[gmx-users]_Energy_difference_-_Gromacs, _Autodock?=

[David van der Spoel]

Mark Abraham wrote:
>> Yes, that was my mistake - PE energy of the whole system is about 65
>> thousands kcal/mol. But Protein-Ligand Coul SR energy is in the range of
>> 50-100 kcal/mol, so it seems to me to be strange that it's much higher
>> than Autodock's predicted value of binding energy.
> 
> Is Autodock predicting a binding *free* energy?
> 
yes.

one can discuss how good it is, but quite good anyway.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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