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

From: Lachele Foley <>
Date: Wed, 10 Jun 2015 14:37:04 -0400

Thanks for the ref and info, Dave!

If you want, you can always make your own charges. You should
probably start with our charges and run an MD from which you extract a
few hundred frames. Then, compute and average the partial charges
over all of the frames. It is probably worthwhile to check the
distribution of charges on those hydrogens, just to see if setting a
charge is statistically relevant.

If you want charges that change, you will need to use a force field
designed for that. It will be computationally more expensive, and
someone else will have to comment about those force fields.

On Wed, Jun 10, 2015 at 2:20 PM, David A Case <> wrote:
> 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
> ....dac
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Wed Jun 10 2015 - 12:00:02 PDT
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