AMBER Archive (2003)

Subject: Re: How to calculate new force field?

From: Jose Ramon Blas (jramon_at_ub222059.pcb.ub.es)
Date: Mon Feb 03 2003 - 13:06:24 CST

Hi,
I propose three ways of doing this:

i) web-searching. Maybe your molecule has been parametrized by someone
before (surprises exist!). Look at http://pharmacy.man.ac.uk/amber/

ii)if your molecule is not too strange, what I propose is to assign to
all the atoms in your system an existing atom_type of amber parm99.dat force
field (BE VERY CAREFUL ON THIS!! this is a parametrization) and check that
all the bonds, angles, torsions exist in the parm99.dat file. If there are
missing terms you can take them from similar ones in parm99.dat.

iii) try antechamber and GAFF (see instructions in AMBER7 home page, it is
very easy and fast). Remember, however, to check if you agree with
antechamber in the atom_types assignment to your particular system.

Hope this helps,

Jose Ramon

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona

On Mon, 3 Feb 2003, k.watanabe wrote:

> hi,
>
> We need to calculate a MD of the protein with a small molecule.
> So, We calculated point charges of small molecule using gaussian
> and resp (in amber) .
> To run MD, We also need bond, angle, torsion, improper torsion
> and VDW parameters of a small molecule.
>
> Does anyone know any information (e.g. web or paper)
> for beginners that indicate how to calculate it?
>
> K, Watanabe.
> Hitachi ulsi systems co. ltd.
>
>