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naming inconsistency with CHARMM #358
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Additionally, the C-terminal GLU is named The protonated version of HIS appears to be named correctly. |
PDB2PQR appears to be treating these changes like CHARMM patches (e.g., see openmm/openmmforcefields#22) rather than renaming full residues. This is done in various places in the code by an
However, I don't think this is the desired behavior; I can't think of a good reason for it. It is likely a bug that came from an over-literal interpretation of the CHARMM forcefield files during initial implementation. I'm going to change it to rename the full residue unless @orbeckst or @speleo3 can think of a reason I should keep it. Thanks! |
Actually, it looks like this code is never used. The Line 363 in 8db8d94
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The input parameter file must be incomplete. Some debugging information can be obtained by dumping the residue map immediately after this line: Line 197 in 8db8d94
The GLU-related items from this dump are:
Unfortunately, it looks like GLUP is missing some atoms. |
This will be easier to fix if we don't have to deal with XML-format data files; it might finally be time to replace those. |
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I am trying to get the pka for 1tiv.pdb and write the output using the CHARMM naming scheme. It appears that the residues names are inconsistently named. Namely, pdb2pqr 1tiv.pdb 1tiv.pqr --ffout=CHARMM --titration-state-method=propka --with-ph=3 produces a 1tiv.pqr file that name GLU as GLUP. Can you please help?
Thanks,
Nihit
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