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View Code? Open in Web Editor NEWRamirez Lab WIKI, where you could find Tutorials, Script Library, Gallery, FAQ, and a little bit more
License: MIT License
Ramirez Lab WIKI, where you could find Tutorials, Script Library, Gallery, FAQ, and a little bit more
License: MIT License
Hola ! Soy estudiante de maestría en química en la Universidad de los Andes. En primer lugar me gustaría agradecerles por estos recursos online. Muy útil e interesante uso del autodock vina.
Recientemente he usado el script de MassiveDockingVina sin embargo creo que una parte complementaria de clustering se puede adicionar fácilmente con el fin de obtener algunos análisis de forma automática. Se puede usar bitclust (doi: 10.1021/acs.jcim.9b00828 y documentación: https://bitclust.readthedocs.io/en/latest/ )
el código para generar el análisis seria:
cp receptor.pdbqt pdbqt/
cd pdbqt/
obabel -ipdbqt receptor.pdbqt -opdb -O receptor.pdb
count=1
for i in {1..100};
do
cd splitpdbqt$i
for j in {01..10}; do
echo "$i $j"
obabel -ipdbqt ligand"$j".pdbqt -opdb -O ligand"$j".pdb ---errorlevel 0
#Generate a complex file with all poses and the receptor
echo "MODEL $count" >> ../Complexes.pdb
grep "REMARK\|HETA" ligand"$j".pdb >> ../Complexes.pdb
grep "ATOM" ../receptor.pdb >> ../Complexes.pdb
echo "ENDMDL" >> ../Complexes.pdb
#Generate a Poses file with all poses in pdb format
echo "MODEL $count" >> ../Poses.pdb
grep "REMARK\|HETA" ligand"$j".pdb >> ../Poses.pdb
echo "ENDMDL" >> ../Poses.pdb
((count++))
done
cd ..
done
#Generate clustering anaylsis folder.
bitclust -top splitpdbqt1/ligand1.pdb -traj Complexes.pdb -odir Analysis -cutoff 3 -sel "resname UNK"
Lo dejo porque puede una posible adición al recurso!
Muchas gracias por su tiempo.
David
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