Thanks Hai. I am trying to run script below, but I get error
in <module>
gmx_top = GromacsTopologyFile('topol.top')
NameError: name 'GromacsTopologyFile' is not defined
------------------------------------------------------------------------------------------
from parmed import gromacs, amber, unit as u
gmx_top = GromacsTopologyFile('topol.top')
gmx_gro = GromacsGroFile.parse('em.gro')
gmx_top.box = gmx_gro.box # Needed because .prmtop contains box info
gmx_top.positions = gmx_gro.positions
amb_prm = AmberParm.from_structure(gmx_top)
amb_prm.write("prmtop")
amb_inpcrd = amber.AmberAsciiRestart("inpcrd", mode="w")
amb_inpcrd.coordinates = gmx_top.coordinates
amb_inpcrd.box = gmx_top.box
amb_inpcrd.close()
On 5 July 2016 at 01:34, Hai Nguyen <nhai.qn.gmail.com> wrote:
> It's Python so you need to make a file with .py extension (e.g my.py) then
> put the content, then run
>
> python my.py
>
> Hai
>
> On Mon, Jul 4, 2016 at 4:26 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> > Hi List (Jason),
> >
> > I compiled ParmEd after downloading from git source. It compiled (python
> > setup.py install) without any errors.
> >
> > I am interested in converting gromacs topologies to AMBER. However, using
> > the below command, I get commands not recognised. Am I missing libraries
> or
> > toolkits? How can I install these?
> >
> > import parmed as pmd
> >
> > Kindly help.
> >
> >
> >
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Vice Chancellor's Research Fellow,
> > Queensland University of Technology,
> > 2 George Street, Brisbane, QLD 4000
> > Australia
> > LinkedIn
> > Research Gate
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Mon Jul 04 2016 - 18:30:02 PDT
