Re: [AMBER] protons

From: Carlos Romero <carlos.rom.74he.gmail.com>
Date: Tue, 10 Apr 2018 04:45:54 +0000

Thanks a lot.

El lun., 9 abr 2018 8:42 p. m., David A Case <david.case.rutgers.edu>
escribió:

> On Mon, Apr 09, 2018, Carlos Romero wrote:
> >
> > Could someone help me insert H+ atom as an ion?
>
> H+ is just a proton, and there is no straightforward molecular mechanics
> way of describing an entity with no electrons (and hence no "size"
> comparable to other ions.)
>
> What is called "H+" is actually some combination of H3O+, H5O2+, etc.
> Amber doesn't offer any built-in way to describe such species. Don't
> forget that under most biochemical conditions (say pH 5 and greater),
> the concentration of free "H+" ions is *very* small.
>
> Basically, a hydrogen ion is really quite different from a lithium or
> sodium ion.
>
> ...regards...dac
>
>
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Received on Mon Apr 09 2018 - 22:00:03 PDT
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