Fix charge reading from PDBQTParser

MDAnalysis · Sep 6, 2023 · c316306 · c316306
1 parent c289b7f
commit c316306
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -24,6 +24,7 @@ Fixes
     their original type value (np.float64 and np.nan) (PR #4272)
   * Fixes a case where qcprot.CalcRMSDRotationalMatrix would return a
     RMSD of None
+  * Fix atom charge reading in PDBQT parser (PR #4283)
 
 Enhancements
   * Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64

diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py
@@ -87,7 +87,8 @@ class PDBQTReader(base.SingleFrameReaderBase):
     47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
     55 - 60        Real(6.2)     occupancy    Occupancy.
     61 - 66        Real(6.2)     tempFactor   Temperature  factor.
-    67 - 76        Real(10.4)    partialChrg  Gasteiger PEOE partial charge *q*.
+    67 - 70        LString(4)    footnote     Usually blank. IGNORED.
+    71 - 76        Real(6.4)     partialChrg  Gasteiger PEOE partial charge *q*.
     79 - 80        LString(2)    atomType     AutoDOCK atom type *t*.
     =============  ============  ===========  =============================================
 

diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py
@@ -97,7 +97,6 @@ class PDBQTParser(TopologyReaderBase):
      - charges
 
     Guesses the following:
-     - elements
      - masses
 
     .. versionchanged:: 0.18.0
@@ -140,7 +139,7 @@ def parse(self, **kwargs):
                 icodes.append(line[26:27].strip())
                 occupancies.append(float(line[54:60]))
                 tempfactors.append(float(line[60:66]))
-                charges.append(float(line[66:76]))
+                charges.append(float(line[70:76]))
                 atomtypes.append(line[77:80].strip())
 
         n_atoms = len(serials)