mattwthompson
commented
3 years ago What version of everything are you using? conda list or pip freeze
Closed samuele-giannini closed 2 years ago
mattwthompson
commented
3 years ago What version of everything are you using? conda list or pip freeze
samuele-giannini
commented
3 years ago Hi, thanks for the answer. I was trying to install InterMol within a conda environment (with python 3.6), because I managed to install ParmEd in that way. However for the installation of InterMol I followed your guidelines: pip install .
In the following you can see the list you requested:
#
_anaconda_depends 2019.03 py36_0
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
anaconda custom py36_1
anaconda-client 1.7.2 py_0 conda-forge
anaconda-project 0.8.3 py_0 conda-forge
asn1crypto 1.3.0 py36_0 conda-forge
astroid 2.3.3 py36_1 conda-forge
astropy 4.0 py36h516909a_1 conda-forge
atomicwrites 1.3.0 py_0 conda-forge
attrs 19.3.0 py_0 conda-forge
babel 2.8.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
backports 1.0 py_2 conda-forge
backports.os 0.1.1 py36_1001 conda-forge
backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge
beautifulsoup4 4.8.2 py36_0 conda-forge
biopython 1.78
AxillaryPower
commented
2 years ago I came here to ask about the same issue; it appears that newer versions of ParmEd no longer have parmed.utils.six in its utils folder, where evidently it used to. InterMol (or at least convert.py) may need to be updated to be compatible with more recent ParmEd.
I was able to eliminate the error by editing convert.py; the only thing it was using parmed.utils.six for was to
from parmed.utils.six import string_types
and string_types is,
if PY3:
string_types = str,
...
else:
string_types = basestring,so in the one place where convert.py, you can change that line
mattwthompson
commented
2 years ago I have a fix running in #380 but if you're using a local build, you should be able to modify line 10 in intermol/convert.py to just be from six import string_types to get it running again. That module in ParmEd is copy-pasted from another one that's probably installed in every Python environment these days.
mattwthompson
commented
2 years ago To any future travelers sent here by the Google machine: this should be fixed in the master branch via the linked PR. That change will also go into a release and conda package at some point.
Hi All, sorry to disturb. I have a problem running InterMol: python convert.py --des_in validation/inputs/Desmond/UnitTest/frag_opls2001/frag_opls2001.cms --gromacs --odir test_output -e Traceback (most recent call last): File "convert.py", line 10, in
from parmed.utils.six import string_types
ModuleNotFoundError: No module named 'parmed.utils.six'
I did a bit of googling but cannot find a way to install parmed.utils.six. Any help would be appreciated. Sam