Hi everyone,
Thanks for useful suggestions. We are wroking on it. Will get back to you
once we check everything.
On Tue, 13 Nov 2018, 17:28 Lachele Foley <lf.list.gmail.com wrote:
> The last response from Anselm (and possibly others - I didn't read
> everything carefully) seems right. Most likely, a residue somewhere isn't
> bonded to another residue correctly.
>
>
> On Tue, Nov 13, 2018 at 7:51 AM Dr. Anselm Horn <anselm.horn.fau.de>
> wrote:
>
> > Dear Maryam,
> >
> > I'd also encourage you identify the residue charges and thus to see
> > whether there are unexpected discrepancies.
> >
> > For a recent publication (doi.org/10.1038/s41598-018-23624-8) we had to
> > generate glycam parameters for glucose. There we learned that suger
> > residues possess charges of 0.194, 0.0, or -0.194 when they have a
> > single valence without bridging oxygen, two valences with one bridging
> > oxygen, or a single valence with one bridging oxygen, respectively.
> > Thus, the value you see as an residual non-integer charge, -0.388, fits
> > well into that residue charge scheme (cf.
> > $AMBERHOME/dat/leap/prep/GLYCAM_06j-1.prep).
> >
> > Thus, there is most probably an issue with open valences in your system
> > or the correct bonds between residues or the residue definition itself,
> > because the glycam force field was created to provide residue charge
> > blocks summing up to 0 (AFAIK). And in turn, I'd recommend you to find
> > the reason for the unbalanced charge in your system.
> >
> > However, people more experienced with the glycam force field might be
> > able to provide you with a more directed piece of advice.
> >
> > Best regards,
> >
> > Anselm
> >
> >
> > Am 13.11.2018 um 08:49 schrieb David Cerutti:
> > > That could explain it. Check the overall charges of one individual
> > residue
> > > by using the CheckMD program (installed with AmberTools). Do this:
> > >
> > > ${AMBERHOME}/bin/CheckMD -p <topology> -c <inpcrd>
> > >
> > > That will print resID.txt, containing tables of every residue type in
> > your
> > > simulation. It should be obvious which residues have non-integer
> > charges.
> > >
> > > Dave
> > >
> > >
> > > On Tue, Nov 13, 2018 at 2:42 AM maryam azimzadehirani <
> > > maryamai1988.gmail.com> wrote:
> > >
> > >> 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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>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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Received on Tue Nov 13 2018 - 06:30:03 PST
