-I: Adding /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/prep to search path.
-I: Adding /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib to search path.
-I: Adding /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm to search path.
-I: Adding /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source buildit-full.in.

Welcome to LEaP!
Sourcing: ./buildit-full.in
----- Source: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/cmd/leaprc.ff12SB
----- Source of /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib
Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib
Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/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: 60
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.140355 angstroms between .R<U5 1>.A<H3' 23> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 2
Unit is OK.
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.140355 angstroms between .R<U5 1>.A<H3' 23> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 2
Unit is OK.
  Solute vdw bounding box:              11.879 17.721 9.286
  Total bounding box for atom centers:  33.781 33.781 33.781
      (box expansion for 'iso' is  61.1%)
  Solvent unit box:                     18.774 18.774 18.774
  Volume: 49828.855 A^3 
  Total mass 20131.776 amu,  Density 0.671 g/cc
  Added 1087 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 (-5.00, -0.72, 3.86).

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 (5.56, 2.09, 8.69).
(Replacing solvent molecule)
Placed Cl- in m at (4.33, 10.91, 10.54).
(Replacing solvent molecule)
Placed Na+ in m at (6.87, 13.54, 9.97).
(Replacing solvent molecule)
Placed Cl- in m at (8.40, 1.26, 8.29).
(Replacing solvent molecule)
Placed Na+ in m at (13.03, 0.62, 8.27).
(Replacing solvent molecule)
Placed Cl- in m at (14.57, 3.57, 6.83).
(Replacing solvent molecule)
Placed Na+ in m at (12.59, 7.22, 5.02).
(Replacing solvent molecule)
Placed Cl- in m at (10.79, 9.32, 5.03).
(Replacing solvent molecule)
Placed Na+ in m at (0.70, 8.47, 10.21).
(Replacing solvent molecule)
Placed Cl- in m at (2.56, 6.37, 10.61).

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 12 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