AMBER Archive (2008)

Subject: RE: AMBER: CG and HC atoms partial charges in AMBER

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Thu Nov 20 2008 - 10:40:43 CST

The GLYCAM06 release in AMBER 10 includes parameters for lipids as well as
carbohydrates. The atom type "CG" is used for sp3 C in the lipid tail, but
you can see this in the GLYCAM06 lipids paper:

Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers
and Glycolipids. M. B. Tessier, M. L. DeMarco, A. B. Yongye and R. J. Woods.
Molecular Simulation, 2008. Vol 34 Issue 4, pages 349 - 364.

Matthew Tessier
mbt3911_at_uga.edu
matthew.tessier_at_gmail.com
Woods' Lab Room 1092
Complex Carbohydrate Research Center - University of Georgia

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Stephane Abel
Sent: Thursday, November 20, 2008 11:26 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: CG and HC atoms partial charges in AMBER

Thanks David for your (quick) response.

In my previous mail, I said that I used GLYCAM06 for the dodecan
molecule, because i would like to simulate, in the futur, a glycolipid
molecule (e.g. dodecyl maloside, DDM). So I constructed only the
dodecane with the CG and HC parameters available in GLYCAM06. Moreover,
in the paper of Kirschner et al. about GLYCAM06 (JCC, 29, 4, 622) CG are
considered as a sp3 atom for hydrocarbon. So do you think that i can use
only the parameters in the GLYCAM06 force field for all the DDM ? Or
should I mix GAFF and GLYCAM for the alkyl tail and the maltose
headgroup, respectively ?

Thank you for your response.

David A. Case wrote:

> On Thu, Nov 20, 2008, Stephane Abel wrote:
>
>> I would like to simulate a dodecan chain with the AMBER force field
>> but *without* the AMBER code (i use an other MD package). So I construct
>> manually the topology and the parameter for this molecule. For
>> subsequent simulations, I will use GLYCAM_06. So I have a little
>> question about the partial charge of the carbon (CG) and hydrogen atoms
>> (HC). How to obtain them ?
>>
>
> The only Amber force field that would be appropriate for a general
molecule
> (like dodecane) would be GAFF. You would need to run antechamber, and
choose
> a charge model (either bcc or resp). See the AmberTools manual for
details,
> and tutorial B4 for a worked-out example.
>
> ...dac
>
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