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how_to_proceed

1. Gaussian output with antechamber –> mol2 (RESP charges)

antechamber -fi gout -fo mol2 -i name.log -o name.mol2 -c resp -at sybyl -pf yes

2. mol2 –> PDBQT (ADT)

mol2topdbqt -l name.mol2 -C -U \\“”“ -o name.pdbqt

(mol2pdbqt = /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py)

3. Docking…

(input file) Using ADT (Grid, Docking) (docking)

/usr/local/autodock/autodock4 -p name.dpf -l name.dlg

Life can made a lot easier if the PyMOL plugin for AutoDock/Vina created by Daniel Seeliger is used. If interested, check in:

http://www.pymolwiki.org/index.php/Autodock_plugin

and read the paper published in J. Comput.-Aided Mol. Des. 24:417-422 (2010):

https://www.mpibpc.mpg.de/276097/Seeliger_2010_JCAMD_24_417-422.pdf

Note: it is always a good idea to visualize the energy maps to check that there are no gross mistakes! (but for this you have to make sure the grid is a real cube (a=b=c) to avoid artifacts in PyMOL)

how_to_proceed.txt · Last modified: 2016/04/18 06:37 by root