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 - 12:00:04 PDT
