Re: [AMBER] Using 6-12 / 10-12 potential in AMBER

From: Jason Swails <>
Date: Tue, 23 Mar 2010 13:12:09 -0400


On Tue, Mar 23, 2010 at 11:44 AM, Alessandro Nascimento
<> wrote:
> 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.

This has been discussed several times on the mailing list and these
discussions point to websites/pdf files on the amber webpage.

> >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)

I do not believe 10-12 parameters are used in ff99SB. You can tell,
however, if an index points to a 10-12 interaction by examining the
values of the integer pointers under the section %FLAG
NONBONDED_PARM_INDEX in the prmtop. Those are indexes into the
non-bonded array (and therefore, only positive values have meaning as
there is no -2nd position of an array...). If one of those values are
negative, then it is a flag to the code to use a 10-12 potential as
opposed to a 6-12. In the prmtops i've looked at, I have not seen any
negative values in that section.

> Again, sorry for the long message and thanks a lot in advance,
> --
> [ ]s
> Alessandro S. Nascimento
> UFABC - Brazil

Hope this helps,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Mar 23 2010 - 10:30:03 PDT
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