My apologies. I've been in China for a few weeks, and I was too
lazy to figure out how to check my gmail messages while I was there.
I just got back a couple days ago and am slowly going through old
1) Firstly, thank you very much for reporting the bug. The issue
you reported is new (to me) and serious enough that I will fix it
soon. The problem appears to be specific to pypi, not anaconda. (I
am using python 3.6.5 with anaconda as well.)
I just uploaded a new version of moltemplate to pypi. (version
2.10.5) Can you try uninstalling moltemplate and then running "pip
install moltemplate" again? Does that solve your issue? (Please
reply only to me. No need to continue the debugging conversation on
the mailing list.)
3) In the mean time, you should be able to get around the problem
by downloading moltemplate from git using:
git clone https://github.com/jewettaij/moltemplate moltemplate
(or just click on the "releases" link, and download a .zip or .tar.gz file)
and installing it by going to the moltemplate directory and entering
pip install .
4) ... another pypi-specific bug:
(missing force fields when using "pip install moltemplate")
I have occasionally run into bugs when using "pip install moltemplate"
(ie using pypi to download moltemplate instead of github). If you
installed it that way, then ".lt" files that contain force fields, and
some random stuff like popular water molecules might not get copied to
the correct place. If you use any of these force fields or water
molecules in your simulations, moltemplate will complain that it can't
find the .lt file for that force field. (eg "oplsaa.lt").
If you run into this problem, there are 2 easy solutions:
a) Just download the file you need from:
...and then move it to the directory where you are running
moltemplate, and try running moltemplate.sh again.
b) Alternatively, try downloading moltemplate from git instead
(bypassing pypi), and install it by changing to the "moltemplate"
directory and entering:
pip install .
(instead of "pip install moltemplate")
This problem only occurred when python 3, not python 2.7, in
conjunction with pypi. And, again, this problem never occurred when
downloading moltemplate directly from git (or from the moltemplate.org
web page, regardless of whether you were using python 3 or 2.7). The
bug is probably in the "package_data" section of the "setup.py" file:
...because the .LT files in the "force_fields" directory are not being
copied to the correct location (when using "pip install moltemplate"
in python 3). I have been too lazy to figure out why this is going
on, but I'm open to suggestions.
Until then, I generally suggest people use git and avoid pypi. If
you think this issue is serious enough to remove moltemplate from
pypi, I will consider that.
Cheers and thanks again for reporting this bug.