-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-vac.in.

Welcome to LEaP!
Sourcing: ./buildit-vac.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
Could not open file frcmod.tip3p: not found
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)
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.140192 angstroms between .R<G5 1>.A<H3' 27> and .R<A3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 2
Unit is OK.
Writing pdb file: init.pdb
	Quit