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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Investigate broken tests #277

Closed sobolevnrm closed 2 years ago

sobolevnrm commented 2 years ago

In testing the long list of molecules mentioned in #36, three entries failed:

These structures should be tested more thoroughly to understand why PDB2PQR is failing.

sobolevnrm commented 2 years ago

It looks like 1EJG does have a gap in the backbone:

REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     PRO A  22    N

Ideally, PDB2PQR would be able to fix a 1-atom gap but it cannot right now so I think this is a legitimate structure to skip in tests.

sobolevnrm commented 2 years ago

4MGP also has a gap in the backbone:

REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     LYS A  11    CE   NZ                                             
REMARK 470     LYS A  14    CG   CD   CE   NZ                                   
REMARK 470     SER A  23    CA   C    O    CB   OG

The gap at SER 23 is definitely beyond PDB2PQR's current capabilities to fix.

sobolevnrm commented 2 years ago

2V75 also has a gap in the backbone:

REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     ASN A  95    CA   C    O    CB   CG   OD1  ND2

The gap at ASN 95 is also too big for PDB2PQR to currently fix.