Re: AMBER: calculating charges to modified 4GA unit

From: Karl Kirschner <>
Date: Wed, 07 Nov 2007 14:37:42 +0100

Hi Nagaraja,

        There is a simple semi-correct answer for obtaining a charge set
that would be appropriate, and then there is the right answer. First
the right answer.

        The charges for the carbohydrate residues in Glycam04, and in the
present state of Glycam (see Glycam website), were generated using
100 to 200 structures (an ensemble) that were extracted from an
explicitly solvated MD simulation. The initial charges for the
simulation were generated using RESP, with a HF/6-31G(d)//HF/6-31G(d)
molecular electrostatic potential (MEP) and a restraint weight of
0.01 (this value is set in the file). All aliphatic hydrogens
where summed into their adjoined carbon atom (also set in the
file). The ensemble of structures were extracted systematically from
the coordinate file using ptraj. The rotatable exocyclic bonds were
constrained to their MD angle values, and each molecule was optimized
(i.e. constrained optimization) at the HF/6-31G(d) level of theory
(i.e. 100-200 QM calculations). A RESP calculation was performed, as
stated above, on each resulting MEP, and then each partial atomic was
averaged over all structures. For terminal carbohydrate residue the
overall charge is adjusted to -0.194 au, which is neutralized when
the -OCH3 (+0.194 au; prep file residue abbreviation is OME) is added
to the C1 position. For non-terminal residue are adjusted to have an
overall charge of 0 au. Thus, each carbohydrate has has an ensemble-
averaged charge set, which does not "favor" a particular conformation
for the hydroxy groups orientations. This process is time consuming
and actually doing this is somewhat complicated.

        If you do not wish to do the above charge derivation, then I would
suggest exploring the following. 1) Try using R.E.D. II, or 2) use
the existing OME and 4GA in Glycam to create your carbohydrate.
Modify the existing 4GA prep file by removing the appropriate -OH
groups. In LEAP, load the modified glucose prep file and the OME prep
file, and form a bond between each OME and your modified 4GA prep
file (use LEAP's bond command); calculated the resulting overall
charge. If the overall charge is non-zero (I am assuming your
polysaccharide does not have a charge residue present) then adjust
the partial atomic charges on the carbon atoms that have the new -
OCH3 groups added to them. This method should provide you with an
adequate charge set that will be compatible with Glycam parameters.

        The paper that describes this can be found at the following web

        I hope this answers your question. Good luck.

Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Hamilton College, Clinton NY 13323

On Nov 7, 2007, at 12:26 PM, nag raj wrote:

> Dear Amber Users,
> My system consist of CH3 group in
> place of primary and secondary hydroxyl hydrogen atom
> of alpha-D-Glucose (Unit name is 4GA in glycam04 force
> field of Amber8.0. Primary and secondary hydroxyl
> hydrogen atoms in 4GA are replaced by CH3 group). As
> per the example given in tutorial
>, I
> calculated the RESP charges to with and without adding
> CH3 group to 4GA unit. The charges of 4GA unit without
> adding CH3 group do not match with 4GA unit of
> glycam04.
> My question is:
> How to calculate the charges to a system consist of
> CH3 group in place of primary and secondary hydroxyl
> hydrogen atom of alpha-D-Glucose.
> Any suggestion is appriciated.
> Thank you in advance.
> with best regards,
> Nagaraja Mulpuri

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Received on Sun Nov 11 2007 - 06:07:08 PST
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