[Users-list] Electrostatics using GLUE

[Marco Neves]

Dear users,

I'm trying to use GLUE to predict the binding mode of a couple of 
inhibitors to an enzyme.
The output of the docking looks like this:

# LIGAND FILE: ligand.kout
# TARGET FILE: protein_in.kout
# ESTIMATED BINDING ENERGY: -23.107 KCAL/MOL
# ENERGY CONTRIBUTIONS: SR=0.439, HP=-23.130, RHB=0.000, ES=-0.416  KCAL/MOL

@<TRIPOS>MOLECULE
ligand.kout
 47 50 0 0 0
SMALL
NO_CHARGES

#                                                              CHARGE   
EPHOBE    EESTER    EESTAT    EHBQQ
@<TRIPOS>ATOM
(...)                                                           0.000  
-1.6007    0.0000    0.0127    0.0000
(...)                                                           0.000  
-1.0700    0.0000   -0.0108    0.0000
(...)                                                           0.000  
-1.1400    0.0000    0.0039    0.0000
(...)                                                           0.000  
-0.6237    0.1079    0.0193    0.0000
(...)                                                           0.000  
-1.3918    0.0000    0.0062    0.0000
(...)                                                           0.000  
-0.7407    0.0000   -0.0050    0.0000
(...)                                                           0.000  
-2.3606    0.2554   -0.0479    0.0000
(...)                                                           0.000  
-2.6282    0.0000    0.1372    0.0000
(...)                                                           0.000  
-2.0047    0.0000   -0.0059    0.0000
(...)                                                           0.000  
-1.5699    0.0752   -0.0034    0.0000
(...)                                                           0.000  
-1.5846    0.0000    0.0031    0.0000
(...)                                                           0.000  
-1.1301    0.0000   -0.0355    0.0000
(...)                                                           0.000  
-0.8789    0.0000   -0.0020    0.0000
(...)                                                           0.000  
-0.7740    0.0000    0.0063    0.0000
(...)                                                           0.000  
-0.8532    0.0000   -0.0216    0.0000
(...)                                                           0.000  
-0.4080    0.0000    0.0053    0.0000
(...)                                                           0.000  
-0.5412    0.0000    0.0255    0.0000
(...)                                                           0.000  
-0.7836    0.0000    0.0107    0.0000
(...)                                                           0.000  
-0.0007    0.0000   -0.1670    0.0000
(...)                                                           0.000  
-0.0026    0.0000   -3.0594    0.0000                                   
     (...)                                                           
0.000  -1.0425    0.0000   -0.0045    0.0000

I suppose that in the header of the columns located after of the omitted 
atomic coordinates, SR stands for steric repulsion, HP for hydrophobic 
probe, RHB for hydrogen bonding and ES for electrostatic, but I would 
like to know how these values are calculated.

Also I notice that the SR, HP and RHB terms are the sum of the atom 
contributions located at the bottom the EESTER, EPHOBE and EHBQQ 
columns, respectively. The same don't happen with the ES term. Is there 
some scaling factor or penalty to apply when converting the atom 
contributions to the final total energy?
I would be very greatful is someone could give a little help.
Thanks,

Marco Neves