-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
Created a new atom named: U5' within residue: .R<U5 1>
  Added missing heavy atom: .R<U5 1>.A<C2 20>
  Added missing heavy atom: .R<U5 1>.A<N3 18>
  Added missing heavy atom: .R<U5 1>.A<O2 21>
  Added missing heavy atom: .R<U5 1>.A<C4 16>
  Added missing heavy atom: .R<U5 1>.A<C5 14>
  Added missing heavy atom: .R<U5 1>.A<O4 17>
  Added missing heavy atom: .R<U5 1>.A<C5' 3>
  Added missing heavy atom: .R<U3 2>.A<C2 22>
  Added missing heavy atom: .R<U3 2>.A<N3 20>
  Added missing heavy atom: .R<U3 2>.A<O2 23>
  Added missing heavy atom: .R<U3 2>.A<C4 18>
  Added missing heavy atom: .R<U3 2>.A<C5 16>
  Added missing heavy atom: .R<U3 2>.A<O4 19>
  total atoms in file: 41
  Leap added 19 missing atoms according to residue templates:
       13 Heavy
       6 H / lone pairs
  The file contained 1 atoms not in residue templates
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
FATAL:  Atom .R<U5 1>.A<U5' 29> does not have a type.
Warning: Close contact of 1.309695 angstroms between .R<U5 1>.A<O2 21> and .R<U5 1>.A<HO5' 1>
Warning: Close contact of 1.090276 angstroms between .R<U5 1>.A<H5'' 5> and .R<U5 1>.A<U5' 29>
Warning: Close contact of 1.089872 angstroms between .R<U5 1>.A<H5' 4> and .R<U5 1>.A<U5' 29>
Warning: Close contact of 0.156907 angstroms between .R<U5 1>.A<C5' 3> and .R<U5 1>.A<U5' 29>
Warning: Close contact of 1.397229 angstroms between .R<U5 1>.A<O5' 2> and .R<U5 1>.A<U5' 29>
Warning: Close contact of 1.131155 angstroms between .R<U3 2>.A<O3' 30> and .R<U3 2>.A<H4' 9>
Warning: Close contact of 1.307451 angstroms between .R<U3 2>.A<O3' 30> and .R<U3 2>.A<C4' 8>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Errors:  1   Warnings: 8
Writing pdb file: init-run2.pdb
	Quit