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

From: David A Case <>
Date: Wed, 10 Jun 2015 14:20:39 -0400

On Wed, Jun 10, 2015, Lachele Foley wrote:

> Aliphatic hydrogens
> (hydrogens attached to a carbon) do not*, participate in hydrogen
> bonding.

This is somewhat controversial. But even with force fields that have (small)
non-zero charges for hydrogens bonded to carbon, CH--O hydrogen bonds are
probably understabilized, compared to "reality". But, as Lachele noted, you
are not losing much by having zero charges in Glycam.

Here is an old, but (I think) still relevant analysis:

%A R. Vargas
%A J. Garza
%A D.A. Dixon
%A B.P. Hay
%T How Strong Is the Calpha-H***O = C Hydrogen Bond?
%J J. Am. Chem. Soc.
%V 122
%P 4750-4755
%D 2000


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Received on Wed Jun 10 2015 - 11:30:04 PDT
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