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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 16:10:15 PST
