[gmx-users] Conversion Amber to Gromacs

[Thomas Piggot]

Hi,

The multiplicity/periodicity is the same but always positive in GROMACS. 
Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by 
IDIVF (the entry after names in AMBER file). The phase is the same.

For more info on why see ambermd.org/formats.html#parm.dat

Cheers

Tom

On 23/10/17 10:09, Elisa Pieri 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.
>
> 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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-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.