Subject: Free energy of binding in AutoDock

From: Carsten Detering <[email-masked]>
Date: Thu, 20 Mar 2003 15:40:29 -0800

Hi all,

I was posting a similar question a while ago, however never really 
having resolved the problem.
Obviously, the calculated free energy of binding (with 'epdb' and 
AutoDock being in command mode (-c flag)) seems to be dependent on the 
atom types allowed for the receptor (specified in autocomm.h under 
ATOMTYPES and in gpf3gen.awk under PROTEIN_ATOMTYPES), without some 
actually being present in the molecule.
For different sets of allowed atom types, I get different free energies 
of binding (for always the same ligand and receptor; the receptor is an 
RNA containing the atom types CNOPH), whether I allow also Fluorine 
and/or Iodine, or none of the latter. When I use only CNOPH, autogrid 
gives a segmentation fault.
The first column gives the atom types that I specified in both 
autocomm.h and gpf3gen.awk, followed by the EFEB extracted from the .clg 
file:

CNOPHXM    Estimated Free Energy of Binding    =   -8.84 kcal/mol
CNOPHXMFI  Estimated Free Energy of Binding    =   -8.74 kcal/mol
CNOPHXMI   Estimated Free Energy of Binding    =   -8.56 kcal/mol
CNOPHXMIF  Estimated Free Energy of Binding    =   -9.03 kcal/mol
CNOSHXMP   Estimated Free Energy of Binding    =   -8.39 kcal/mol
CNOSHXMPI  Estimated Free Energy of Binding    =   -8.87 kcal/mol
CNOSHXMPIF Estimated Free Energy of Binding    =   -8.87 kcal/mol

It may have just a simple explanation, but I cannot explain that to me.

Thanks for any help on this,

Carsten

-- 

Carsten Detering, Ph.D.
University of Washington
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665