Be careful. It sounds to me like your calculation is not set up right.
Changing the protonation of the N should definitely change the partial
charge, and your overall charge seems wrong. I would not trust these
charges until you resolve that.
On Wed, Jul 27, 2022, 8:06 PM Liao via AMBER <amber.ambermd.org> wrote:
> Thanks Shiji this information is very helpful.
>
> Sent from my iPhone
>
> > On Jul 27, 2022, at 4:25 PM, Shiji Zhao <shijiz.uci.edu> wrote:
> >
> >
> > Hi Liao,
> >
> > The charges for amino acids in the ff14SB force field were derived using
> a method called RESP (REstrained Electrostatic Potential), which fits
> charges to reproduce QM calculated electrostatic potentials (ESPs) around
> molecules. In contrast, AM1-BCC is an empirical method that applies one set
> of parameters into any molecule. In theory, RESP should give better charges
> than AM1-BCC since it takes the molecular details of target molecules into
> account. However, many studies have shown that AM1-BCC derived charges give
> ideal performances in molecular modeling tasks such as MD simulation. For
> example, this one https://pubs.acs.org/doi/10.1021/acs.jcim.0c01384
> >
> > My advice is that, if you don't have easy access to QM software to
> calculate QM ESPs, you can simply use the AM1-BCC method for charging. If
> you have QM softwares such as Gaussian or GAMESS, you can use the RESP
> method (There are two programs in the AmberTools package that can perform
> RESP charging: resp and py_resp.py), or you can compare the performances of
> both methods.
> >
> > Best,
> > Shiji Zhao
> >
> >> On Wed, Jul 27, 2022 at 1:45 PM Liao via AMBER <amber.ambermd.org>
> wrote:
> >> Dear experts,
> >>
> >> Today when looking at partial charges on my molecules, I found quite a
> big difference, between the side chain N on Lysine, and an alkyl NH3+ on a
> small molecule. The small molecule has its partial charges calculated by
> sqm in UCSF chimera for AM1-BCC charges, and the Lysine charges are from
> ff14SB library.
> >>
> >> I drew the standalone lysine and added charges to it, and the big
> difference still stands, that the side chain N on Lysine is +0.374 (in NH3+
> state), and the newly calculated lysine treated as a small molecule is
> +0.851. Changing the small molecule lysine from NH3+ to NH2 the
> non-protonated state didn't make a significant difference, that the
> recalculated charge after minimization is +0.909.
> >>
> >> I remember from reading, and from my own experience, that good charges
> are one of foremost important factors in modeling. So I'm quite surprised
> by this difference, that AM1-BCC charges are known to be good, and so are
> well established FF charges, but they differ so much in the case of NH3+.
> >>
> >> Which one should I prefer?
> >>
> >> Thanks!
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Received on Thu Aug 04 2022 - 13:37:33 PDT
