-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/prep to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source buildit-full.in.

Welcome to LEaP!
Sourcing: ./buildit-full.in
----- Source: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/cmd/leaprc.ff12SB
----- Source of /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading PDB file: ./init.pdb
  total atoms in file: 66
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 1
Unit is OK.
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 1
Unit is OK.
  Solute vdw bounding box:              13.722 11.507 9.543
  Total bounding box for atom centers:  33.722 33.722 33.722
      (box expansion for 'iso' is  22.2%)
  Solvent unit box:                     18.774 18.774 18.774
  Volume: 49828.855 A^3 
  Total mass 20176.838 amu,  Density 0.672 g/cc
  Added 1086 residues.
1 Na+ ion required to neutralize.
Adding 1 counter ions to "m" using 1A grid
Grid extends from solute vdw + 1.37  to  7.47
Resolution:      1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-5.88, 0.62, -6.20).

Done adding ions.
Na+ has a charge of 0.
Adding the ions anyway.
Adding 10 counter ions to "m" using 1A grid
Grid extends from solute vdw + 5.59  to  11.69
Resolution:      1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-9.89, -0.54, 6.13).
(Replacing solvent molecule)
Placed Cl- in m at (-11.52, -3.12, 2.77).
(Replacing solvent molecule)
Placed Na+ in m at (-11.87, -7.94, 3.24).
(Replacing solvent molecule)
Placed Cl- in m at (-7.98, -9.45, 5.03).
(Replacing solvent molecule)
Placed Na+ in m at (-7.00, -10.33, 11.14).
(Replacing solvent molecule)
Placed Cl- in m at (-1.72, -11.28, 12.29).
(Replacing solvent molecule)
Placed Na+ in m at (-10.78, -5.96, 0.74).
(Replacing solvent molecule)
Placed Cl- in m at (-10.98, -10.67, -1.69).
(Replacing solvent molecule)
Placed Na+ in m at (-1.90, -11.36, 8.77).
(Replacing solvent molecule)
Placed Cl- in m at (-3.95, -7.89, 5.53).

Done adding ions.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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

	WAT	1075
  )
 (no restraints)
	Quit