Hello,
Many thanks for the suggestion. The sulphate moeity itself is charged
here (SO3-). It is part of the keratan sulphate glycosaminoglycan.
Regards,
On 17/05/2021 12:42, Dr. Anselm Horn wrote:
> Hi Rajas,
>
> from what you described it seems that the sulfate moiety is the origin
> of the non-integer charge; where do its charges come from?
>
> IMHO it would be save to ignore the charge deviation, since it only
> accounts for +0.008 a.u., and you probably have a sound literature
> reference for it.
> However, a practical workaround to obtain an integer charge would be to
> modify the atomic charges of the sulfate moiety to account for the
> inaccuracy.
>
> But other may comment here as well.
>
> Best regards,
>
> Anselm
>
> NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
>
> On 05/14/2021 06:24 PM, RAJAS MALLENAHALLI RAO wrote:
>> Hello all,
>>
>> I'm using Amber to simulate a glycoprotein containing keratan sulfate
>> glycans with sialic acid cap. I built the system using glycoprotein
>> builder of glycam.org, and I replaced the glycosylated Asparagine
>> residues with NLN. I'm using ff14SB for protein & Glycam06-j1 for
>> sugars. When I loaded the protein on tleap and checked for its charge,
>> it gives me a non-integer value:
>>
>>> test = loadpdb prot1a.pdb
>> Loading PDB file: ./prot1a.pdb
>> total atoms in file: 4343
>> Leap added 3978 missing atoms according to residue templates:
>> 3978 H / lone pairs
>>> charge test
>> Total unperturbed charge: -49.992000
>> Total perturbed charge: -49.992000
>>
>>
>> I tried to check where this is coming from, I tried on unglycosylated
>> system, it gives integer value; on glycosylated system (w/o any
>> charged
>> residues as well as with sialic acid) it gives integer value. The
>> problem starts when I add the sulfate groups. Is it advisable to
>> fiddle
>> with the NLN residue library to even out the non-integer value? or is
>> it
>> safe to ignore it altogether? Many thanks for suggestions/ help in
>> advance.
>>
>
>
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--
Rajas M Rao
Postdoctoral researcher
Laboratoire MEDyC CNRS UMR-7369
Université de Reims Champagne-Ardenne
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Received on Mon May 17 2021 - 05:30:02 PDT
