First of all, sorry for the long message, but it is a fundamental question!
Studying the VDW parameter in AMBER FF/program, I got troubles trying
to understand how VDW parameters are actually computed in the prmtop
file.
>From the documentation, its quite clear that :
rij = ri+rj, both radi given in FF files such as parm99.dat
eij = sqrt(ei*ej) , epsilons also given in FF files.
Both radius and well depth are combined to generate Acoef/Bcoef:
Acoef = eij*rij^12
Bcoef = 2*eij*rij^6
Finally, EVDW = (Acoef/dij^12 ) – (Bcoef/dij^6) , where dij is the
distance between atoms i and j.
So far, so good. A problem shows up with the definitions of ICO (índex
to the nonbonded parameters). According to the PRMTOP file format, if
ICO < 0, a 10-12 potential is used intead of the typical Lennard-Jones
6-12 potential.
As far as I know, the 10-12 potential is (was?) used to model H-bonds.
However, reading Cornell et al, 1994 (JACS) and Ferguson & Kollman
1991 (J. Computat. Chem.), it seems that 10-12 potential was not
really necessary to model Hbonds accuratelly.
So, my questions are:
* Is 10-12 potential actually used in current Amber FFs ? (e.g. ff99SB)
* If so, how ICO is defined? (couldn´t find in leap codes)
Again, sorry for the long message and thanks a lot in advance,
--
[ ]s
Alessandro S. Nascimento
UFABC - Brazil
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Received on Tue Mar 23 2010 - 09:00:02 PDT
