ADL: Protein+molecule complex - computation of charges

Giulia Canevari giulia.canevari at gmail.com
Tue Feb 19 01:48:50 PST 2008


Hi,

I'm still an absolute beginner with Autodock4 and I need some advice:

I'm docking some ligands to a protein+a FAD molecule; I'm wondering whether
it is better to compute (with PMV) the Gasteiger charges of the
(protein+FAD) complex or to add the Kollman charges to the protein alone and
compute Gasteiger of the FAD molecule alone and then produce a pdbqt file
for the complex by putting these two together.

I've already tried both these approaches and they lead to different results.
I've also tried removing the FAD molecule and the result is different from
the above. Another computation, made without the FAD molecule and with
Autodock 3, led to another, different, result.

What is the best way to deal with this problem?

Thanks,

Giulia


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