Peter Eastman
Peter Eastman
If you've already created an XML file defining the force field then yes, of course. Did you have a more specific question?
That ought to be possible. There are a few changes required. We would need to add PDB files for them to the `templates` folder. It provides a structure for each...
Oops, sorry for not replying. > What would the standard three residue codes for these be? SEP and PTR? Here are the definitions of [SEP](http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=sep&operation=ccid) and [PTR](http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=ptr&operation=ccid). Look them over...
Sounds great! soft.xml was created based on Amber99SB-ILDN. Since I don't think it includes those residues, it's fine to regenerate it based on Amber14. The differences should be minor.
That's fine. It doesn't really create a dependency. That script is just run by us to generate the file that gets checked into the repository. Users don't need openmmforcefields installed.
It looks like the type of that field has changed since the script was written. It used to store a tuple `(class, mass, element)`. It now stores an `_AtomType` object:...
It's the same thing. It used to be a tuple whose first element was the class. Change `[0]` to `.atomClass`.
This was added in #296.
I can reproduce the problem. I'm investigating now.
Thanks for the extra information. I've made some progress toward debugging this, but it involves a lot of complicated interactions between different parts of the code. It's related to the...