Re: [AMBER] Charges for H-atoms in GLYCAM?

From: Lachele Foley <>
Date: Wed, 10 Jun 2015 13:44:33 -0400

Only the aliphatic hydrogens are set to zero. Aliphatic hydrogens
(hydrogens attached to a carbon) do not*, participate in hydrogen
bonding. The hydroxyl hydrogens (hydrogens attached to an O) all have
non-zero partial charges. The aliphatic hydrogens are set to zero
because in general their computed partial charges are very small and
oscillate around zero. So, rather than set a small and arbitrary
charge on them, one that might artificially bias their dynamics and
interactions, they are set to zero.

* At least, not in these sorts of systems. It is conceivable that
such hydrogens in some strange molecule could do that, but that
behavior is definitely not expected here.

On Wed, Jun 10, 2015 at 1:32 PM, Chris <> wrote:
> Dear All!
> When using GLYCAM force field, I noticed that the partial atom charges for hydrogen atoms are all seted to ZERO. I can't understand why generating GLYCAM in such a manner. And if I want to analyze H-bond interaction between my sugar ligand and protein, as the charges for H atom are 0, does it is resonable for my system's MD simulation under GLYCAM?
> thx!
> Chris
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Wed Jun 10 2015 - 11:00:03 PDT
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