From: Axel Kohlmeyer (
Date: Mon Mar 30 2009 - 20:24:24 CDT

On Mon, 2009-03-30 at 14:27 -1000, Irene Newhouse wrote:

hello irene,

> Got distracted by other work, and have just gotten back to the
> question of adding
> heme to the dowser dictionary & parameters. I got one of the free
> distributions of gromos, and
> put that up, & started looking through the ffgmx* files, as
> recommended on a link
> from the dowser plugin page. To make sure I had the right thing, I
> started looking for values
> identical to those listed for N:
> This is in dowser:
> REMARK atomtype LJ-a LJ-b MS-radius
> TYPE N 49.36 1300.0 2.40 # any Nitorgen
> While the closest thing I can seem to find is in ffmgxnb.rtp, where
> the apparently relevant
> comment line reads:
> ;name at.num mass charge ptype c6 c12
> & N reads:
> N 7 14.00670 0.000 A 0.24362E-02
> 0.16924E-05
> Am I looking at the right thing? If so, how do I transmogrify the c6 &
> c12 values into those
> in dowser?

well, one of them are espilon/sigma from the more commonly used
representation of the LJ potential and the second the prefactors
to the powers of 1/r. best you have a look at, e.g. the gromacs
manual (i just looked it up, page 50, point 4.1.1 of the version 4.0
manual) and you see how to convert it. now all you need to find out
is what unit epsilon is in (note that gromacs uses nanometers as length
and not angstroms), and whether the epsilon in dowser does contain the
4 or not. in most cases it is not, but in some it is.

hope that helps,

> Thanks!
> Irene Newhouse
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.