Conversion gromacstoamber -ParmEd

[Viswanath Vittaladevaram]

Hi,

I am finding this error when I'm trying to prepare amber files using gromacs files.

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

I need help on this!

Thanks,

[Mario Sergio Valdes]

Make sure that the itp file for the ea10 molecule is in the same directory as the topology file.

Consider using the latest version of ambertools and parmed.
Please note that this group is for problems related to gmx_MMPBSA. For problems with ambertools and parmed, consider reporting them to the appropriate channel.

[Viswanath Vittaladevaram]

Hi,

thanks for replying. I was able to sort out the problem. The problem identified was inside itp file the gold atoms were striped out earlier and when I ran it by keeping gold atoms.It worked.

Thanks.

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