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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jun 19 09:30:24 CEST 2007

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?

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

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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