Re: Using CHARMM Compatible Amber Parameters

From: Ehsan Ban (
Date: Sun Oct 23 2011 - 12:57:03 CDT

The purpose is to have a comparison and I think Amber is more widely used
with simulating the structure of DNA.

Thank you very much for your helpful remarks, specially with modifying
the1-4scaling parameter.

I don't clearly understand why there should be a difference between the two
codes. But, my concern was regarding to this paragraph in the topology file
for the converted Amber force field:

! Differences in the electrostatic energies:
! (*) The conversion from charge units to kcal/mol in CHARMM is based
! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173.
! The actual value is somewhat lower than both these values
! (~331.843)! To convert the charges to "CHARMM", they should be
! multiplied by 1.000058372. This was not done within this file.
! [When this is done, the charges are not rounded and therefore
! non-integral charges for the residues are apparent.] To get around
! this problem either the charges can be scaled within CHARMM (which
! will still lead to non-integral charge) or in versions of CHARMM
! beyond c25n3, and through the application of the "AMBER" keyword in
! pref.dat, the AMBER constant can be used. By default, the "fast"
! routines cannot be used with the AMBER-style impropers. In the
! later versions of CHARMM, the AMBER keyword circumvents this
! problem.

Thanks again,

On Thu, Oct 20, 2011 at 12:34 PM, Axel Kohlmeyer <> wrote:

> On Wed, Oct 19, 2011 at 9:10 PM, Ehsan Ban <> wrote:
> > Hi Everyone,
> > I'm trying to use CHARMM compatible Amber parameters to simulate dsdna
> from:
> >
> > Because Amber and CHARMM use different values to convert charge values to
> > kcal/mol changes should be made to CHARMM program's pref.dat to work with
> > these parameter files. Does anyone know how to get around this in NAMD?
> how can this be?
> the unit of charge (1 elementary charge) and the unit of length (1
> angstrom) is
> apparently the same in both codes and since you want the same unit of
> energy
> (kcal/mol) you have to get the same result in both cases. is there
> something
> that i am missing here?
> axel.
> > Regards
> > Ehsan Ban
> > Rensselaer Polytechnic Institute
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

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