[gmx-users] Conversion Amber to Gromacs

Tue Oct 24 19:41:10 CEST 2017

Please, get it here

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

Interestingly, but Google code still holds the correct information too:

https://code.google.com/archive/p/acpype/

On 24 October 2017 at 18:34, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hello Elisa,
>
> "J'arrive après la bataille" To be sure that you have correct Amber
> parameters for GROMACS, you could also use the acpype suite*. This suite
> converts  Amber params in gromacs format. The program generates the
> (non)ffbonded.itp and top files in gromacs format from the Amber's LeaP
> tool. It also provides some gromacs and Amber files to perform and a single
> point energy to test if the conversion is correctly done.
>
> I used successfully this code  to convert the Amber lipid14 params for
> POPC lipid in the GROMACS format.
>
> *http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder
>
> HTH
>
> Stéphane
>
> ------------------------------
>
> Message: 3
> Date: Tue, 24 Oct 2017 17:17:08 +0200
> From: Elisa Pieri <elisa.pieri at univ-amu.fr>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Conversion Amber to Gromacs
> Message-ID:
>         <CANYcjuZAF9n7tM=c-FGaR--ctbA=hedtP6BnPv77-FpOB8Y63A at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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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