-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: ../../../../../scripts/leaprc.ff99bsc0
----- Source of ../../../../../scripts/leaprc.ff99bsc0 done
Log file: ./leap.log
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.parmbsc0
Reading force field modification type file (frcmod)
Reading title:
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_nucleic94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_amino94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminoct94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminont94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/DNA_CI.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/ions94.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/RNA_CI.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 parameters: ../../../../../scripts/frcmod.ff99Chen-Garcia
Reading force field modification type file (frcmod)
Reading title:
glycosdic bond torsion modifications to parm99 from Chen and Garcia (PNAS, 2013, 110, 16820)
Loading PDB file: ./init.pdb
  total atoms in file: 67
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:              13.656 11.773 9.587
  Total bounding box for atom centers:  33.726 33.726 33.726
      (box expansion for 'iso' is  20.4%)
  Solvent unit box:                     18.774 18.774 18.774
  Volume: 49828.855 A^3 
  Total mass 20210.854 amu,  Density 0.674 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 + 1.87  to  7.97
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 + 5.49  to  11.59
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 (-8.80, -0.84, 2.77).
(Replacing solvent molecule)
Placed Cl- in m at (-11.30, -1.18, 0.87).
(Replacing solvent molecule)
Placed Na+ in m at (-15.17, -4.40, -1.52).
(Replacing solvent molecule)
Placed Cl- in m at (-15.70, -4.08, -5.45).
(Replacing solvent molecule)
Placed Na+ in m at (-14.46, -3.83, -8.04).
(Replacing solvent molecule)
Placed Cl- in m at (-11.91, -5.24, -8.80).
(Replacing solvent molecule)
Placed Na+ in m at (-10.74, -8.33, -13.27).
(Replacing solvent molecule)
Placed Cl- in m at (-7.35, -6.60, -13.32).
(Replacing solvent molecule)
Placed Na+ in m at (-9.02, -5.50, -9.10).
(Replacing solvent molecule)
Placed Cl- in m at (-10.05, -7.54, -5.00).

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