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 - 11:09:16 CST

Stephane,
Yes, that is correct. The carbohydrate charges are meant to be used as
residues that can be added to proteins or lipid tails without charge
modification. The benefit to developing charges for the lipid tails is that
it requires less sampling for ensemble charge development than
carbohydrates. That paper explains our work in developing charges for lipid
tails.

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 11:51 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: CG and HC atoms partial charges in AMBER

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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