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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 02 2021 - 10:00:02 PDT
