Update imports for latest openmm version

[shudipto-amin]

The problem

Using newer version of openmm installed according to this page, running python ffaffurr.py results in the following error:

Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
File "ffaffurr.py", line 15, in <module>
from simtk.openmm.app.internal import *
ModuleNotFoundError: No module named 'simtk.openmm.app.internal' 

It appears that the import error is due to using deprecated code.

Suggested solution

• On local machine, install openmm using conda, as per official OpenMM instructions.
• Create a new branch for modifying the scripts.
• Modify ffaffurr.py to import scripts correctly, using OpenMM suggestion as a guide.
• Test script using new installation.
• Make a pull request to merge code.

[XiaojuanHu]

Which version of openmm are you using? I'm using 7.4.2 and didn't see this error came out.

[shudipto-amin]

Which version of openmm are you using? I'm using 7.4.2 and didn't see this error came out.

The version I get when I install it is 7.7. It is possible that when you update an older version, it only updates to the latest backward compatible version.

[shudipto-amin]

It is possible to avoid the problem by installing an older version of openmm (< 7.5), but it takes a few extra steps:

conda --prepend channels omnia
conda install -c omnia openmm=7.4.2

But openmm has moved away from using omnia channel, and they have replaced all documentation for older versions with newer ones. A user not familiar with the older version (or even users who are) will be lost. Also, as omnia version gets older, it will become more and more depracated probably.

I also ran into some issues with numpy installation after doing it this way - so we would have to provide instructions on installing all packages in the right order. I would very much prefer to use the newer version.