Re: [AMBER] Amber to gromacs topology

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Thu, 4 Oct 2018 15:20:09 +0000 (UTC)

For amber to gromacs topology which command should I use?

Thanks and Regards,
Saikat Pal



 

    On Thursday, 4 October, 2018, 8:47:18 PM IST, Matias Machado <mmachado.pasteur.edu.uy> wrote:
 
 well... you are then supposed to type some commands to perform whatever you want to do... ;-)

Best,

Matías

------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[http://pasteur.uy/en/laboratorios-eng/lsbm]
[http://www.sirahff.com]

----- Mensaje original -----
De: "Saikat Pal" <saikatpaliitg.yahoo.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 4 de Octubre 2018 11:34:34
Asunto: Re: [AMBER] Amber to gromacs topology

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 <mmachado.pasteur.edu.uy> wrote: 
 
 Dear Saikat,

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

Best,

Matias

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

------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[http://pasteur.uy/en/laboratorios-eng/lsbm]
[http://www.sirahff.com]

----- Mensaje original -----
De: "Saikat Pal" <saikatpaliitg.yahoo.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
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/__init__.py", 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/__init__.py", 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/__init__.py", 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/__init__.py", 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/__init__.py", 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/__init__.py", 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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Received on Thu Oct 04 2018 - 08:30:03 PDT
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