Re: [AMBER] Assignment of partial charge to a molecule

From: Aron Broom <>
Date: Tue, 6 Mar 2012 13:18:47 -0500

How large is your fullerene? If it's something like a C60 couldn't you
just randomize them outside of XLEaP and then enter those in manually by
editing the molecule? That assumes you aren't making a large number of

But honestly, that seems like a very sketchy way of getting what you want,
what is the basis of those random charges? I think to do that properly
you'd need to get your fullerene working with a polarizable forcefield,
such that your polar compounds get trapped in a more physically meaningful
manner (that is, through dipole induced dipole interactions). I've no idea
how difficult it would be to add the fullerene properties to something like
Amoeba or DFTB.

Just my opinion.


On Tue, Mar 6, 2012 at 1:05 PM, gargi borgohai <> wrote:

> Respected Sir,
> In order to induce polar confinement to a fullerene
> molecule I want a random distribution of charges on each of the carbon
> atoms. The command at XLEAP : " set default pdbwritecharges on" is not
> working. Sir, how can I add charges to the molecule successfully.
> Thanking you.
> Gargi Borgohain.
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Tue Mar 06 2012 - 10:30:03 PST
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