Re: [AMBER] Glycophosphate parametrization using GLYCAM

From: Lachele Foley <>
Date: Thu, 19 Jun 2014 11:46:31 -0400

>> You'd still need to set atom
>> types for the attaching carbon (Cp).
> And this might be the reason... we'll try.

That should do it.

> 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.

This is correct. But, if you follow our procedures for generating the
partial charges, you should be fine.

> 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.

All GLYCAM carbohydrate residues have a very easily predictable total
charge. You are correct that this is necessary for them to be used in
the modular fashion. Not all are exactly the same, but they are

Here it is:

* Every reducing end C1 carries with it a charge of +0.194. So, the
0GA residue has a total charge of +0.194.

* Every non-reducing Ox carries a charge of -0.194. So, the 4GA
residue has a total charge of 0, YGA has a total charge of -0.194, and
so forth.

* The reducing end aglycons all have a charge of -0.194. So, the
combination ROH-0GA is neutral.

When we started looking into adding derivatives (SO3, Me, etc.), we
found that we could not retain that "0.194" standard and get
reasonable charge distributions. So, the rules for attaching them are
a little more complex. The rules are at the page I referenced at the
start of this thread.

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Jun 19 2014 - 09:00:03 PDT
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