PaDEL-ADV
Introducing another new software, PaDEL-ADV. This is a software to perform virtual screening using AutoDock Vina.
PaDEL-ADV reads a directory containing ligands files. For each ligand, the structural file is converted into a pdb file, if necessary, using The Chemistry Development Kit. The pdb file is then converted to pdbqt using the prepare_ligand4.py script provided by AutoDockTools. AutoDock Vina is then used to dock the ligand with the receptor. Individual binding modes are extracted from the output pdbqt file using vina_split. The pdbqt files are then converted to pdb files using the pdbqt_to_pdb.py script provided by AutoDockTools. Results for each binding modes are extracted from the log file and placed into the results CSV file. The log file and all the related pdb and pdbqt files are then compressed into a zip file.
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January 18th, 2010 at 11:50 pm
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Best, Holger
February 24th, 2010 at 7:58 pm
Dear sir,
I am very glad to know about padel-ADV for virtual screening but when i try to run on ubuntu linux getting following error and on windows 7 MGLTools path is not being recognized. please help me to solve this problem
Thank you
With regards,
vamsi
Error:
ImportError: liblapack.so.3: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py”, line 7, in
from MolKit.pdbWriter import PdbWriter
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/pdbWriter.py”, line 16, in
from MolKit.pdbParser import PdbParser
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/pdbParser.py”, line 50, in
from MolKit.moleculeParser import MoleculeParser
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/moleculeParser.py”, line 15, in
from MolKit.molecule import Atom
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/molecule.py”, line 25, in
from mglutil.util import misc
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/mglutil/util/misc.py”, line 19, in
import numpy.oldnumeric as Numeric
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/__init__.py”, line 103, in
import linalg
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/linalg/__init__.py”, line 4, in
from linalg import *
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/linalg/linalg.py”, line 29, in
from numpy.linalg import lapack_lite
ImportError: liblapack.so.3: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py”, line 7, in
from MolKit.pdbWriter import PdbWriter
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/pdbWriter.py”, line 16, in
from MolKit.pdbParser import PdbParser
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/pdbParser.py”, line 50, in
from MolKit.moleculeParser import MoleculeParser
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/moleculeParser.py”, line 15, in
from MolKit.molecule import Atom
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/MolKit/molecule.py”, line 25, in
from mglutil.util import misc
File “/home/vamsi/MGLTools-1.5.4/MGLToolsPckgs/mglutil/util/misc.py”, line 19, in
import numpy.oldnumeric as Numeric
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/__init__.py”, line 103, in
import linalg
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/linalg/__init__.py”, line 4, in
from linalg import *
File “/home/vamsi/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/linalg/linalg.py”, line 29, in
from numpy.linalg import lapack_lite