On Thu, Oct 13, 2022, FyD via AMBER wrote:
>
>The total charge value of the molecular fragments in the Amber force
>field libraries takes 'most of the time' an integer value. This is the
>case for the terminal and central fragments of the amino-acids. This
>is also true for the central fragments of the nucleotides. However,
>this is not correct for the terminal fragments of the nucleotides,
>where the sum of the total charges of the 2 terminal fragments has
>that integer value.
>
>I wonder if there is an importance of having such an integer value for
>a molecular fragment in the electrostatic interaction computation of a
>protein/polynucleotide for instance, when running MD simulation in
>condensed phase using the Particle mesh Ewald algorithm/a periodic
>box.
Periodic calculations in Amber use PME, which will add a neutralizing
background charge if the molecule has a net charge. It doesn't really care
if the charge is integral or not.
The fact that you need both a 5' nucleotide and a 3' nucleotide on the same
strand in order to get an integral charge represents our best (simple) guess
of the actual charge distribution.
...hope this helps...dac
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Received on Fri Oct 14 2022 - 09:30:03 PDT
