Lester Hedges

I have code to detect water molecules in a Sire system. However, what would we expect for crystal waters loaded from a PDB file. Do these always appears as two...

I'm afraid we haven't fully added this feature yet. We do support situations where there are existing water molecules in the system that are complete (not just a lone oxygen)...

I managed to solvate it just fine: ```python import BioSimSpace as BSS # Load the system. system = BSS.IO.readMolecules("pro.*") # Print the coordinates of the first water molecule. system[1].coordinates() [(-66.3700...

Just to note that all of the water molecules in the original protein system seem to have identical z-coordinates. (Each molecule has a different z-coord, but within a molecule they...

Ah, okay, that's good to know. In this case you can just swap the order of `pro` and `pert` when creating the complex, i.e.: ```python sys = pert + pro...

Actually, it's still giving the non-continuous error. Will try to figure it out when I get a moment.

It looks like the molecule ordering isn't preserved when creating the `sys` object, which is something that we _should_ have fixed lately. Will try to debug.

If you do the following then you can create a complex with the ligand first, then protein, then waters: ```python # You don't need to do the toSystem bit, since...

No problem. I've just pushed a couple of commits that fix these issues. Molecule ordering is now preserved when adding two `System` objects and existing water molecules are moved to...

Hi @jmichel80. Having not run these simulations before I'm not sure what is involved in the setup. Do you have any good references for setting up and running absolute free...