Re: [AMBER] Non-integer/zero charges from RESP fitting?

From: Kenneth Huang <>
Date: Wed, 13 Jan 2021 13:50:29 -0500

Hi David,

Ah, that's good to know- I assumed it would be working with 1E-6 since
that's what it reports in, not something even more precise like 1E-12. I'll
try to see if there aren't any 'good' positions where I can just add on the
missing value.



On Wed, Jan 13, 2021 at 8:15 AM David A Case <> wrote:

> On Tue, Jan 12, 2021, Kenneth Huang wrote:
> >The odd thing I've noticed is that while the canonical nucleosides
> >themselves add up to zero, my modified NAs are all very slightly off
> >(0.000001). My instinct is that it's a rounding error, but when I check
> the
> >output, it says the net charge should be 0,
> >
> >>
> >> Reading input for molecule 6 weight: 1.000
> >> inosine
> >>
> >> Total charge (ich): 0
> >> Number of centers: 30
> The "Total charge (ich)" look like an integer, not a real number.
> >Which from my limited understanding of it, looks like it should restrict
> >the charge to N decimal places (6?) which leaves me puzzled as why it'd be
> >unable to zero the charges, instead of leaving them at 0.000001? Or am I
> >missing something very obvious?
> It's actually quite tricky to take a list of floating point numbers that
> add
> up to zero (to some very small tolerance, like 10^-12 or better), and
> convert them into a list that, when printed with an F12.6 format, appear to
> add to zero with no roundoff. Ideas are welcome; maybe Dave Cerutti knows
> how this problem is handled in mdgx.
> If you are making just a limited number of units, the only workaround I
> know
> of is to just hand-edit the output .mol2 or .off files, and force the
> charges to add up to exactly zero. Or, just ignore the problem.
> ...dac
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Received on Wed Jan 13 2021 - 11:00:02 PST
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