[gmx-users] Re: converting parmbsc0 dihedrals to RB function

Alan alanwilter at gmail.com
Wed Apr 7 23:50:47 CEST 2010

>From ffamber (in e.g. .../gromacs/top/ffamber99sbbon.itp):

- impropers treated as propers in GROMACS to use correct AMBER analytical
- propers treated as RBs in GROMACS to use combine multiple AMBER torsions
per quartet

I followed these instructions while building acpypi (acpypi.googlecode.com/

You can study my code and see how the conversion is done (I put the details
inside acpypi.py).

I didn't test acpypi with an amber prmtop/inpcrd input with parmbsc0
parameters, but it would be interesting to see what I would get.

Bear in mind that if parmbsc0 were "simple" to port, then it would have been
done since the first version of ffamber, but I know Eric Sorin is working on
that now.


On Wed, Apr 7, 2010 at 22:00, <gmx-users-request at gromacs.org> wrote:

> > Dear Users,
> >
> > I am trying to port the new parmbsc0 forcefield
> > (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
> > simulations.
> >
> > While unit conversions are sufficient to convert many of the parameters
> > from AMBER to GROMACS format, dihedral angle conversion does not seem to
> > be straight forward - the dihedral parameters need to be converted to
> > the Ryckaert-Bellemans parameters.
> Why? GROMACS can probably do the non-RB form - IIRC you can implement a
> sum of multiple instances of 4.61 with different n.
> > I went through the GROMACS 4.0
> > manual, especially equations 4.61-4.65 to understand the procedure. The
> > procedure involves comparing the fourier expansion of the IUPAC
> > convention of dihedral potential (equation 4.65) with the
> > Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
> > to get the Cn's of the RB function. However, I am not able to understand
> > how to account for the phase angles. (Also to note, the parmbsc0
> > forcefield contains phase angles other than 0 and 180.)
> Elegant conversion formulae require those angles to be convenient...
> Mark

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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