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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Received on Fri Dec 05 2008 - 16:09:57 PST
