This PDB is not properly neutralized

[leeping]

I think the charge on this protein is -15, but PDBFixer only adds 9 positive ions.

https://www.dropbox.com/s/r6sv73mglmu966f/3chy_native.pdb

I replaced the nonstandard amino acid with CYS, deleted all heterogens and used a pH of 7.0 . I chose ionic strengths of zero and 50 mM, and in both cases it added a total of +9 charge.

[leeping]

I think it has something to do with the initial molecular geometry. After I minimized the (incorrectly charged) protein and ran it through PDBFixer again, it correctly added 15 positive ions.

[jchodera]

We should still add a check where an Exception is raised if the system was requested to be net neutral and doesn't end up that way....