Re: [AMBER] Error with PDB4AMBER

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Tue, 19 Oct 2021 21:43:08 +0200

Amith,

while it may be that your installation is broken, did you actually
*source* the amber.sh file, which resides in the Amber installation
directory ($AMBERHOME)?
It not only sets the AMBERHOME and PATH variable, so that executables
and scripts are found, but also setups the python environment.

All the best,

Anselm



On 10/19/2021 08:51 PM, Rangarajan, Amith wrote:
> Hi,
>
> thanks for the suggestion. I tried to see if i had sourced it
> avranga1008.dev1 ~
> $ which pmemd
> /opt/amber20/bin/pmemd
>
> avranga1008.dev1 ~
> $ $AMBERHOME/
> -bash: /opt/amber20/: Is a directory
>
> avranga1008.dev1 ~
> $ $AMBERHOME/bin/pdb4amber
> Traceback (most recent call last):
> File "/opt/amber20/bin/pdb4amber", line 11, in <module>
> load_entry_point('pdb4amber==1.7.dev0', 'console_scripts', 'pdb4amber')()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 476, in load_entry_point
> return get_distribution(dist).load_entry_point(group, name)
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2700, in load_entry_point
> return ep.load()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2318, in load
> return self.resolve()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2324, in resolve
> module = __import__(self.module_name, fromlist=['__name__'], level=0)
> File "/opt/amber20/lib/python3.6/site-packages/pdb4amber-1.7.dev0-py3.6.egg/pdb4amber/__init__.py", line 1, in <module>
> from . import pdb4amber
> File "/opt/amber20/lib/python3.6/site-packages/pdb4amber-1.7.dev0-py3.6.egg/pdb4amber/pdb4amber.py", line 7, in <module>
> import parmed
> ModuleNotFoundError: No module named 'parmed'
> it seems some thing in the installation is wrong with pdb4amber.
>
> thanks,
> amith
> ________________________________
> From: Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
> Sent: Tuesday, October 19, 2021 11:33 AM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Re: [AMBER] Error with PDB4AMBER
>
> Hello Amith,
>
> Did you "source amber.sh" before calling pdb4amber?
>
> Best,
>
> Vinícius Wilian D. Cruzeiro, PhD
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: @vwcruzeiro
> ________________________________
> From: Rangarajan, Amith <Amith.Rangarajan.ucsf.edu>
> Sent: Tuesday, October 19, 2021 11:28 AM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: [AMBER] Error with PDB4AMBER
>
>
> hI,
>
> upon calling pdb4amber ( pdb4amber -h) , i am getting this error message .
> File "/opt/amber20/bin/pdb4amber", line 11, in <module>
> load_entry_point('pdb4amber==1.7.dev0', 'console_scripts', 'pdb4amber')()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 476, in load_entry_point
> return get_distribution(dist).load_entry_point(group, name)
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2700, in load_entry_point
> return ep.load()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2318, in load
> return self.resolve()
> File "/usr/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2324, in resolve
> module = __import__(self.module_name, fromlist=['__name__'], level=0)
> File "/opt/amber20/lib/python3.6/site-packages/pdb4amber-1.7.dev0-py3.6.egg/pdb4amber/__init__.py", line 1, in <module>
> from . import pdb4amber
> File "/opt/amber20/lib/python3.6/site-packages/pdb4amber-1.7.dev0-py3.6.egg/pdb4amber/pdb4amber.py", line 7, in <module>
> import parmed
> ModuleNotFoundError: No module named 'parmed'
> Not sure what is needed to fix this or if i am doing something wrong.
>
> please share your thoughts and suggestions.
>
> best,
> amith
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Received on Tue Oct 19 2021 - 13:00:02 PDT