AMBER Archive (2009)

Subject: Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP

From: FyD (
Date: Sun May 31 2009 - 07:51:50 CDT

Dear Xueqin Pang,

> I am doing computational stimulation on GPCR with Amber10 now, and
> have the following problems when adding lipid membrane (which has
> already been stabilised) into the system
> 1. Can I get my topolygy of dppc with Antechember (GAFF), and then
> get the partial charges with RESP after optimization with Gauss?


> 2. Someone do it as follows :"General Amber force field (GAFF)
> parameters were assigned to ligands and DPPC molecules, while the
> partial charges were calculated using the AM1-BCC method as
> implemented in the Antechamber suite of AMBER 8." Is the result
> reliable? (Journal of Medicinal Chemistry, 2006, Vol. 49, No. 14)

Why not.

> 3. Someone have treat the partial charges of CH3 and CH2 as 0, can
> we do the same thing in Amber. (J. Phys. Chem. B, Vol. 108, No. 14,
> 2004)

Why not. For instance, Glycam FF uses H set to zero.

Did you try one of these approaches ?

regards, Francois

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