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
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
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Received on Tue Nov 13 2018 - 05:00:02 PST
