-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
Could not open file ./leaprc.ff99bsc0: No such file or directory
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/RNA_CI.lib
Could not open file frcmod.tip3p: not found
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)
Could not open file frcmod.ff99Chen-Garcia: not found
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.127838 angstroms between .R<RC5 1>.A<H3' 24> and .R<RC3 2>.A<H5'1 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Could not find bond parameter for: OS - P
Could not find bond parameter for: OH - HO
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - OH
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - CT
Could not find bond parameter for: CT - OS
Could not find bond parameter for: C - O
Could not find bond parameter for: NC - C
Could not find bond parameter for: N2 - H
Could not find bond parameter for: N2 - H
Could not find bond parameter for: CA - N2
Could not find bond parameter for: CA - NC
Could not find bond parameter for: CM - HA
Could not find bond parameter for: CM - CA
Could not find bond parameter for: CM - H4
Could not find bond parameter for: CM - CM
Could not find bond parameter for: N* - CM
Could not find bond parameter for: N* - C
Could not find bond parameter for: CT - H2
Could not find bond parameter for: CT - N*
Could not find bond parameter for: CT - CT
Could not find bond parameter for: OS - CT
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - OS
Could not find bond parameter for: CT - CT
Could not find bond parameter for: CI - H1
Could not find bond parameter for: CI - H1
Could not find bond parameter for: CI - CT
Could not find bond parameter for: OH - CI
Could not find bond parameter for: HO - OH
Could not find bond parameter for: OH - HO
Could not find bond parameter for: OH - HO
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - OH
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - CT
Could not find bond parameter for: CT - OH
Could not find bond parameter for: C - O
Could not find bond parameter for: NC - C
Could not find bond parameter for: N2 - H
Could not find bond parameter for: N2 - H
Could not find bond parameter for: CA - N2
Could not find bond parameter for: CA - NC
Could not find bond parameter for: CM - HA
Could not find bond parameter for: CM - CA
Could not find bond parameter for: CM - H4
Could not find bond parameter for: CM - CM
Could not find bond parameter for: N* - CM
Could not find bond parameter for: N* - C
Could not find bond parameter for: CT - H2
Could not find bond parameter for: CT - N*
Could not find bond parameter for: CT - CT
Could not find bond parameter for: OS - CT
Could not find bond parameter for: CT - H1
Could not find bond parameter for: CT - OS
Could not find bond parameter for: CT - CT
Could not find bond parameter for: CI - H1
Could not find bond parameter for: CI - H1
Could not find bond parameter for: CI - CT
Could not find bond parameter for: OS - CI
Could not find bond parameter for: P - O2
Could not find bond parameter for: P - O2
Could not find bond parameter for: P - OS
Checking for angle parameters.
Could not find angle parameter: OS - P - O2
Could not find angle parameter: OS - P - O2
Could not find angle parameter: OS - P - OS
Could not find angle parameter: H1 - CT - OH
Could not find angle parameter: CT - CT - OS
Could not find angle parameter: CT - OH - HO
Could not find angle parameter: H1 - CT - CT
Could not find angle parameter: H1 - CT - OS
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: CT - OS - P
Could not find angle parameter: NC - C - O
Could not find angle parameter: H - N2 - H
Could not find angle parameter: N2 - CA - NC
Could not find angle parameter: CA - N2 - H
Could not find angle parameter: CA - N2 - H
Could not find angle parameter: CA - NC - C
Could not find angle parameter: HA - CM - CA
Could not find angle parameter: CM - CA - N2
Could not find angle parameter: CM - CA - NC
Could not find angle parameter: H4 - CM - CM
Could not find angle parameter: CM - N* - C
Could not find angle parameter: CM - CM - HA
Could not find angle parameter: CM - CM - CA
Could not find angle parameter: N* - CT - CT
Could not find angle parameter: N* - CM - H4
Could not find angle parameter: N* - CM - CM
Could not find angle parameter: N* - C - NC
Could not find angle parameter: N* - C - O
Could not find angle parameter: H2 - CT - N*
Could not find angle parameter: H2 - CT - CT
Could not find angle parameter: CT - N* - CM
Could not find angle parameter: CT - N* - C
Could not find angle parameter: CT - CT - CT
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: OS - CT - CT
Could not find angle parameter: OS - CT - H2
Could not find angle parameter: OS - CT - N*
Could not find angle parameter: OS - CT - CT
Could not find angle parameter: H1 - CT - OS
Could not find angle parameter: H1 - CT - CT
Could not find angle parameter: CT - OS - CT
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - CT
Could not find angle parameter: CT - CT - OS
Could not find angle parameter: H1 - CI - CT
Could not find angle parameter: H1 - CI - H1
Could not find angle parameter: H1 - CI - CT
Could not find angle parameter: CI - CT - H1
Could not find angle parameter: CI - CT - OS
Could not find angle parameter: CI - CT - CT
Could not find angle parameter: OH - CI - H1
Could not find angle parameter: OH - CI - H1
Could not find angle parameter: OH - CI - CT
Could not find angle parameter: HO - OH - CI
Could not find angle parameter: H1 - CT - OH
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: CT - OH - HO
Could not find angle parameter: H1 - CT - CT
Could not find angle parameter: H1 - CT - OH
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: CT - OH - HO
Could not find angle parameter: NC - C - O
Could not find angle parameter: H - N2 - H
Could not find angle parameter: N2 - CA - NC
Could not find angle parameter: CA - N2 - H
Could not find angle parameter: CA - N2 - H
Could not find angle parameter: CA - NC - C
Could not find angle parameter: HA - CM - CA
Could not find angle parameter: CM - CA - N2
Could not find angle parameter: CM - CA - NC
Could not find angle parameter: H4 - CM - CM
Could not find angle parameter: CM - N* - C
Could not find angle parameter: CM - CM - HA
Could not find angle parameter: CM - CM - CA
Could not find angle parameter: N* - CT - CT
Could not find angle parameter: N* - CM - H4
Could not find angle parameter: N* - CM - CM
Could not find angle parameter: N* - C - NC
Could not find angle parameter: N* - C - O
Could not find angle parameter: H2 - CT - N*
Could not find angle parameter: H2 - CT - CT
Could not find angle parameter: CT - N* - CM
Could not find angle parameter: CT - N* - C
Could not find angle parameter: CT - CT - CT
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: OS - CT - CT
Could not find angle parameter: OS - CT - H2
Could not find angle parameter: OS - CT - N*
Could not find angle parameter: OS - CT - CT
Could not find angle parameter: H1 - CT - OS
Could not find angle parameter: H1 - CT - CT
Could not find angle parameter: CT - OS - CT
Could not find angle parameter: CT - CT - H1
Could not find angle parameter: CT - CT - CT
Could not find angle parameter: CT - CT - OH
Could not find angle parameter: H1 - CI - CT
Could not find angle parameter: H1 - CI - H1
Could not find angle parameter: H1 - CI - CT
Could not find angle parameter: CI - CT - H1
Could not find angle parameter: CI - CT - OS
Could not find angle parameter: CI - CT - CT
Could not find angle parameter: OS - CI - H1
Could not find angle parameter: OS - CI - H1
Could not find angle parameter: OS - CI - CT
Could not find angle parameter: O2 - P - OS
Could not find angle parameter: O2 - P - O2
Could not find angle parameter: O2 - P - OS
Could not find angle parameter: P - OS - CI
There are missing parameters.
check:  Warnings: 2
Unit is OK.
Writing pdb file: init.pdb
	Quit