Re: [AMBER] Charge calculation methods for RED server

From: FyD <>
Date: Thu, 09 Jan 2014 21:05:58 +0100

Dear Yew Mun,

> I'm not sure if this is the right place to ask about the R.E.D
> server, so I'm just going to give it a shot.

You can post your questions to the Amber mailing list or to the
q4md-fft mailing list at as you wish.

> I'm planning to simulate a zinc finger where the zinc ion is
> coordinated to 4 other Cys residues. I plan to calculate the charge
> of the Zn ion since coordination would definitely have changed its
> +2 charge.

If you want to have a +2 charge on the Zn(II) (not that obvious) you
will have to set an intra-molecular charge constraint of +2 on this
Zinc atom otherwise the atomic charges of Zn(II) is likely to be far
lower than +2.

See to compare
charges for Fe(III) with an integer charge value (i.e. +3) vs a
non-integer charge value.

> I know I can rely on the RED server for this, but under the charge
> method (e.g. Resp-A1A), how do I know which one is suitable.?

RESP-A1A means HF/6-31G*//HF/6-31G*
do you think HF/6-31G* is suitable for bioinorganic complexes?
See once again:

> Also, while the RED website has a tutorial for metal inorganic
> complexes, is there a step by step guide as well on using the RED
> server for deriving charges of metals in proteins.?

See projects in R.E.DD.B.

I hope this helps.

regards, Francois

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Received on Thu Jan 09 2014 - 12:30:03 PST
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