> test2 = loadpdb POR-2a2b.pdb
Loading PDB file: ./POR-2a2b.pdb
  Added missing heavy atom: .R<CSER 620>.A<OXT 12>
  Added missing heavy atom: .R<FAD 621>.A<C4A 8>
  Added missing heavy atom: .R<FAD 621>.A<C5A 10>
  total atoms in file: 5062
  Leap added 4820 missing atoms according to residue templates:
       3 Heavy
       4817 H / lone pairs
> saveAmberParm test2 test2.prmtop test2.inpcrd
Checking Unit.
WARNING: There is a bond of 16.116888 angstroms between: 
-------  .R<FAD 621>.A<N3A 52> and .R<FAD 621>.A<C4A 53>
WARNING: There is a bond of 16.770245 angstroms between: 
-------  .R<FAD 621>.A<C5A 47> and .R<FAD 621>.A<C6A 48>
WARNING: There is a bond of 14.378186 angstroms between: 
-------  .R<FAD 621>.A<N7A 46> and .R<FAD 621>.A<C5A 47>
WARNING: There is a bond of 13.779173 angstroms between: 
-------  .R<FAD 621>.A<C4A 8> and .R<FAD 621>.A<N9A 44>
WARNING: The unperturbed charge of the unit: -19.000000 is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 9774 9775 duplicates bond ('triangular' bond) or angle ('square' bond)

1-4: angle 9773 9775 duplicates bond ('triangular' bond) or angle ('square' bond)

1-4: angle 9773 9774 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
old PREP-specified impropers:
 <FAD 621>:  C4A  N3   C4   O4  
 <FAD 621>:  N3   N1   C2   O2  
 <FAD 621>:  C4A  N10  C10  N1  
 <FAD 621>:  C4   C10  C4A  N5  
 <FAD 621>:  C6   C9A  C5A  N5  
 <FAD 621>:  C7M  C6   C7   C8  
 <FAD 621>:  C8M  C9   C8   C7  
 <FAD 621>:  C9   C5A  C9A  N10 
 <FAD 621>:  C1*  C9A  N10  C10 
 <FAD 621>:  C1*  C3*  C2*  O2* 
 <FAD 621>:  C2*  C4*  C3*  O3* 
 <FAD 621>:  C5*  C3*  C4*  O4* 
 <FAD 621>:  C5A* C3A* C4A* O4A*
 <FAD 621>:  C2A* C4A* C3A* O3A*
 <FAD 621>:  C3A* C1A* C2A* O2A*
 <FAD 621>:  C2A* N9A  C1A* O4A*
 <FAD 621>:  C8A  C1A* N9A  C4A 
 <FAD 621>:  C6A  C4A  C5A  N7A 
 <FAD 621>:  N6A  C5A  C6A  N1A 
 <FAD 621>:  C5A  N3A  C4A  N9A 
 <FMN 622>:  C4A  N3   C4   O4  
 <FMN 622>:  N3   N1   C2   O2  
 <FMN 622>:  C4A  N10  C10  N1  
 <FMN 622>:  C4   C10  C4A  N5  
 <FMN 622>:  C6   C9A  C5A  N5  
 <FMN 622>:  C7M  C6   C7   C8  
 <FMN 622>:  C8M  C9   C8   C7  
 <FMN 622>:  C9   C5A  C9A  N10 
 <FMN 622>:  C1*  C9A  N10  C10 
 <FMN 622>:  C1*  C3*  C2*  O2* 
 <FMN 622>:  C2*  C4*  C3*  O3* 
 <FMN 622>:  C5*  C3*  C4*  O4* 
 <NAP 623>:  C5A* C3A* C4A* O4A*
 <NAP 623>:  C4A* C2A* C3A* O3A*
 <NAP 623>:  C3A* C1A* C2A* O2A*
 <NAP 623>:  C2A* N9A  C1A* O4A*
 <NAP 623>:  C8A  C1A* N9A  C4A 
 <NAP 623>:  C6A  C4A  C5A  N7A 
 <NAP 623>:  N6A  C5A  C6A  N1A 
 <NAP 623>:  C5A  N3A  C4A  N9A 
 total 2063 improper torsions applied
 40 improper torsions in old prep form
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

        res     total affected

        CSER    1
        NGLN    1
  )
 (no restraints)
>