[gmx-users] Amber OPLS dihedral conversion to GROMACS RB

[Malcolm Gillies]

Hi David,

The conversion formula you need is on page 62 of the GROMACS manual
(equation 4.54). Assuming the phase angles for PN= 1, 2 and 3 are 0,
180, and 0 degrees, respectively, then Vn in equation 4.54 is equal to
PK / IDIVF for the line where PN=n

e.g.

    X -C -CA-X    4   14.50        180.0             2.         

gives a V2 = 14.5 / 4 = 3.625 kcal/mol

For a particular dihedral, you need to accumulate all the Vn terms from
different lines of the AMBER parameter file and then convert them into a
single set of RB parameters.

See also

    http://amber.scripps.edu/doc6/html/AMBER-sh-19.3.html

under "Dihedral parameters" for the AMBER torsional energy function.

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University

On Wed, 2003-08-06 at 22:21, DaJustice1 at aol.com wrote:
> Dear GMX Users,
> 
> I am attempting to convert Amber OPLS dihedral parameters to GMX RB
> parameters, but I’m having some trouble.  I have searched through the
> archives and found replies about the same problem.  The replies state
> that the conversion is described in the GMX Users manual.  I have read
> the force field section covering dihedral conversion to RB, but I
> still am not sure how to proceed.  Amber OPLS has multiple definitions
> for dihedrals using different PN, but GMX only has one line containing
> the six RB parameters C 0-5.  If someone in the list has experience
> with these conversions, please enlighten me.
> 
> Thank you,
> 
> David Justice
> Researcher
> Gogonea Computational Chem. Group