[gmx-users] OPLS 1-4 interactions & intramolecular contributions to interaction energies ...

[Michael Brunsteiner]

dear all,

Can anybody tell me what the proper way of including
1-4 non-bonded interactions with the OPLSAA FF is ?
>From previous messages in this list I gather that
there seems to be no unique definition and the scaling
factor for the 1-4 interactions including H-atoms seems
to be different in different Gromacs versions. What is
this factor in 3.2.1, what is it in 3.1.4 and which is the
"correct" one ?

I came accross this qustion when calculating adsorption
energies of different molecules on a surface and I found
that I can get a diferrent ranking of the relative
adsorption energies depending on whether I include 1-4 
and/or intramolecular interactions or not in the calculated
Delta U. I do wonder how physically meaningful the intramolecular
FF-terms are when it comes to comparing interaction energies 
between different molecules and a surface or, say, a receptor.
AFAIK many programs that compare, e.g., interaction energies 
between proteins & ligands do not account for variations in the 
intramolecular FF terms. The same is true for Aqvists LIE method. 
Has anybody out there given this question some consideration ?

cheers,
Michael








		
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - Send 10MB messages!
http://promotions.yahoo.com/new_mail