Following output am getting when I ran
amber.python -c "from parmed.scripts import clapp; print(clapp)"
----------[sunitap.ycn2 amber18]$ amber.python -c "from parmed.scripts
import clapp; print(clapp)"
Traceback (most recent call last):
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
line 25, in <module>
from simtk.unit import *
ModuleNotFoundError: No module named 'simtk'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/__init__.py",
line 22, in <module>
from parmed import unit, utils
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
line 27, in <module>
from parmed.unit.unit import Unit, is_unit
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/unit.py",
line 35, in <module>
from parmed.utils.six import iterkeys
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/__init__.py",
line 3, in <module>
from parmed.utils.pairlist import find_atom_pairs
File
"/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/pairlist.py",
line 5, in <module>
import numpy as np
ModuleNotFoundError: No module named 'numpy'
-----------------
On Wed, Aug 21, 2019 at 11:42 AM Hai Nguyen <nhai.qn.gmail.com> wrote:
> In this case, I don't think install another MIniconda will help.
>
> The error message comes from the code in AmberTools/test/test_check.sh
>
> try:
>
> from parmed.scripts import clapp
>
> except ImportError:
>
> if os.path.exists(os.path.join(ambhome, 'bin/parmed')):
>
> sys.stderr.write('\\nError: Could not import Amber Python modules!
> \\n'
>
> ' Probably your Amber Python environment was not set up
> correctly.\\n\\n')
>
> error()
>
>
>
> What's the output of the below command
> amber.python -c "from parmed.scripts import clapp; print(clapp)"
>
> Hai
>
> On Wed, Aug 21, 2019 at 1:45 AM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
>
> > I am manually downloading Miniconda and installing it.
> > Let me see if it can solve my problem.
> >
> > On Wed, Aug 21, 2019 at 10:56 AM Sunita Patel <sunita.patel.cbs.ac.in>
> > wrote:
> >
> > > Dear David,
> > >
> > > When I tried intalling Miniconda Python package. But, am getting
> > following
> > > problem. I need your help to solve Amber 18 installation issue.
> > >
> > > ./configure_python
> > >
> > > This script will download and install a version of Python compatible
> > >
> > > with every component of AmberTools and install all required and
> optional
> > >
> > > prerequisites. The Python distribution is downloaded for your operating
> > >
> > > system from Miniconda.
> > >
> > >
> > > Downloading Python 2.7 Miniconda
> > >
> > > Detected Linux kernel. Downloading the Linux installer
> > >
> > > Downloading the latest Miniconda distribution
> > >
> > > Detected 64-bit Linux
> > >
> > > --2019-08-20 11:44:34--
> > > https://repo.continuum.io/miniconda/Miniconda2-4.3.21-Linux-x86_64.sh
> > >
> > > Resolving repo.continuum.io... failed: Name or service not known.
> > >
> > > wget: unable to resolve host address `repo.continuum.io'
> > >
> > > On Tue, Aug 20, 2019 at 5:54 PM David A Case <david.case.rutgers.edu>
> > > wrote:
> > >
> > >> On Tue, Aug 20, 2019, Sunita Patel wrote:
> > >> >
> > >> >System was having older python 2.6 so installed Phython3.6 locally
> and
> > >> set
> > >> >path.
> > >>
> > >> We strongly recommend allowing the configure script to download a
> > >> Miniconda python package; that ensures that you have all the required
> > >> packages available. It is installed within your Amber tree, so it
> won't
> > >> interfere with any existing ("system") python you may have.
> > >>
> > >> ....dac
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 21 2019 - 01:30:02 PDT
