ADL: Redocking and Binding energy

zhaojunwei zhaojunwei2004 at
Mon Mar 3 04:40:59 PST 2008

Hi, all

I'm using AutoDock4 for docking of enzyme and inhibitors. There're two questions about autodock confusing me.

1. The receptor I used to do redocking is a dimer, then shall I use one of the monomers only, or shall I  use the two monomers together to prepare receptor files? Do these two approaches make same results?

2. I've tried the method mentioned by Mr Wim Nerinckx in this list when setting parameters ga_num_evals and ga_num_generations. And finally I run my docking with a maximum number of 25,000,000 energy evalutions, and a maximum number of 5,000 generations. But the binding energy seems about 2-3 kcal/mol higher than experiment data. When doing this using AutoDock3.05, with the same parameter, the binding energies were closer to experiment data, but consumed more time. What should I do to deal with this situation?

Any input will be greatly appreciated.


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