Re: [AMBER] Non - integral charge o unperturbed unit

From: FyD <>
Date: Fri, 23 Mar 2012 15:58:26 +0100

Dear Ashwini,

in general the total charge of a molecular fragment has an integer
charge value although in some cases this is not true (see some GYCAM
units as well as the 3' & 5'-terminal fragments of nucleotides).

I would carefully check the charge derivation procedure and the
constraints used during the fit to generate the molecular fragment.

regards, Francois

> I am doing a metalloprotein simulation. My system contains two Fe metal,
> each metal site is disconnected and present at different domains of the
> protein. I used MCPB to get charge parameters for each metal site
> independently. The charges for each metal site were derived by keeping the
> charge of the fragment as 0. When i combine these two metal sites and
> generate the inpcrd and prmtop file using leap, I get the following error :
> ERROR: The unperturbed charge of the unit: -0.318694 is not integral.
> WARNING: The unperturbed charge of the unit: -0.318694 is not zero.
> Leap further ignores the warning and creates the inpcrd and prmtop file.
> Is it OK if this error is ignored ??
> What is the solution to get the net charge of the system = 0

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Received on Fri Mar 23 2012 - 08:00:03 PDT
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