1. Execute xleap, and add counter ions.
$ xleap &
> unit = loadpdb protein.pdb
> charge unit
Total unperturbed charge: -1.00
Total perturbed charge: -1.00
> addions unit Na+ 0.0
1 Na+ ion required to neutralize.
Adding 1 counter ions to "a" using 1A grid
Total solute charge: -1.00 Max atom radius: 2.00
Grid extends from solute vdw + 1.87 to 7.87
Box:
Bla Bla ..
Calculating grid charges
charges: 33 sec
(No solvent overlap)
Placed Na+ in a at (30.81, -3.42, -12.87).
Done adding ions.
>
2. "Seclect the ion" by clicking it, and then solvate the protein.
> solvatebox unit WATBOX216 10.0
Solute vdw bounding box: 48.108 46.574 48.991
Total bounding box for atom centers: 68.108 66.574 68.991
Solvent unit box: 18.774 18.774 18.774
Bla Bla ..
Total vdw box size: 71.546 69.707 72.229 angstroms.
Volume: 360226.023 A^3
Total mass 172264.490 amu, Density 0.794 g/cc
Added 8427 residues.
>
3. Click "move", and move the ion away from the protein by dragging your mouse.
Drop it at the corner of the water box with no solvent overlap.
4. Save the input files, and terminate xleap.
> check unit
Warning ..
Warning ..
Bla Bla ..
Unit is OK.
> savepdb unit input.pdb
Writing pdb file: input.pdb
Shortening residue name for PDB format: NALA -> ALA
Shortening residue name for PDB format: CSER -> SER
> saveamberparm unit input.top input.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Bla Bla ..
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CSER 1
NALA 1
WAT 8596
)
(no restraints)
> quit