Re: [AMBER] Gromacs towards Amber conversion

From: Karl Kirschner <k.n.kirschner.gmail.com>
Date: Sun, 29 Mar 2015 12:12:51 +0200

Hello Simone,

  As Carlos said, it is difficult to use Gromacs parameter with the Amber's
Sander program. Gromacs contains a variety of different mathematical
equations that can be used to model the different terms within the
force-field equation (e.g. different torsion function, different nonbonded
functions). If the Gromacs parameters are used in the same force-field
equation as found in Amber, then the conversion can be done. However, if a
different force-field equation is employed, then the conversion is not as
straight forward. Because of this, and as far as I know, no one has yet
developed a Gromacs --> Amber force field conversion script/program. If you
do find one, make sure that the parameters can be used in the same
force-field equation.

Bests,
Karl

-- 
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
On Sat, Mar 28, 2015 at 3:25 PM, Simone Fulle <fulle.bio.mx> wrote:
> Hi,
>
> I would like to use force field parameter of modified amino acids, which
> are already available in the Gromacs format. As I would like to use Amber
> for the simulations, I am aiming to transform these parameters into the
> classical Amber .lib and .frcmod format. I found solutions to convert Amber
> towards Gromacs file formats but, unfortunately, not the other way around
> (i.e. Gromacs towards Amber). Maybe I just missed it - are there any
> scripts or functions which I could use for the conversion?
>
>
> Best,
>
> Simone
>
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Received on Sun Mar 29 2015 - 03:30:02 PDT