Re: [AMBER] Amber to gromacs topology

From: Saikat Pal <>
Date: Thu, 4 Oct 2018 14:34:34 +0000 (UTC)

Thank you, sir, for your reply. I have followed your command now I stuck in   :
Reading input from STDIN...

Thanks and Regards,
Saikat Pal


    On Thursday, 4 October, 2018, 7:50:13 PM IST, Matias Machado <> wrote:
 Dear Saikat,

Have you source the file $AMBERHOME/ or $AMBERHOME/amber.csh before executing parmed?



PD: I think this is the top recurrent issue in the mailing list...

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Saikat Pal" <>
Para: "AMBER Mailing List" <>
Enviados: Jueves, 4 de Octubre 2018 8:37:46
Asunto: [AMBER] Amber to gromacs topology

I want to convert amber topology to gromacs topology. So I have tried using parmed but it fails. Here is the command i have used:/home/saikat/softwares/AMBER/amber18/bin/parmed -p 148d-wat-0-reduce-oct.prmtop -c 148d-wat-0-reduce-oct.inpcrd
Error shows:
Traceback (most recent call last):
  File "/home/saikat/softwares/AMBER/amber18/bin/parmed", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 2985, in <module>
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 2971, in _call_aside
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 2998, in _initialize_master_working_set
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 662, in _build_master
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 675, in _build_from_requirements
  File "/home/saikat/softwares/AMBER/amber18/miniconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/", line 854, in resolve
pkg_resources.DistributionNotFound: The 'ParmEd==3.0.0+57.g74a84d30' distribution was not found and is required by the application

Thanks and Regards,
Saikat Pal

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