ADL: How to assign total charge for small molecule

Michele Lunelli efunit at yahoo.it
Wed Feb 13 08:32:26 PST 2008


Dear all,

in the active site of my enzyme I have a quinone as cofactor, which has charge 
-1 at physiological pH. However, when I calculate Gasteiger charges for this 
small molecule in ADT, its net total charge is 0. Is it possible to set it 
correctly?

Alternatively, is it consistent to use ESP (= Merz-Kollman) charges only for 
this cofactor for docking simulation with autodock 4, while all the amino acids 
and the ligand have Gasteiger charges?


Thank you in advance,
Michele Lunelli


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