AMBER Archive (2008)

Subject: Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein.

From: Gustavo Seabra (
Date: Wed Jul 16 2008 - 09:08:45 CDT

On Wed, Jul 16, 2008 at 8:15 AM, SeungPyo Hong <> wrote:
> Dear Amber users,
> I want to perform MD simulation with a ligand, however I don't know whether
> I am going to the right direction.
> Any command of yours will be a great help for me.
> I need to generate force field of ligands, and made one using the following
> commands:
> $ antechamber -i DRGML2.TOPH -fi mol2 -o ligand.prepin -fo prepi -c bcc -s 2
> MAXOPT=20000"
> $ parmchk i lipid_a.prepin f prepi o ligand.frcmod
> * The charge of the ligand is '-4'.
> * As many had already noticed, the 3D structure is generated from DUNDEE
> PRODRG server.
> However, I just remember that the consistency of the force field is
> important.
> I will use AMBER03 FORCE FIELD in the simulation.
> However, I don't know whether the AM1 can be used with AMBER03 force field,
> because as I remember AMBER03 force field was generated with more
> complicated methods and basis functions.

You're right, you may have a consistency problem here. If you use
antechamber the way you describe, you get AM1-BCC charges, which where
parametrized to reproduce the HF/6-31* charges used in gaff and other
Amber parameter sets, while in the ff03 charges were derived from a
b3lyp/cc-pVTZ//HF/6-31G** calculation in an implicit solvent model.
So, to be strictly consistent here, maybe you should either derive
your charges from a full QM calculation following the procedure
described in the ff03 paper, or use a force field compatible with the
HF/6-31G* charges. In this case, the recommended one would be the 99SB
force field.

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