-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: 67
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.140355 angstroms between .R<G5 1>.A<H3' 27> and .R<G3 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<G5 1>.A<H3' 27> and .R<G3 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:              9.862 20.615 11.904
  Total bounding box for atom centers:  33.787 33.787 33.787
      (box expansion for 'iso' is  97.6%)
  Solvent unit box:                     18.774 18.774 18.774
  Volume: 49828.855 A^3 
  Total mass 20246.886 amu,  Density 0.675 g/cc
  Added 1089 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 (5.56, -0.13, 2.85).

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 (4.31, -3.83, -8.04).
(Replacing solvent molecule)
Placed Cl- in m at (2.97, -2.07, -14.79).
(Replacing solvent molecule)
Placed Na+ in m at (-2.60, 1.02, -15.23).
(Replacing solvent molecule)
Placed Cl- in m at (0.83, -2.67, -10.32).
(Replacing solvent molecule)
Placed Na+ in m at (3.94, 0.79, -12.80).
(Replacing solvent molecule)
Placed Cl- in m at (-0.02, 3.91, -15.66).
(Replacing solvent molecule)
Placed Na+ in m at (-0.12, -6.96, -10.61).
(Replacing solvent molecule)
Placed Cl- in m at (2.19, -8.91, -6.68).
(Replacing solvent molecule)
Placed Na+ in m at (0.08, -13.19, -5.38).
(Replacing solvent molecule)
Placed Cl- in m at (6.68, -1.87, -8.66).

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