Re: [AMBER] D-N-Sulfate-glucosamine net charge

From: FyD <>
Date: Thu, 01 Dec 2011 08:40:45 +0100

Dear Massimiliano,

Several comments:

- The paper of Huige & Altona is indeed a reference but is a little old.

- You could create totally new unit(s) for any type of
sulfated/modified monosaccharide units for GAGs. A key problem in your
case will be how you will connect the new force field libraries to the
existing ones. This problem can be solved by applying specific charge
constraint(s) during the charge fitting step; i.e. for a
monosaccharide unit: intra-molecular charge constraint(s); and between
two monosaccharide units: inter-molecular charge constraint(s) (see

- Obviously, making a new unit compatible with existing ones by
applying this type of constraints will impact the charge fitting step.
Thus, another approach would be to generate a new set of force field
libraries for your oligosaccharide(s); i.e. following a totally
independent and highly homogeneous approach. Here, the approach is
highly related to the structure of your oligosaccharide: does it
contain a single or several chemical modifications?

- You can find examples of charge derivation and force field library
building for chemically engineered olgosaccharides and glycoconjugates
in R.E.DD.B. where all the computational data are described and are
freely available.

- You can also use R.E.D. Server and automatically generate a new set
of force field libraries for any particular GAG sequence.

- You will find tutorials about this topic as well .

Finally, if you connect to the q4md-fft mailing list . I know you
will be able to discuss with users, which have developed new force
field libraries for GAGs. (You can also look at the archives but we
have a bug, which makes these archives difficult to read so far).

regards, Francois

> I am attempting to do MD simulations of certain glycosaminoglycans (GAG)
> interacting with proteins.
> With regard to the partial charges, from the Amber archives I
> understood that I should use the sulfate.prep
> file from GLYCAM website, whilst having a look at the GLYCAM website FAQs
> I should use the parameters given in J. Comp. Chem. Huige and Altona,
> Vol. 16, 56 (1995).
> To familiarise with the tleap oligosaccharides building procedure I
> am starting
> from monomer D-N-Acetylglucosamine in which I want to substitute the acetyl
> with the sulfate group (at the N atom in position 2).
> The total charge of the new sulfated compound should obviously be -1 .
> If I implement the partial charges given in "sulfate.prep" file downloaded
> from GLYCAM website ( )
> I get a net charge equal to -0.909000
> whereas
> if I implement the partial charges given in J. Comp. Chem. Huige and
> Altona, Vol. 16, 56 (1995),
> I get a net charge equal to
> -0.982000
> which is closer to the unit (in this case I implemented the charges
> derived for Isopropyl-Sulfamate and I used also the N and H atoms charges
> in addition to those of SO_3).
> For helping I enclosed the input file I use for tleap (where there are
> several comments for
> clarity).
> Am I doing right or missing something here?
> Should I recalculate the partial charges through a RESP procedure?
> But if this is the case, why is there a sulfate.prep file in GLYCAM
> website and how
> should one use it?
> Any hint/suggestion would be really appreciated.
> Best,
> --
> Dr Massimiliano Porrini

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Received on Thu Dec 01 2011 - 00:00:04 PST
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