Dear All,
The issue is solved. We were missing to rename two of the glycosylated Asn
to NLN. The net charge is now integral.
Thank you for your help.
On Tue, Nov 13, 2018 at 5:36 PM maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> 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 - 23:30:02 PST
