Re: [AMBER] convert amber topology and coordinates files into gromacs topology

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 3 Jul 2016 22:57:49 -0400

On Sun, Jul 3, 2016 at 8:27 PM, Ming Tang <m21.tang.qut.edu.au> wrote:

> Dear list,
>
> I am studying glycoprotein. As amber is very slow on CPUs, I really want
> to do my simulations in gromacs. I found that gromacs has amber99sb.ff. So
> I want to convert amber topology and coordinates files into gromacs
> topology using Antechamber. My concerns are:
>
> 1) amber16 has leaprc.protein.ff14SB now, then is it reliable to
> study my glycoprotein using amber99sb.ff in gromacs?
>

‚ÄčThis question does not fully make sense. ff14SB is a different force
field than ff99SB. The former is significantly newer (~8 years newer), and
has been substantially improved in many regards.

If you are using antechamber and converting the result to GROMACS, I would
suggest just doing the whole system in Amber and converting the prmtop and
inpcrd files to a GROMACS topology and gro file. You can do this with
ParmEd if you want to.

HTH,
Jason
‚Äč
-- 
Jason M. Swails
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Received on Sun Jul 03 2016 - 20:00:02 PDT
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