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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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PDB2PQR incorrectly reconstructing missing atoms in 4E8M #267

Closed sobolevnrm closed 2 years ago

sobolevnrm commented 2 years ago

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

Originally posted by @sobolevnrm in https://github.com/Electrostatics/pdb2pqr/issues/256#issuecomment-1003118601