-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-vac.in.

Welcome to LEaP!
Sourcing: ./buildit-vac.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 PDB file: ./pattern.pdb
  Added missing heavy atom: .R<G5 1>.A<C4 25>
  Added missing heavy atom: .R<G5 1>.A<C5 15>
  Added missing heavy atom: .R<G5 1>.A<N3 24>
  Added missing heavy atom: .R<G5 1>.A<N7 14>
  Added missing heavy atom: .R<G5 1>.A<C6 16>
  Added missing heavy atom: .R<G5 1>.A<C2 20>
  Added missing heavy atom: .R<G5 1>.A<O6 17>
  Added missing heavy atom: .R<G5 1>.A<N1 18>
  Added missing heavy atom: .R<G5 1>.A<N2 21>
  Added missing heavy atom: .R<G3 2>.A<C4 27>
  Added missing heavy atom: .R<G3 2>.A<C5 17>
  Added missing heavy atom: .R<G3 2>.A<N3 26>
  Added missing heavy atom: .R<G3 2>.A<N7 16>
  Added missing heavy atom: .R<G3 2>.A<C6 18>
  Added missing heavy atom: .R<G3 2>.A<C2 22>
  Added missing heavy atom: .R<G3 2>.A<O6 19>
  Added missing heavy atom: .R<G3 2>.A<N1 20>
  Added missing heavy atom: .R<G3 2>.A<N2 23>
  total atoms in file: 41
  Leap added 26 missing atoms according to residue templates:
       18 Heavy
       8 H / lone pairs
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.
Writing pdb file: init-run2.pdb
	Quit