That's also true.
Anyway, I briefly checked the charge of NLN residue, that is, modified ASN for N-linkages for glycosilated protein.
The charge is equal to -0.194, exactly one half of the reported -0.388 value.
Probably there are some connecting residues, which are not properly set by the user.
________________________________________
Da: David Cerutti [dscerutti.gmail.com]
Inviato: martedì 13 novembre 2018 8.24
A: AMBER Mailing List
Oggetto: Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 13 2018 - 00:00:02 PST
