x = 137.393510491
size_y = 77.8062347665
size_z = 187.127904172

Get top 20 with following command
python vina_screen_get_top.py 20 > urvishatop20.txt

Get Binding energy from all log files for vina results
Copy all_log files in the specific folder

run following commands
wget http://covid19.vnsguhpc.co.in:808/sites/default/files/attachment/vs_anal...
mv vs_analysis.py_.txt vs_analysis.py
python vs_analysis.py

Help for Viralrecall

su - vishal1
Enter password

cd /data/backup_user/vishal1/viralrecall/
python viralrecall.py -i FASTA/LS.fasta -p FASTA/LS_OUT -t 2 -f

python viralrecall.py -i '/data/backup_user/vishal1/Dekstop/FASTA/LS/LS.fasta' -p '/data/backup_user/vishal1/Dekstop/FASTA/LS/out' -t 2 -f

Change LS.fasta to input name and LS_OUT to outpur folder

wait for successful completion of command,
The out folder contains the output files