This is an issue of psfgen that reconstructs the coordinates of Hs based on CHARMM topology file.
See the input pdb of ubiquitin (1D3Z_mod1.pdb.gz) and output pdb generated by pdbrx (1D3Z_mod1_charmm.pdb.gz).
The below shows H bound to N of the first 3 residues of input and output pdb files.
========================================================
In 1D3Z_mod1.pdb
ATOM 29 H GLN A 2 49.145 -89.006 8.595 1.00 0.00 H
ATOM 45 H ILE A 3 48.474 -87.484 4.379 1.00 0.00 H
ATOM 67 H PHE A 4 46.627 -83.490 3.877 1.00 0.00 H
========================================================
In 1D3Z_mod1_charmm.pdb
ATOM 21 HN GLN A 2 49.058 -88.992 8.574 0.00 0.00 A H
ATOM 38 HN ILE A 3 48.497 -87.437 4.318 0.00 0.00 A H
ATOM 57 HN PHE A 4 46.557 -83.439 3.873 0.00 0.00 A H
This is an issue of psfgen that reconstructs the coordinates of Hs based on CHARMM topology file. See the input pdb of ubiquitin (1D3Z_mod1.pdb.gz) and output pdb generated by pdbrx (1D3Z_mod1_charmm.pdb.gz).
The below shows H bound to N of the first 3 residues of input and output pdb files.
======================================================== In 1D3Z_mod1.pdb
ATOM 29 H GLN A 2 49.145 -89.006 8.595 1.00 0.00 H
ATOM 45 H ILE A 3 48.474 -87.484 4.379 1.00 0.00 H
ATOM 67 H PHE A 4 46.627 -83.490 3.877 1.00 0.00 H
======================================================== In 1D3Z_mod1_charmm.pdb ATOM 21 HN GLN A 2 49.058 -88.992 8.574 0.00 0.00 A H ATOM 38 HN ILE A 3 48.497 -87.437 4.318 0.00 0.00 A H ATOM 57 HN PHE A 4 46.557 -83.439 3.873 0.00 0.00 A H
========================================================
I could fix it by writing a simple psfgen script. Do we need to add some codes to modify psfgen part in pdbrx to treat this issue?