Hi,
Before to perform MD simulations with you "large" system I will try to figure out why the addition of glycans leads a system with a non integral charge. For instance did you check if the charges of residues linked to the glycans are correct? Are some Hs missing? Do not forget that you will have to justify your model when you will submit your work for publication. And I am not sure that any reviewers will be satisfied by a system with a non integral charge.
Stéphane
________________________________________
De : maryam azimzadehirani [maryamai1988.gmail.com]
Envoyé : lundi 12 novembre 2018 13:05
À : AMBER Mailing List
Objet : Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
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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> >
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Received on Mon Nov 12 2018 - 05:30:02 PST
