gromacs to amber files conversion : Parmed exception.Gromacs error: No template defined

[Viswanath Vittaladevaram]

Hi everyone.

I'm trying to prepare amber files from files generated using gromacs. When I tried to run gromacs to amber script I see the following error message. I checked itp and gro files, it looks alright! What could be the problem here?

traceback (most recent call last):
  File "<stdin>", line 2, in <module>
  File "/ichec/packages/amber/18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/formats/registry.py", line 214, in load_file
    return cls(filename, *args, **kwargs)
  File "/ichec/packages/amber/18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/ichec/packages/amber/18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/gromacs/gromacstop.py", line 444, in read
    'template defined' % molname)
parmed.exceptions.GromacsError: Structure contains ea10 molecules, but no template defined

[Richard Gowers]

Hi Viswanath

Welcome to the mailing list. Your script looks like it isn’t using MDAnalysis and is mostly using parmed, so you might get better answers asking on their support channels.

That said, it also looks like you’re using Python 2.7 and likely a very old version of Parmed, so updating might fix the problem.

Sorry I couldn’t help more

Richard

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[Viswanath Vittaladevaram]

Hi,

I am finding this error mentioned below

Using 1 MPI thread
Using 12 OpenMP threads


WARNING: This run will generate roughly 3729 Mb of data

starting mdrun 'CG MA10 self-assembled monolayer in water'
250000000 steps, 5000000.0 ps.
step 0Segmentation fault (core dumped)

Need inputs on this!

Thanks,