[gmx-users] Conversion Amber to Gromacs

[Elisa Pieri]

Hello again,

Thank you very much for your answers, we got to convert everything. We used
pdb2gmx with no problems, and the conf.gro file looks fine (on VMD at
least). Then, we tried with a simple input file (from
http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf), but grompp
reports a fatal error and a few warnings:

This is an example of the warnings:
WARNING 15 [file ffnonbonded.itp, line 78]: Too few parameters on line
(source file
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line 338)

And this is the fatal error:
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/people/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c,
line: 742
Fatal error: Unknown bond_atomtype hE

This is one of the new atomtypes we introduced, but we double checked the
connectivity and the bonding parameters for hE and it looks fine. Any idea?
Should I send you the force field files?

Thank you very much in advance,
Elisa

On Mon, Oct 23, 2017 at 1:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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> > > >>
> > > >
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