[AMBER] converting gromacs topology to amber

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Sun, 2 May 2021 19:32:31 +0300

Dear all,
I have run a simulation on gromacs.
I know that we can convert the topology and gro files using parmed to amber
format. the script file i think is this

import parmed as pmd
gromacs.GROMACS_TOPDIR = "/mnt/d/Najwan/cynaroside"
gmx_top = pmd.load_file('topol.top', xyz='complex.gro')
gmx_top.save('complex.top', format='amber')
gmx_top.save('complex.crd', format='rst7')

I save it as parmd.in

my command line is

parmed top_to_prm.in > -l convert.log

i get the file the following

*parmed.tools.exceptions.ParmError: Could not determine file type of
top_to_prm.in <http://top_to_prm.in>*

could someone please guide me to the correct usage?

I also tried using cpptraj but it also throws me the error of

*Molecule NLU1 is not defined in gromacs topology.*

NLU1 is the ligand

is the ligand.itp required or gro file required

thanks you

Ayesha Fatima
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Received on Sun May 02 2021 - 10:00:02 PDT
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