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 - 06:00:02 PST
