ADL: How should I prepare the Ligand PDBQT file with ADT for a single metal ion?
forli at scripps.edu
Mon Sep 27 14:19:39 PDT 2010
AutoDock is designed and tuned to work with small molecules. Working with single atoms is
an 'exotic' usage of the software, but it's also rather trivial, in principle, not having
torsions or orientations to be evaluated.
Therefore, the docked position of your atom *should be* the absolute lowest value of the
Mg map calculated with AutoGrid.
You can use ADT to load and visualize that map.
Hope this helps,
Jian Huang wrote:
> Dear ADT developers and Dockers,
> I have been trying to use ADT and Autodock to dock a single metal ion (mecury ion) in the active site of a protein. However, I get lots of errors from ADT when I try to enter the mecury ion as a ligand in PDB format. I am guessing this is because ADT expects to find some bonds in the ligand. How should I prepare the Ligand PDBQT file with ADT for a single metal ion? Is it possible to dock a single metal ion using Autodock?
> Does anyone in the comunity have experience in this situation?
> I would be very grateful if anyone can help me with this.
> Thanks in advance.
> Jian Huang
> School of Life Science and Technology
> University of Electronic Science and Technology of China
> Chengdu, 610054 P. R. China
> Phone: +86-28-83208232, Fax: +86-28-83208238
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Stefano Forli, PhD
Olson Molecular Graphics Laboratory
Dept. Molecular Biology, MB-112
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: (858) 784-2055
fax: (858) 784-2860
email: forli at scripps.edu
More information about the autodock