Residue name conflict with Amber ions and RNA

[chapincavender]

Many of the ports of the Amber ion parameters use the residue name "U" for the uranium cation U4+, which conflicts with the residue uracil in RNA force fields. This leads to an error when these force fields are combined.

MWE:

>>> from openmm import app
>>> ff = app.ForceField("amber/RNA.OL3.xml", "amber/ions/ionslm_126_opc.xml")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openmm/app/forcefield.py", line 214, in __init__
    self.loadFile(files)
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openmm/app/forcefield.py", line 334, in loadFile
    self.registerResidueTemplate(template)
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openmm/app/forcefield.py", line 471, in registerResidueTemplate
    raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel))
ValueError: Residue template U with the same override level 0 already exists.

The following files are affected.

$ grep -l 'Residue name="U"' openmmforcefields/ffxml/amber/ions/*.xml
openmmforcefields/ffxml/amber/ions/ions234lm_126_spce.xml
openmmforcefields/ffxml/amber/ions/ions234lm_126_tip3p.xml
openmmforcefields/ffxml/amber/ions/ions234lm_126_tip4pew.xml
openmmforcefields/ffxml/amber/ions/ions234lm_hfe_spce.xml
openmmforcefields/ffxml/amber/ions/ions234lm_hfe_tip3p.xml
openmmforcefields/ffxml/amber/ions/ions234lm_hfe_tip4pew.xml
openmmforcefields/ffxml/amber/ions/ions234lm_iod_spce.xml
openmmforcefields/ffxml/amber/ions/ions234lm_iod_tip3p.xml
openmmforcefields/ffxml/amber/ions/ions234lm_iod_tip4pew.xml
openmmforcefields/ffxml/amber/ions/ionslm_126_fb3.xml
openmmforcefields/ffxml/amber/ions/ionslm_126_fb4.xml
openmmforcefields/ffxml/amber/ions/ionslm_126_opc3.xml
openmmforcefields/ffxml/amber/ions/ionslm_126_opc.xml
openmmforcefields/ffxml/amber/ions/ionslm_hfe_fb3.xml
openmmforcefields/ffxml/amber/ions/ionslm_hfe_fb4.xml
openmmforcefields/ffxml/amber/ions/ionslm_hfe_opc3.xml
openmmforcefields/ffxml/amber/ions/ionslm_hfe_opc.xml
openmmforcefields/ffxml/amber/ions/ionslm_iod_fb3.xml
openmmforcefields/ffxml/amber/ions/ionslm_iod_fb4.xml
openmmforcefields/ffxml/amber/ions/ionslm_iod_opc3.xml
openmmforcefields/ffxml/amber/ions/ionslm_iod_opc.xml

I suggest changing the residue name for all of these to "U4+" as in openmmforcefields/ffxml/amber/tip3p_standard.xml and in lib/atomic_ions.lib in AmberTools.

[epretti]

This should be fixed as of #368.