[gmx-users] Re: Amber to Gromacs

Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Sat Oct 13 17:45:54 CEST 2007

> Dear all,
>  	I hvae used ANTECHAMBER & GAFF of Amber generate a .prmtop and .prmcrd of 
> a small molecular(XK263, a inhibitor of HIV-1 PR). I want to use ffamber99 in
> Gromacs-3.3.1 to do a simulation of it, but I can't get the force field of the 
> molecular used in Gromacs. 
>     On the Homepage of Amber, there is a script to converse the Amber force 
> field to Gromacs. But it can't work without Amber8 or Amber9 installation.
> I didn't get a Amber8/Amber9 package, can anyone help me to do the conversion?
> It will be very appreciated!
>    The attached is the .prmtop and the .prmcrd file, another one is the script.
> They are in a compressed file in the attached.
> The command used may be:
> ./amb2gmx.pl --prmtop XK.prmtop --crd XK.prmcrd --outname XK

Maybe you can convert topology manually by taking force fields
parameters from Amber and converting them into Gromacs terms.
I'm not familiar with Amber but as far as I know energies are
i kcal so you need to convert kcal->kJ. In some programs
parameters of e.g. bond stretches are k(r-r0)^2 while in others
it is (k/2)(r-r0)^2. Also dihedrals might be difficult to convert.
You can use Amber topologies for proteins and compare them with
Gromacs Amber ports from folding at home to find some rules.

Best regards

Vojtech Spiwok

Ing. Vojtech Spiwok, PhD.
Dept. of Biochemistry and Microbiology
Institute of Chemical Technology Prague
Technicka 3, Prague 6, 166 28,
Czech Republic
Tel: +420 22044 3028
Fax: +420 22044 5167
E-mail: spiwokv at vscht.cz
Web: biomikro.vscht.cz/groups/lab211/

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