Re: [AMBER] Leap: addions

From: Jason Swails <>
Date: Thu, 29 Dec 2011 10:25:59 -0500

On Thu, Dec 29, 2011 at 5:27 AM, George Tzotzos <> wrote:

> This may be a trivial question but any "enlightenment" would be most
> welcome.
> tLeap charge COMPLEX gives Total perturbed charge: -7.998000. Yet "addions
> COMPLEX Na+ 0" produces "7 Na+ ions required to neutralize". Shouldn't it
> be 8 ions instead?
> Asking this out of curiosity. Thanks in advance for any answer.

The problem is that the charge is cast as an integer (or supplied to the
floor() function, I don't know which without looking at the code), meaning
that any fractional charge is ignored. As close as 0.998 may be to 1, it
doesn't actually register as a full charge, and as such is not neutralized
by addions.

It doesn't make much sense to have 0.998 of an electron, so you may check
why this charge is coming out this way in the first place. Do you have a
custom residue that you derived charges for? If so, I would suggest
assigning that 0.002 e-charges somewhere on that residue.


> Regards
> George
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Dec 29 2011 - 07:30:04 PST
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