[AMBER] converting gromacs topology to amber

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Wed, 5 May 2021 01:04:26 +0300

Dear all,
i have a gromacs topology and .gro file that I want to convert into amber
however, using several scripts and suggestion on the internet, i am unable
to do so. my errors stem from parmed unable to recognise gromacs, i think.
How do i put it in its path? my parmed is installed within amber18. i found
the gromacsfile. but how to modify it?
 i looked at the scripts and files but there is no gmx_top in the
parmed/gromacs folder but there is gromacstop. so should i change it the
the following script

from parmed import gromacs, amber, unit as u
gromacstop = GromacsTopologyFile('topol.top')
gromacsgro = GromacsGroFile.parse('complex.gro')
gromacstop.box = gromacsgro.box # Needed because .prmtop contains box info
gromacstop.positions = gromacsgro.positions
amb_prm = AmberParm.from_structure(gromacstop)
amb_inpcrd = amber.AmberAsciiRestart("cyn.crd", mode="w")
amb_inpcrd.coordinates = gmx_mpi_toptop.coordinates
amb_inpcrd.box = gmx_mpi_top.box


i also tried with gromber but no luck. first the preprocessors (define
[DEFINE=VAR]) could not be defined as I am not sure what to write for the
variable. now gromber is not recognised at all.

Any suggestions would be great?

Thank you
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Received on Tue May 04 2021 - 15:30:02 PDT
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