Re: Nucleic acid stains parameters

From: Kenno Vanommeslaeghe (
Date: Mon Aug 25 2014 - 10:56:26 CDT

If nobody has them, I'd recommend submitting them to the CGenFF program at prior to refinement with ffTK. That way, you'll have
reliable atom types and most probably also some parameter and charges that
do not need to be optimized. For the ones that do, ffTK is a good option.

But you probably know this already, since you suggested it yourself on the
CHARMM forums:
as far as I am concerned, we'll continue the discussion there.

On 08/25/2014 11:37 AM, Sebastián Gutiérrez wrote:
> Dear NAMD Users,
> i'm looking for CHARMM-compatible parameters for the following molecules:
> -Acridine orange
> -ethidium bromide
> -ethidium homodimer-2
> -evans blue
> -hexidium iodide
> -indocyanine green
> -methylene blue
> -propidium iodide
> -nuclear yellow
> I'm asking only in case someone already has any of these, since i'm going
> to try generating these parameters with the ffTK plugin (for VMD).
> Thanks!
> Sebastián E. Gutiérrez Maldonado
> Graduate student
> Computational Biology Lab (DLab)
> Fundación Ciencia & Vida
> Av. Zañartu 1482, Ñuñoa, Santiago

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