PDB2PQR fails on files with only nucleic acid resides

[sobolevnrm]

On structures like 4E8M, PDB2PQR fails with messages like:

2021-11-25 15:51:05,865 CRITICAL:main.py:791:main_driver:No biomolecule heavy atoms found and no ligand present. Unable to proceed.  You may also see this message if PDB2PQR does not have parameters for any residue in your biomolecule.
2021-11-25 15:51:05,866 CRITICAL:main.py:792:main_driver:Giving up.

Reported by @mishaguy.

[sobolevnrm]

This problem appears to be specific to RNA-only PDB entries. For example, 1NAJ seems to work in the test created in af3caec.

The source of the issue is an inconsistency between NA.xml and PDB nomenclature for nucleic acids. The former uses RA, RC, RG, RU and the latter uses A, C, G, U.

[mishaguy]

the previous versions of pdb2pqr handled these structures without error. I still have it attached to my PyMol on Mac, I get it from Homebrew, and it works without error

[sobolevnrm]

The ANISOU records in 4E8M appear to be part of the problem. After fixing the problem with residue naming (PDB2PQR was expecting RA, etc. and the PDB file had A, etc.), the RNA structure 5V0O without ANISOU records works but 4E8M does not.

[sobolevnrm]

The ANISOU records in 4E8M appear to be part of the problem. After fixing the problem with residue naming (PDB2PQR was expecting RA, etc. and the PDB file had A, etc.), the RNA structure 5V0O without ANISOU records works but 4E8M does not.

Err... that's not correct: grepping the ANISOU records out of 4E8M still gives a file that generates errors in my "fixed" version of PDB2PQR.

[sobolevnrm]

It looks like the problems I'm seeing with 4E8M now are due to PDB2PQR incorrectly reconstructing missing atoms:

REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470       G A  -1    OP2  N9   C8   N7   C5   C6   O6                    
REMARK 470       G A  -1    N1   C2   N2   N3   C4                              
REMARK 470       G A   1    N9   C8   N7   C5   C6   O6   N1                    
REMARK 470       G A   1    C2   N2   N3   C4                                   
REMARK 470       A A 207    N9   C8   N7   C5   C6   N6   N1                    
REMARK 470       A A 207    C2   N3   C4                                        
REMARK 470       G A 311    N9   C8   N7   C5   C6   O6   N1                    
REMARK 470       G A 311    C2   N2   N3   C4                                   
REMARK 470       C A 312    N1   C2   O2   N3   C4   N4   C5                    
REMARK 470       C A 312    C6                                                  
REMARK 470       G A 391    N9   C8   N7   C5   C6   O6   N1                    
REMARK 470       G A 391    C2   N2   N3   C4

[sobolevnrm]

This appears to be a separate problem so I've created a new issue (#267) for it.