Re: [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)

From: FyD <>
Date: Sun, 13 Oct 2013 10:45:33 +0200

Dear Jonathan,

- Concerning Iron(III)Hydroxide:
The difficulty is the presence of iron(III)...
you could use the R.E.D. tools or better R.E.D. Server (Development)
and generate a force field library (FF lib.) for this whole molecule.

- Concerning Enterobactin:
here you could use again R.E.D. Server and split this whole molecule
into elementary (repetitive) building blocks to generate required
molecular fragments, which are then associated to generate Enterobactin.

You can find examples of the building block approach in R.E.DD.B.
see for instance:

Tutorials are available at:

Writing a tutorial for your project about developing FF lib. for these
2 molecules and how to associate them would be of great use for the

For sure R.E.D. (perl) can handle these cases (without atom typing)
while R.E.D. Python will generate the FF lib. with charge values/atom
types and frcmod files with or without extra-points and united
carbons; all ready to be used in the LEaP prgram...

regards, Francois

> I am sorry to do this, but I only have knowledge in ochem (haven't taken
> pchem yet) so reading "Car-Parrinello Molecular Dynamics" and searching it
> on wikipedia yields no data that I understand.
> So what I'll do to save everyone time is to share what I want to do and ask
> if this software can do it, and if not, do you know of any software that
> can do this?
> My goal is to simulate Iron(III)Hydroxide in a box of water (perhaps
> physiological conditions/ions) with Enterobactin, to see if it will form an
> iron complex.
> Perhaps this is more for a quantum chemistry program? Any that you would
> suggest to use?

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Received on Sun Oct 13 2013 - 02:00:03 PDT
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