[gmx-users] Amber OPLS dihedral conversion to GROMACS RB
malcolm.b.gillies at anu.edu.au
Thu Aug 7 04:54:01 CEST 2003
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
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.
under "Dihedral parameters" for the AMBER torsional energy function.
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
> Gogonea Computational Chem. Group
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