Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar

From: José Daniel Martinez <>
Date: Thu, 29 Nov 2018 08:52:14 +0000

Thanks for your response, David.
I see what you propose is something like a parametrization of a small 'fluorine environment', while keeping the rest of the molecule like is described in GLYCAM. I will carefully read the posts you attached, at first sight the protocol is similar to what you could do with GAUSSIAN, isn’t it?


De: David Cerutti <>
Enviado: miércoles, 28 de noviembre de 2018 19:53
Para: AMBER Mailing List
Asunto: Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar

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The way I'd approach this sugars problem is to take the base parameters
from GLYCAM and try to graft in the fluorine chemistry. GAFF isn't the
tool here, I think--it is for making something from scratch, whereas you
want something that looks like an established parameter set for related
molecules. What I'd do is make your residue, assign charges based on
GLYCAM manually (use your best judgment), then take the mdgx program in
AmberTools. Look at these tutorials:

The first one is about "IPolQ" charges which you don't want if you are
trying to mimic GLYCAM--you want HF/6-31G* or HF/CC-PVTZ. The thing to do
is run mdgx -FITQ to see a list of options for charge fitting, then make a
bunch of configurations and run HF/(your basis set) on them to get charge
grids. mdgx will be able to take those charge grids and run a REsP-like
fit, and you can specify that it hold charges other than the fluorine and
proximal atoms to values from the original GLYCAM for the sugars that
you've decided are the closest match. Then, you can make a bunch of other
configurations by manipulating the fluorine group to sample dihedral
configurations, and refit parameters that impinge on the motion of that
group (I'd recommend angles as well as dihedrals).

This is the "hard core" way to do it, but I made mdgx to make the hardcore
stuff as straightforward as possible. It's mechanistically easier to take
mdgx and make a completely new set of parameters for your molecule, but
it'll take more computational power and the details of telling mdgx to
respect certain parameters from GLYCAM are not that difficult.

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Received on Thu Nov 29 2018 - 01:00:01 PST
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