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PDBFixer fixes problems in PDB files
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How to eliminate hydrogen #243

Closed yhgon closed 2 years ago

yhgon commented 2 years ago

I add heterogen and water and output is expected as input.pdband 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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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