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 <kartheekpi...@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,
karthee...@research.iiit.ac.in,
On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek <kartheekpi...@gmail.com>
wrote:
You can do with ParmEd
On Oct 20, 2017 10:07 PM, "Elisa Pieri" <elisa.pi...@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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