How to carry out docking of few ligands againt set of multiple receptors using aurodock vina. Is any python script available to do this?
Hi Rajesh,
POAP can do what you want.
See its manual.
http://www.sankaranethralaya.org/research-bioinformatics-poap.html
https://github.com/inpacdb/POAP
http://www.sankaranethralaya.org/images/research/bioinformatics/pdf/POAP_Manual.pdf
Thanks Ishikawa, I tried using it earlier in ubuntu 16.04, but could not suceed. Thats why looking for an alternative.
Hi again,
I wrote a shell script for multi-receptor/multi-ligand files, but I have not tested it yet.
vina_multi_receptor.sh
#!/bin/bash
for i in rec_*.pdbqt; do
j=`basename ${i} .pdbqt`
mkdir ${j}
cp ${j}.pdbqt ./${j}
cd ${j}
for f in ../database/*.pdbqt; do
b=`basename $f .pdbqt`
echo Processing ligand $b
vina --config ../${j}_conf.txt --ligand ../database/$f --out ${b}_out.pdbqt --log ${b}_log.txt
done
cd ..
done
In a working directroy, put receptor pdbqt files like rec_2w69.pdbqt and rec_5h6m.pdbqt, and do configure files for the receptors like rec_2w69_conf.txt and rec_5h6m_conf.txt.
In addition, create a "database" directory, and put ligand pdbqt files like a.pdbqt, b.pdbqt, ... under the "database" directory.
If the shell script doesn't work, you can modify it properly.
Thats great. Thank you dear Ishikawa. I will try with this script. But seems that it would require multiple config files for each receptor. I think POAP do it interactively. Its little cumbersome to process more than 300 protein pdbs into pdbqts and config.txt for each.
It would be great help if you suggest some scripts where i can convert protein pdbs into pdbqts. But still I think config files would be the trickest part. I tried with aligning protein structures and defining binding site in single config.txt, but failed. I am going to try your script for multiple receptor multiple ligand docking, but if you have solutions for-
1. Generating pdbqts from protein pdbs in one go.
2. Alternative for defining config.txt files.
Please do share.
Thanks for sharing the script with details of its use.
Hi again,
I suggest some hints for your question:
1. Use prepare_receptor4.py (ADT scripts) or Open Babel in your shell script.
Please check the following VinaLC site:
https://plsuser.llnl.gov/bbs/vinalc/usersGuide.html
2. Try Fpocket. The output file contains the representative coordinates of pockets.
http://bioserv.rpbs.univ-paris-diderot.fr/services/fpocket/
https://sourceforge.net/projects/fpocket/
http://bioserv.rpbs.univ-paris-diderot.fr/services/fpocket/doc/manual_fpocket1.0.pdf
Hi again,
I edited the shell script:
1) changed the 5th line as "cp $i ./${j}"
2) modified the 10th line as follows:
"vina --config ../${j}_conf.txt --receptor $i --ligand ../database/$f --out ${b}_out.pdbqt --log ${b}_log.txt"
Has anyone else already tried this script? If so, how successful it was?
Yes, the script works fine for muti-receptor and multi-ligand docking.
1. Put receptor.pdbqts and receptor.txt (config.txt) in working directory
2. Put ligand pdbqts in database directory inside working directory
Run the script. It generates directories with each receptor names contaning docking output and log files.
The script works fine in Windows platform. However, I run it in Cygwin as it's a bash script. Just save this script in working directory as script.sh, put the protein/s.pdbqt file/s along with configuration.txt and put the ligands in a subdirectory named database in the working directory.
If you have compiled vina in cygwin, just issue the command-
bash script.sh
You can use this script for simple vina docking or for ensemble docking.
You may need to modify the contents of script as per the names of protein/s.pdbqts.
Hope, it would help. In case, if you face any specific issue, share the issue or error message here.
Best luck
u better execute multiple commands in one go separated by && in window cmd prompt; or in linux its very simple to make a shell script.
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