ADL: How should I prepare the Ligand PDBQT file with ADT for a single metal ion?

Jian Huang hj at uestc.edu.cn
Sat Sep 18 06:54:22 PDT 2010


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
http://immunet.cn/hlab
 
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




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