Hi Dave,
120 monosaccharides in total (20 oligosaccharides of 6 units each). Can you
explain more about what is minute adjustments to each of them?
thanks
On Tue, Nov 13, 2018 at 10:54 AM David Cerutti <dscerutti.gmail.com> wrote:
> One thing that I don't see in this discussion is "how many residues have
> you added?" If the answer is a very large number of them, then the excess
> charge is going to be distributed over them all, and what you should
> probably do is make minute adjustments to each of them to neutralize the
> system as a whole. This is probably what's happening. A lot of sugar
> moieties come out with slightly non-integer charge, IIRC.
>
> Dave
>
>
> On Mon, Nov 12, 2018 at 9:11 AM maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Dear Stephane,
> > Obviously we will solve the issue. This is why I wrote to this mailing
> list
> > in the first place and we are not discussing publication or peer review
> > process and your personal comments on that matter. But thank you for your
> > advice.
> > No hydrogens are not missing.
> > Thanks
> >
> >
> > On Mon, 12 Nov 2018, 16:53 ABEL Stephane <Stephane.ABEL.cea.fr wrote:
> >
> > > 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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Received on Tue Nov 13 2018 - 00:00:02 PST
