-I: Adding /share/apps/amber/cpu/21/dat/leap/prep to search path.
-I: Adding /share/apps/amber/cpu/21/dat/leap/lib to search path.
-I: Adding /share/apps/amber/cpu/21/dat/leap/parm to search path.
-I: Adding /share/apps/amber/cpu/21/dat/leap/cmd to search path.
-f: Source 6OFV_tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./6OFV_tleap.in
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/oldff/leaprc.ff14SB
----- Source of /share/apps/amber/cpu/21/dat/leap/cmd/oldff/leaprc.ff14SB done
Log file: ./leap.log
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/amino12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/aminoct12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/aminont12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/nucleic12.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/solvents.lib
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff
----- Source of /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.water.tip3p
----- Source of /share/apps/amber/cpu/21/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/atomic_ions.lib
Loading library: /share/apps/amber/cpu/21/dat/leap/lib/solvents.lib
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /share/apps/amber/cpu/21/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: /share/apps/amber/cpu/21/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading Mol2 file: ./AP1.mol2
Reading MOLECULE named AP1
Loading Mol2 file: ./AN1.mol2
Reading MOLECULE named AN1
Loading Mol2 file: ./SR1.mol2
Reading MOLECULE named SR1
Loading Mol2 file: ./GU1.mol2
Reading MOLECULE named GU1
Loading Mol2 file: ./MG1.mol2
Reading MOLECULE named MG1
Loading Mol2 file: ./MG2.mol2
Reading MOLECULE named MG2
Loading Mol2 file: ./MG3.mol2
Reading MOLECULE named MG3
Loading Mol2 file: ./PP1.mol2
Reading MOLECULE named PP1
Loading Mol2 file: ./WT1.mol2
Reading MOLECULE named WT1
Loading Mol2 file: ./WT2.mol2
Reading MOLECULE named WT2
Loading Mol2 file: ./WT3.mol2
Reading MOLECULE named WT3
Loading Mol2 file: ./WT4.mol2
Reading MOLECULE named WT4
Loading Mol2 file: ./WT5.mol2
Reading MOLECULE named WT5
Loading Mol2 file: ./WT6.mol2
Reading MOLECULE named WT6
Loading Mol2 file: ./WT7.mol2
Reading MOLECULE named WT7
Loading parameters: ./POP.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading parameters: /share/apps/amber/cpu/21/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: ./6OFV_mcpbpy.frcmod
Reading force field modification type file (frcmod)
Reading title:
REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY
Loading PDB file: ./6OFV_mcpbpy.pdb

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (AP1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (AN1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (SR1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (GU1) missing connect0 atom.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.
  total atoms in file: 5468
Writing pdb file: 6OFV_dry.pdb

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NALA -> ALA

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CASN -> ASN
Checking Unit.

/share/apps/amber/cpu/21/bin/teLeap: Warning!
The unperturbed charge of the unit (-10.999998) is not zero.

/share/apps/amber/cpu/21/bin/teLeap: Note.
Ignoring the warning from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.

/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5436 5437 duplicates bond ('triangular' bond) or angle ('square' bond)


/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5441 5460 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
 total 1224 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

	AN1	1
	AP1	1
	CASN	1
	GU1	1
	NALA	1
	PP1	1
	SR1	1
	WT1	1
	WT2	1
	WT3	1
	WT4	1
	WT5	1
	WT6	1
	WT7	1
  )
 (no restraints)
  Solute vdw bounding box:              64.605 53.427 57.449
  Total bounding box for atom centers:  84.605 73.427 77.449
  Solvent unit box:                     18.774 18.774 18.774
  Total vdw box size:                   87.721 76.664 80.740 angstroms.
  Volume: 542981.221 A^3 
  Total mass 269294.346 amu,  Density 0.824 g/cc
  Added 12749 residues.
11 Na+ ions required to neutralize.
Adding 11 counter ions to "mol" using 1A grid
Grid extends from solute vdw + 3.38  to  9.48
Resolution:      1.00 Angstrom.
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
(Replacing solvent molecule)
Placed Na+ in mol at (21.60, 22.41, 1.06).
(Replacing solvent molecule)
Placed Na+ in mol at (28.87, 11.65, 1.62).
(Replacing solvent molecule)
Placed Na+ in mol at (22.01, -13.91, 7.15).
(Replacing solvent molecule)
Placed Na+ in mol at (-2.10, -21.87, 3.36).
(Replacing solvent molecule)
Placed Na+ in mol at (13.43, 23.52, -0.99).
(Replacing solvent molecule)
Placed Na+ in mol at (24.65, -24.58, -11.00).
(Replacing solvent molecule)
Placed Na+ in mol at (14.09, 14.51, -6.64).
(Replacing solvent molecule)
Placed Na+ in mol at (7.55, -21.34, -12.79).
(Replacing solvent molecule)
Placed Na+ in mol at (27.07, -7.78, 9.76).
(Replacing solvent molecule)
Placed Na+ in mol at (-17.85, 15.70, 3.24).
(Replacing solvent molecule)
Placed Na+ in mol at (25.42, 17.68, 8.63).

Done adding ions.
 0.000002 0 1 0
0 Cl- ion required to neutralize.
Adding 0 counter ions to "mol" using 1A grid
Writing pdb file: 6OFV_solv.pdb
   printing CRYST1 record to PDB file with box info

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NALA -> ALA

/share/apps/amber/cpu/21/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CASN -> ASN
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.

/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5436 5437 duplicates bond ('triangular' bond) or angle ('square' bond)


/share/apps/amber/cpu/21/bin/teLeap: Note.
1-4: angle 5441 5460 duplicates bond ('triangular' bond) or angle ('square' bond)

Building improper torsion parameters.
 total 1224 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

	AN1	1
	AP1	1
	CASN	1
	GU1	1
	NALA	1
	PP1	1
	SR1	1
	WAT	12738
	WT1	1
	WT2	1
	WT3	1
	WT4	1
	WT5	1
	WT6	1
	WT7	1
  )
 (no restraints)
	Quit

Exiting LEaP: Errors = 0; Warnings = 13; Notes = 5.
