AMBER Archive (2008)

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

From: Stephane Abel (Stephane.Abel_at_cea.fr)
Date: Thu Nov 20 2008 - 10:51:25 CST

Thanks Mattew,

Indeed i read your paper. So i understand well, if I use GLYCAM06 for my
glycolipid molecule, i need to compute the partial charge for only the
atoms of the alkyl tail ? Because In the Kirshner paper the partial
charge for the maltose are given. It is correct ?

Thank you

Matthew Tessier wrote:

> 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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>
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