Re: [AMBER] Glycophosphate parametrization using GLYCAM

From: FyD <>
Date: Fri, 20 Jun 2014 10:46:35 +0200

Dear Jochen,

> My train of thought was that the bond, torsion and dihedral terms used
> in GLYCAM would by carefully balanced with the partial charges to
> reproduce the certainly subtle details of the conformational equilibria
> of the different carbohydrates. Therefore I assumed that changing those
> would not be a good idea. I also assumed that in order to be used as a
> "building block", all GLYCAM carbohydrate moieties would have the same
> total charge, which obviously is not the case, as you mentioned in your
> last email.

the same phosphate building block is connected to different positions
of different molecules with different total charge values; obviously
you could fine tune the charge fit and involve different phosphate
building blocks to improve the RRMS of the fit; in our case this did
not help that much...

>> the charge of the monosaccharide units are different and the charges
>> of the phosphate groups can be identical or different depending on the
>> number of building blocks used for the phosphate groups; that being
>> said - I would first simplify the problem and use a single building
>> block for the phosphate groups...

> Yes. But what I do not get is this: If each monosaccharide unit can have
> a different total charge, we obviously can not use the same partial
> charges for the phosphate group atoms when bound to different
> monosaccharides and need to carry out RESP-fitting for all
> monosaccharide-phosphates that occur in our simulation. For the sulfate
> moiety as used in the carbohydrate builder, this is obviously not needed.

Sugar1-OH Me-POH(2-)
       inter-mcc 1
Sugar2-OH Me-POH(2-)
       inter-mcc 2

       -> Sugar1-POH(2-) + Sugar2-POH(2-)

   Whatever is the total charge of Sugar1-OH & Sugar2-OH...

   inter-molecular equivalencing is even applied to different
nucleosides (but the C1' & H1' to relax the system) ...

regards, Francois

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Received on Fri Jun 20 2014 - 02:00:04 PDT
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