Thank you for these explanations
Stefane
Matthew Tessier wrote:
> 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.uga.edu
> matthew.tessier.gmail.com
> Woods' Lab Room 1092
> Complex Carbohydrate Research Center - University of Georgia
>
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
> Stephane Abel
> Sent: Thursday, November 20, 2008 11:51 AM
> To: amber.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.uga.edu
>> matthew.tessier.gmail.com
>> Woods' Lab Room 1092
>> Complex Carbohydrate Research Center - University of Georgia
>>
>>
>> -----Original Message-----
>> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
>>
> Of
>
>> Stephane Abel
>> Sent: Thursday, November 20, 2008 11:26 AM
>> To: amber.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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>
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Received on Fri Dec 05 2008 - 16:10:35 PST
