How to eliminate hydrogen

[yhgon]

I add heterogen and water and output is expected as input.pdb and output.pdb
however, when I delete heterogen with fixer.removeHeterogens(False) option as below del_het.pdb
it still have Hydrogen atom. how to eliminate it?

input PDB

ATOM      1  N   MET A   1      -0.522   1.364   0.000  1.00  0.00           N  
ATOM      2  CA  MET A   1       0.000   0.000   0.000  1.00  0.00           C  
ATOM      3  C   MET A   1       1.520   0.000   0.000  1.00  0.00           C  
ATOM      4  O   MET A   1       2.145  -0.050   1.058  1.00  0.00           O  
ATOM      5  CB  MET A   1      -0.507  -0.774  -1.206  1.00  0.00           C  
ATOM      6  CG  MET A   1      -2.013  -0.981  -1.209  1.00  0.00           C  
ATOM      7  SD  MET A   1      -2.587  -1.914  -2.650  1.00  0.00           S  
ATOM      8  CE  MET A   1      -1.935  -3.537  -2.272  1.00  0.00           C  

output.pdb

REMARK   1 CREATED WITH OPENMM 7.7, 2022-02-14
ATOM      1  N   MET A   1      -0.522   1.364   0.000  1.00  0.00           N  
ATOM      2  H   MET A   1       0.266   2.221  -0.271  1.00  0.00           H  
ATOM      3  H2  MET A   1      -1.263   1.765  -0.863  1.00  0.00           H  
ATOM      4  H3  MET A   1      -1.329   1.485   0.881  1.00  0.00           H  
ATOM      5  CA  MET A   1       0.000   0.000   0.000  1.00  0.00           C  
ATOM      6  HA  MET A   1      -0.206  -0.581   1.024  1.00  0.00           H  
ATOM      7  C   MET A   1       1.520   0.000   0.000  1.00  0.00           C  
ATOM      8  O   MET A   1       2.145  -0.050   1.058  1.00  0.00           O  
ATOM      9  CB  MET A   1      -0.507  -0.774  -1.206  1.00  0.00           C  
ATOM     10  HB2 MET A   1      -0.582  -0.598  -2.388  1.00  0.00           H  
ATOM     11  HB3 MET A   1       0.076  -1.805  -1.068  1.00  0.00           H  
ATOM     12  CG  MET A   1      -2.013  -0.981  -1.209  1.00  0.00           C  
ATOM     13  HG2 MET A   1      -2.397  -1.366  -0.145  1.00  0.00           H  
ATOM     14  HG3 MET A   1      -3.032  -0.447  -1.541  1.00  0.00           H  
ATOM     15  SD  MET A   1      -2.587  -1.914  -2.650  1.00  0.00           S  
ATOM     16  CE  MET A   1      -1.935  -3.537  -2.272  1.00  0.00           C  
ATOM     17  HE1 MET A   1      -0.990  -3.536  -1.554  1.00  0.00           H  
ATOM     18  HE2 MET A   1      -2.900  -4.001  -1.744  1.00  0.00           H  
ATOM     19  HE3 MET A   1      -1.848  -3.810  -3.429  1.00  0.00           H  

del_het.pdb

REMARK   1 CREATED WITH OPENMM 7.7, 2022-02-14
ATOM      1  N   MET A   1      -0.522   1.364   0.000  1.00  0.00           N  
ATOM      2  H   MET A   1       0.266   2.221  -0.271  1.00  0.00           H  
ATOM      3  H2  MET A   1      -1.263   1.765  -0.863  1.00  0.00           H  
ATOM      4  H3  MET A   1      -1.329   1.485   0.881  1.00  0.00           H  
ATOM      5  CA  MET A   1       0.000   0.000   0.000  1.00  0.00           C  
ATOM      6  HA  MET A   1      -0.206  -0.581   1.024  1.00  0.00           H  
ATOM      7  C   MET A   1       1.520   0.000   0.000  1.00  0.00           C  
ATOM      8  O   MET A   1       2.145  -0.050   1.058  1.00  0.00           O  
ATOM      9  CB  MET A   1      -0.507  -0.774  -1.206  1.00  0.00           C  
ATOM     10  HB2 MET A   1      -0.582  -0.598  -2.388  1.00  0.00           H  
ATOM     11  HB3 MET A   1       0.076  -1.805  -1.068  1.00  0.00           H  
ATOM     12  CG  MET A   1      -2.013  -0.981  -1.209  1.00  0.00           C  
ATOM     13  HG2 MET A   1      -2.397  -1.366  -0.145  1.00  0.00           H  
ATOM     14  HG3 MET A   1      -3.032  -0.447  -1.541  1.00  0.00           H  
ATOM     15  SD  MET A   1      -2.587  -1.914  -2.650  1.00  0.00           S  
ATOM     16  CE  MET A   1      -1.935  -3.537  -2.272  1.00  0.00           C  
ATOM     17  HE1 MET A   1      -0.990  -3.536  -1.554  1.00  0.00           H  
ATOM     18  HE2 MET A   1      -2.900  -4.001  -1.744  1.00  0.00           H  
ATOM     19  HE3 MET A   1      -1.848  -3.810  -3.429  1.00  0.00           H  

[peastman]

Heterogens and hydrogens are totally different things. Heterogens are residues other than standard amino acids and nucleotides. If you don't want to add hydrogens, don't call addMissingHydrogens().

[yhgon]

These Hydrogens came from Add Hydrogen, Add Solvent process to prepare OpenMM simulation. I want to delete hydrogens after OpenMM simulation compare Rg with original PDB. So I make these simple step to reproduce my situation.

I want to know any option to eliminate these hydrogens in protein residues without any external tools.

[peastman]

You can use Modeller.delete() to do that. See http://docs.openmm.org/latest/userguide/application/03_model_building_editing.html and http://docs.openmm.org/latest/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.delete. Something like this:

hydrogens = [a for a in topology.atoms() if a.element == element.hydrogen]
modeller.delete(hydrogens)

[yhgon]

thanks what I want. I hope PDFFixer would add this feature in additional function.