added OC1 and OC2 to default list of hydrogen bond acceptors

- added C-terminus  OC1 and OC2 (Amber FF) to default list of acceptors in HydrogenBondAnalysis
- closes #1342 
- updated docs
- updated CHANGELOG

package/CHANGELOG

@@ -44,6 +44,8 @@ Fixes
   * Fixed AnalysisBase class provides numerical start,stop,step values (PR #1340)
   * Fixed PSFParser not creating multiple residues for identical resids in
     different segments. (Issue #1347, PR #1348)
+  * Add the OC1 and OC2 from amber99sb-ildn to hydrogen bond acceptors (issue #1342)
+
 
 Changes
   * Enable various pylint warnings to increase python 3 compatibility

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -148,7 +148,8 @@
    =========== ==============  =========== ====================================
    group       donor           acceptor    comments
    =========== ==============  =========== ====================================
-   main chain  N               O
+   main chain  N               O, OC1, OC2 OC1, OC2 from amber99sb-ildn
+                                           (Gromacs)
    water       OH2, OW         OH2, OW     SPC, TIP3P, TIP4P (CHARMM27,Gromacs)
 
    ARG         NE, NH1, NH2
@@ -386,6 +387,8 @@ class HydrogenBondAnalysis(object):
         GLU OE1/OE2, HIS ND1/NE2, MET SD, SER OG, THR OG1, TYR OH
       *GLYCAM06*
         N,NT,O,O2,OH,OS,OW,OY,P,S,SM
+      *amber99sb-ildn(Gromacs)*
+        OC1, OC2 of the main chain
 
     See Also
     --------
@@ -415,7 +418,7 @@ class HydrogenBondAnalysis(object):
     #: use the keyword `acceptors` to add a list of additional acceptor names.
     DEFAULT_ACCEPTORS = {
         'CHARMM27': tuple(set([
-            'O', 'OH2', 'OW', 'OD1', 'OD2', 'SG', 'OE1', 'OE1', 'OE2', 'ND1', 'NE2', 'SD', 'OG', 'OG1', 'OH'])),
+            'O', 'OC1', 'OC2', 'OH2', 'OW', 'OD1', 'OD2', 'SG', 'OE1', 'OE1', 'OE2', 'ND1', 'NE2', 'SD', 'OG', 'OG1', 'OH'])),
         'GLYCAM06': tuple(set(['N', 'NT', 'O', 'O2', 'OH', 'OS', 'OW', 'OY', 'SM'])),
         'other': tuple(set([]))}
 

testsuite/MDAnalysisTests/analysis/test_hbonds.py

@@ -102,6 +102,20 @@ def test_atoms_too_far():
         h.run(verbose=False)
         assert_equal(h.timeseries, [[]])
 
+    @staticmethod
+    def test_acceptor_OC1_OC2():
+        gro = '''test
+3
+    1ALA    OC1    1   0.000   0.000   0.000
+    2ALA      N    2   0.300   0.000   0.000
+    2ALA     H1    3   0.200   0.000   0.000
+7.29748 7.66094 9.82962'''
+
+        u = MDAnalysis.Universe(StringIO(gro), format="gro")
+        h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u)
+        h.run(verbose=False)
+        assert_equal(h.timeseries[0][0][4], 'ALA2:H1')
+
     @staticmethod
     def test_true_traj():
         u = MDAnalysis.Universe(GRO, XTC)