ADL: Magnesium Ion

kbarakat at ualberta.ca kbarakat at ualberta.ca
Mon Jan 26 15:25:59 PST 2009


Hello,

I am trying to use Autodock4 on a receptor that contains a Magnesium  
ion coordinated by 3 ASP residues and 3 water molecules. the receptor  
structure has been equilibrated using MD simulation using the  
amber99sb force field. When I load the structure into ADT it crashes  
and doesn't generate the pdbqt file.

when I remove the MG ion, it works well and generates the pdbqt file.

I am wondering if someone can help me to keep the MG ion in its place  
within the Binding site and generate the pdbqt file?

your help is appreciated

with my best regards
khaled





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