It is probably unrelated, but I also had problems with running Modeller
from Anaconda on Windows. Apparently the complicated Modeller directory
structure used in the standalone Windows version is not relevant under
Anaconda.
...
File "C:\Users\genie\.conda\envs\modeller\lib\os.py", line 1109, in
add_dll_directory
cookie = nt._add_dll_directory(path)
FileNotFoundError: [WinError 3] The system cannot find the path
specified:
I'm guessing you are using Python 3.8? You're absolutely right - the
standalone installer includes some logic to make it work with multiple
Python versions, which isn't necessary with Anaconda since the Anaconda
environment handles that already. It's a harmless addition for Python up
to 3.7 as it just adds a (non-existent) directory to the search path,
but Python 3.8 changed the way the path was handled, and (as you saw)
reports an error if a path element doesn't exist.
The simple fix here is to edit Modeller's top-level __init__.py (on your
system in
C:/Users/genie/.conda/envs/modeller/Library/modeller/modlib/modeller)
and remove this logic, lines 30 through 94 (or just the call to
add_dll_directory() on lines 72 & 73).