Re: [AMBER] antechamber: why the net charge does not sum up to zero?

From: FyD <>
Date: Tue, 17 Jan 2017 07:04:01 +0100

Dear Dr Case,

I just sent an email entitled:
Fwd: [AMBER-Developers] non-neutral ethane from antechamber
date: 03/02/2012 (10:13:37 CET)

I remember other emails were also sent to the amber mailing list
(might be about other errors?).
Anyway this email with Michael is one example:
This is about ethane and an error of +0.00200 was reported.

A rounding off error of 0.002 for a charge accuracy of +/-1.10-3 e
makes sense for ethane (this error might be corrected by adding
-1.10-3 on each of the chemically equivalent carbon atom; or not
corrected because this error is considered as neglectible).
An error of +0.00200 for a charge accuracy of 1.10-5 is more strange;
except if a charge accuracy of 1.10-3 was _in fact_ used and 2 zeros
are added to reach a 'pseudo' 1.10-5 accuracy? Anyway I do not think
an error of 200.10-5 is a rounding off error if a 1.10-5 charge
accuracy was used in the case of ethane.

regards, Francois

Quoting FyD <>:

> Dear Dr Case,
> Ups, excuse me, I missed your email...
>>> that being said - an error of +/- 0.001 i.e. +/-
>>> 0.0010 for a charge accuracy of 1.10-4 (i.e. 0.0001) is _not_ normal
>> Are we sure what the error we are talking about is? Is there a simple
>> example that shows this?
> In PyRED we have encountered the following problems (2 examples
> below), and PyRED should ;-) now correct these problems:
> (CH3)3-CH: i.e. 2-methylpropane
> 1) Let's guess we choose a charge accuracy of 1.10-4 e (to be printed
> in the .mol2 output) and an error of +1.10-4 (because of the rounding
> off procedure at the chosen accuracy - from the 1.10-6 one printed in
> the RESP output) is generated during the charge fit for each of the 9
> hydrogen atoms of the tertiobutyl group and to the CH hydrogen; thus
> one ends up with: 9*1.10-4 + 1.10-4 = 0.0010 e: this case is 'normal'.
> Correcting (a posteriori to the resp fit) the partial charge values
> using -1.10-4 (i.e. using the chosen charge accuracy) of a selection
> of the atoms of 2-methylpropane in agreement with (i) chemical
> equivalencing and (ii) the total charge value (equals zero) is
> possible here (but a little tricky).
> (similarly a chosen charge accuracy of 1.10-3 e can potentially lead
> to an error of 0.010 e for 2-methylpropane; such 1.10-2 errors were
> present in the old GLYCAM force field).
> 2) Then, still for 2-methylpropane we were able to generate errors of
> 3.10-4 because of the use of additional an intra-molecular charge
> constraint (intra-mcc). Thus here correcting this 3.10-4 error in
> agreement with (i) chemical equivalencing (ii) the total charge value
> and (iii) the intra-mcc using the chosen charge accuracy is
> impossible; thus we had to choose to correct using the double of the
> chosen charge accuracy; i.e. -1.10-4 + -2.10-4 (loop twice in the algo).
> uff not easy to describe...
>> In my experience, the internal charges for am1-bcc always add to zero;
>> if they are only printed out to three decimal places, then the
>> usual rounding
>> effects may mean that the sum of the *printed charges* is different
>> from zero.
> Yes exactly.
>> But you seem to be referencing some deeper error, and an example
>> would be most helpful.
>> Apologies if I missed the post that had a good test case.
> Personally I am lost with the errors reported by the users for the
> different versions of Antechamber, and I do not know the source code
> of Antechamber: I remember some Antechamber versions did not apply
> chemical charge equivalencing: the 'sustiva_?' molecule and the 3
> fluorine atoms), then chemical charge equivalencing was applied, and
> then examples with these 'strange' errors were reported. I wonder if
> an example of such an error was not discussed with Michael Crowley in
> the amber developer mailing list: I will try to find the reference to
> that email, uff...
> regards, Francois

           F.-Y. Dupradeau

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Received on Mon Jan 16 2017 - 22:30:02 PST
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