> pro = loadpdb pro.pdb
Loading PDB file: ./pro.pdb
-- residue 1: duplicate [ H2] atoms (total 2)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

  total atoms in file: 1121
  Leap added 1 missing atom according to residue templates:
       1 H / lone pairs
> check pro
Checking 'pro'....
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
Warning: Close contact of 0.042835 angstroms between .R<NMET 1>.A<H3 4> and .R<NMET 1>.A<H1 2>
Checking parameters for unit 'pro'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 2
Unit is OK.

> addions pro Na+ 0
2 Na+ ions required to neutralize.
Adding 2 counter ions to "pro" using 1A grid
Grid extends from solute vdw + 1.87  to  7.87
Resolution:      1.00 Angstrom.
grid build: 0 sec
 (no solvent present)
Calculating grid charges
charges: 0 sec
Placed Na+ in pro at (31.27, 47.54, 35.66).
Placed Na+ in pro at (41.27, 28.54, 38.66).

Done adding ions.

> solvateoct pro TIP3PBOX 9.0
Scaling up box by a factor of 1.342123 to meet diagonal cut criterion
  Solute vdw bounding box:              56.801 35.963 30.635
  Total bounding box for atom centers:  80.960 80.960 80.960
      (box expansion for 'iso' is  99.0%)
  Solvent unit box:                     18.774 18.774 18.774
  Volume: 275277.004 A^3 (oct)
  Total mass 146099.508 amu,  Density 0.881 g/cc
  Added 7657 residues.

> saveamberparm pro pro.top pro.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 227 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

        res     total affected

        CGLN    1
        NMET    1
        WAT     7657
  )
 (no restraints)