Histidines created with Hs at HD1 and HE1

[tdudgeon]

When adding hydrogens I'm finding that histidines are not be handled correctly.

pdbfixer protein.pdb --add-atoms=all --ph=7

Before:

ATOM    303  N   HIS A  41      14.444  -7.662  22.209  1.00 14.91           N  
ATOM    304  CA  HIS A  41      13.763  -7.017  23.355  1.00 16.16           C  
ATOM    305  C   HIS A  41      12.537  -7.853  23.762  1.00 16.81           C  
ATOM    306  O   HIS A  41      11.970  -7.560  24.818  1.00 16.49           O  
ATOM    307  CB  HIS A  41      13.531  -5.540  23.082  1.00 16.04           C  
ATOM    308  CG  HIS A  41      12.405  -5.273  22.162  1.00 16.15           C  
ATOM    309  CD2 HIS A  41      11.094  -5.553  22.274  1.00 17.21           C  
ATOM    310  ND1 HIS A  41      12.569  -4.556  20.983  1.00 19.09           N  
ATOM    311  CE1 HIS A  41      11.384  -4.393  20.422  1.00 14.71           C  
ATOM    312  NE2 HIS A  41      10.479  -5.050  21.149  1.00 19.19           N  

After:

ATOM    605  N   HIS A  41      14.444  -7.662  22.209  1.00  0.00           N  
ATOM    606  H   HIS A  41      14.806  -6.791  21.491  1.00  0.00           H  
ATOM    607  CA  HIS A  41      13.763  -7.017  23.355  1.00  0.00           C  
ATOM    608  HA  HIS A  41      14.435  -7.019  24.335  1.00  0.00           H  
ATOM    609  C   HIS A  41      12.537  -7.853  23.762  1.00  0.00           C  
ATOM    610  O   HIS A  41      11.970  -7.560  24.818  1.00  0.00           O  
ATOM    611  CB  HIS A  41      13.531  -5.540  23.082  1.00  0.00           C  
ATOM    612  HB2 HIS A  41      12.992  -5.092  24.050  1.00  0.00           H  
ATOM    613  HB3 HIS A  41      14.443  -4.817  22.822  1.00  0.00           H  
ATOM    614  CG  HIS A  41      12.405  -5.273  22.162  1.00  0.00           C  
ATOM    615  CD2 HIS A  41      11.094  -5.553  22.274  1.00  0.00           C  
ATOM    616  HD2 HIS A  41      10.264  -5.440  23.117  1.00  0.00           H  
ATOM    617  ND1 HIS A  41      12.569  -4.556  20.983  1.00  0.00           N  
ATOM    618  HD1 HIS A  41      13.396  -3.749  20.719  1.00  0.00           H  
ATOM    619  CE1 HIS A  41      11.384  -4.393  20.422  1.00  0.00           C  
ATOM    620  HE1 HIS A  41      10.868  -3.330  20.637  1.00  0.00           H  
ATOM    621  NE2 HIS A  41      10.479  -5.050  21.149  1.00  0.00           N

Note how HD2 and HE1 are present. This would correspond to the charged form (HIP - see http://ambermd.org/Questions/HIS.html) that would not be expected at pH 7.

[peastman]

HD2 and HE1 are always present, regardless of the form. HD1 and HE2 are the variable ones. The above file has HD1 but not HE2, corresponding to the HID form.

[tdudgeon]

Sorry, got mixed up on this. I'm sure I was seeing H on both Ns, but that is not the case.