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

From: SeungPyo Hong <sp1020.gmail.com>
Date: Thu, 17 Jul 2008 10:50:31 +0900

Thank you Alan and Seabra,

to Alan:
I have to check the options I had used.
Maybe I have done a mistake.

to Seabra:
Your answer is what I needed.
thank you so much.

Sincerely,
Seungpyo Hong

On Wed, Jul 16, 2008 at 11:08 PM, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:

> On Wed, Jul 16, 2008 at 8:15 AM, SeungPyo Hong <sp1020.gmail.com> 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
> > -nc -4 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=BFGS XTEST=0.0001
> > 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.
>
> Gustavo.
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-- 
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'At the same time, he allowed interaction among objects.'
-Seungpyo Hong
Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_.kaist.ac.kr
sp1020.gmail.com
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Received on Sun Jul 20 2008 - 06:07:19 PDT
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