[Users-list] List of energy terms in Glue docking, again

[Lars Olsen]

Hi, 
 
I will try to post the same issue again, since I got no response last time
(in April), and 
I would really interested in solving the problem.
 
My problem concerns the interaction energy between the protein and a ligand.
As I understand 
the manual (section 41.7,
http://www.moldiscovery.com/docs/grid/c82.html#C73.3), the scoring 
function in GLUE is made up of different contributions (Ligand-Target
Enthalpic interaction energy 
and Water bridges between Ligand and Target, Penalty for displacing
pre-bound waters from Target, etc.) 
between Probe Molecule (the ligand) and Target
 
Is there any way to get out the individual energy terms in the scoring
function (i.e. a list with the 
Ligand-Target Enthalpic interaction energy and Water bridges between Ligand
and Target, 
Penalty for displacing  pre-bound waters from Target) ?
 
I have tried to use Grid for estimating these energies, using the following
input file:
 
lont complex.lont
inpt protein.kout
leng -5
levl 3
ligand.kout
iend
 
in which the complex.lont is my outpout file, protein.kout and ligand.kout
are my kout files for the protein
and the ligand, respectively. Is this the right way to get out these
numbers? 
 
I would appreciate any response. Thanks in advance.
 
Lars

 

----------------------------

Lars Olsen, ph.d. 

Biostructural Research Group, Medicinal Chemistry

Danish University of Pharmaceutical Sciences

DK-2200 Copenhagen

Phone: +45 35 306 305

 

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