AMBER Archive (2008)

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

From: David A. Case (
Date: Thu Nov 20 2008 - 09:56:15 CST

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.


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