[gmx-users] Conversion Amber to Gromacs

[Mark Abraham]

On Mon, Oct 23, 2017 at 11:10 AM Elisa Pieri <elisa.pieri at univ-amu.fr>
wrote:

> Hello again,
>
> sorry I wasn't very clear perhaps..we are trying to modify directly the
> ffbonded.itp file (together with all the other interested ones) in the
> Amber94 force field in order to include the Amber Lipids17 force field. We
> added most of the parameters with no problems (bond equilibrium lengths,
> constants, bending and so on), but we were not able to understand what is
> the conversion factor for torsion parameters between the Amber software
> Suite and Gromacs. I know that in the Amber package, the dihedral force
> constant is expressed in Kcal/mol, but I couldn't understand what are the
> units (and therefore how to convert the parameters) in Gromacs.
>

Chapter 2 of the reference manual describes the units. Chapter 4 describes
the functional forms, and e.g. tables in chapter 5 fill in the gaps. That
has always been enough for me when converting stuff to and from AMBER
descriptions.

Mark


> Any idea?
> Elisa
>
> On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek <kartheekpitta at gmail.com>
> wrote:
>
> > ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
> > appropriate software for converting topologies.
> > This is the parm.py  script I have employed, supply amber topologies
> > file.prmtop and file.inpcrd as input and amber.save option will give
> > converted gromacs topologies as output.
> >
> > import parmed as pmd
> > #amber = pmd.load_file('prmtop', 'inpcrd')
> > amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
> > #save a GROMACS topology and GRO file
> > amber.save('new24_ang.top')
> > amber.save('new24_ang.gro')
> >
> >
> > ----------------------------------------------
> > P. Kartheek,
> > PhD Candidate, Computational Biophysical Chemistry,
> > Center for Computational Natural Sciences and Bioinformatics,
> > International Institute of Information Technology,
> > Marimuthu Krishan Group,
> > 9701577399,
> > kartheek.p at research.iiit.ac.in,
> >
> >
> > On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek <kartheekpitta at gmail.com>
> > wrote:
> >
> > > You can do with ParmEd
> > > On Oct 20, 2017 10:07 PM, "Elisa Pieri" <elisa.pieri at univ-amu.fr>
> wrote:
> > >
> > >> Hello GMX users/developers,
> > >>
> > >> we are trying to add the Amber lipids17 forcefield to the Amber99
> > >> forcefield implemented in Gromacs. We are a little bit lost on the
> > torsion
> > >> parameters: how to convert the constant from Amber to Gromacs?
> > >>
> > >> Thank you in advance!
> > >> Elisa
> > >> --
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