Merge pull request #2314 from dprada/dna_amber_names

Adding alternative names of terminal nucleic acids (5' and 3') and atoms H2', H2'', H5' and H5''.

wrappers/python/simtk/openmm/app/data/pdbNames.xml

@@ -25,12 +25,12 @@
   <Atom name="O4'" alt1="O4*"/>
   <Atom name="O5'" alt1="O5*"/>
   <Atom name="H1'" alt1="H1*"/>
-  <Atom name="H2'" alt1="H2*" alt2="1H2*" alt3="1H2'"/>
-  <Atom name="H2''" alt1="2H2*" alt2="2H2'"/>
+  <Atom name="H2'" alt1="H2*" alt2="1H2*" alt3="1H2'" alt4="H2'1"/>
+  <Atom name="H2''" alt1="2H2*" alt2="2H2'" alt3="H2'2"/>
   <Atom name="H3'" alt1="H3*"/>
   <Atom name="H4'" alt1="H4*"/>
-  <Atom name="H5'" alt1="1H5*" alt2="1H5'"/>
-  <Atom name="H5''" alt1="2H5*" atl2="2H5'"/>
+  <Atom name="H5'" alt1="1H5*" alt2="1H5'" alt3="H5'1"/>
+  <Atom name="H5''" alt1="2H5*" atl2="2H5'" alt3="H5'2"/>
   <Atom name="HO2'" alt1="2HO*"/>
   <Atom name="HO3'" alt1="H3T"/>
   <Atom name="HO5'" alt1="H5T"/>
@@ -252,19 +252,19 @@
   <Atom name="H42" alt1="2H4"/>
  </Residue>
  <Residue name="U" alt1="URA" type="Nucleic"/>
- <Residue name="DA" alt1="DAD" type="Nucleic">
+ <Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic">
   <Atom name="H61" alt1="1H6"/>
   <Atom name="H62" alt1="2H6"/>
  </Residue>
- <Residue name="DG" alt1="DGU" type="Nucleic">
+ <Residue name="DG" alt1="DGU" alt2="DG3" alt3="DG5" type="Nucleic">
   <Atom name="H21" alt1="1H2"/>
   <Atom name="H22" alt1="2H2"/>
  </Residue>
- <Residue name="DC" alt1="DCY" type="Nucleic">
+ <Residue name="DC" alt1="DCY" alt2="DC3" alt3="DC5" type="Nucleic">
   <Atom name="H41" alt1="1H4"/>
   <Atom name="H42" alt1="2H4"/>
  </Residue>
- <Residue name="DT" alt1="THY" type="Nucleic">
+ <Residue name="DT" alt1="THY" alt2="DT3" alt3="DT5" type="Nucleic">
   <Atom name="C7" alt1="C5M"/>
   <Atom name="H71" alt1="1H5M"/>
   <Atom name="H72" alt1="2H5M"/>