Thanks for you reply Dave.
I see your point. The system is quite large... I have a dimer of two
protein chains (each about 600 a.a). However the charge of the same system
without glycans is integral. I am comparing the dynamical pattern of the
system with and without attached glycans (each protein chain is
glycosylated with about 10 oligosaccharide chains). As long as the PME
condition works fine, I would rather proceed. Is there anything you could
suggest that we try to fix this issue?
Thank you very much
On Mon, Nov 12, 2018 at 10:33 AM David Cerutti <dscerutti.gmail.com> wrote:
> You can technically run MD, but I'd be worried about the residue(s) you've
> just made. What pmemd (or pmemd.cuda) will do is tell you "Sum of charges
> from parm topology file = 0.37999999." And, since that's greater than 0.01,
> it will say "Assuming uniform neutralizing plasma." This means that it's
> going to lean on the Ewald tinfoil boundary conditions, setting the first
> Fourier frequency value explicitly to zero. It's not that the system
> dynamics is necessarily bad if you have +1, or even -3 proton units' excess
> charge on the system. If you think that it resonates with protons in the
> surrounding water to accumulate that partial charge in a mean sense, this
> is actually not a bad idea--the problem is that all of the other residues
> are neutral or of integer charge, so the rest of the model isn't ready to
> swing the way of your new residues.
>
> Dave
>
>
> On Sun, Nov 11, 2018 at 7:43 AM maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Dear Amber users,
> > I have generated a glycosylated protein using xleap. I am using AMBER
> tools
> > 17 and I have sourced the ff14SB for protein atoms and glycam forcefield
> > for the glycans. All glycosylated Asns are renamed to NLN. However I got
> > this warning from the leap:
> > *The unperturbed charge of the unit: -0.388000 is not integral*
> > can I proceed for MD with such warning?
> > thanks in advance
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Received on Mon Nov 12 2018 - 04:30:02 PST
