Sourav,
I'm guessing your PYTHONPATH and/or AMBERHOME and/or something related to
the always wonderful python package management system
is at work here, unless you haven't installed parmed - which doesn't rule
out python issues, btw.
Can you report the output of the following from the command line?
(1) which parmed
(2) echo $AMBERHOME
those should give something like:
todd.finch:~$ which parmed
/usr/local/amber22/bin/parmed
todd.finch:~$ echo $AMBERHOME
/usr/local/amber22
(3) also try it from a python prompt on the command line, you should see
something like:
todd.finch:~$ python3
Python 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import parmed
>>> dir(parmed)
['AcceptorDonor', 'AmoebaNonbondedExceptionType', 'Angle', 'AngleType',
'Atom', 'AtomList', 'AtomType', 'Bond', 'BondType', 'ChiralFrame', 'Cmap',
'CmapType', 'Dihedral', 'DihedralType', 'DihedralTypeList',
'DrudeAnisotropy', 'DrudeAtom', 'ExtraPoint', 'Group', 'Hybridization',
'Improper', 'ImproperType', 'Link', 'MultipoleFrame', 'NoUreyBradley',
'NonbondedException', 'NonbondedExceptionType', 'OutOfPlaneBend',
'OutOfPlaneBendType', 'OutOfPlaneExtraPointFrame', 'ParameterSet',
'PiTorsion', 'QualitativeBondType', 'RBTorsionType', 'Residue',
'ResidueList', 'StretchBend', 'StretchBendType', 'Structure',
'StructureView', 'ThreeParticleExtraPointFrame', 'TorsionTorsion',
'TorsionTorsionType', 'TrackedList', 'TrigonalAngle',
'TwoParticleExtraPointFrame', 'UnassignedAtomType', 'UreyBradley', 'Vec3',
'__all__', '__author__', '__builtins__', '__cached__', '__doc__',
'__file__', '__loader__', '__name__', '__package__', '__path__',
'__spec__', '__version__', '_version', '_versionre', 'amber', 'charmm',
'constants', 'dlpoly', 'download_CIF', 'download_PDB', 'download_cif',
'download_pdb', 'entos', 'exceptions', 'formats', 'geometry', 'gromacs',
'load_file', 'load_rdkit', 'load_rosetta', 'modeller', 'namd', 'openmm',
'parameters', 'periodic_table', 'rdkit', 'read_CIF', 'read_PDB',
'read_cif', 'read_pdb', 'residue', 'rosetta', 'structure', 'symmetry',
'tinker', 'tools', 'topologyobjects', 'unit', 'utils', 'vec3', 'version']
>>>
Cheers,
Todd
On Mon, Jan 1, 2024 at 5:31 AM Sourav Bhowmik via AMBER <amber.ambermd.org>
wrote:
> Dear users,
> I am trying to convert amber prmtop and inpcrd to gromacs format using
> amb2gro_top_gro.py programme. The following error is encountered. Kindly
> help me.
>
> sic.sic:~/ala$ amb2gro_top_gro.py
> Traceback (most recent call last):
> File "/home/sic/Downloads/amber22/bin/amb2gro_top_gro.py", line 7, in
> <module>
> import parmed as pmd
> ModuleNotFoundError: No module named 'parmed'
> sic.sic:~/ala$
>
> Sourav
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 01 2024 - 09:00:02 PST
