-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-full.in. Welcome to LEaP! Sourcing: ./buildit-full.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 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) Loading PDB file: ./init.pdb total atoms in file: 60 Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. Solute vdw bounding box: 13.016 10.877 9.893 Total bounding box for atom centers: 33.716 33.716 33.716 (box expansion for 'iso' is 17.7%) Solvent unit box: 18.774 18.774 18.774 Volume: 49828.855 A^3 Total mass 20149.792 amu, Density 0.672 g/cc Added 1088 residues. 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Grid extends from solute vdw + 1.37 to 7.47 Resolution: 1.00 Angstrom. grid build: 0 sec Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-3.92, 6.17, -3.35). Done adding ions. Na+ has a charge of 0. Adding the ions anyway. Adding 10 counter ions to "m" using 1A grid Grid extends from solute vdw + 5.59 to 11.69 Resolution: 1.00 Angstrom. grid build: 0 sec Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-3.58, 2.24, 9.56). (Replacing solvent molecule) Placed Cl- in m at (-6.53, 3.90, 10.56). (Replacing solvent molecule) Placed Na+ in m at (-7.99, 6.08, 9.90). (Replacing solvent molecule) Placed Cl- in m at (-6.59, 8.82, 7.78). (Replacing solvent molecule) Placed Na+ in m at (-3.95, 10.88, 5.53). (Replacing solvent molecule) Placed Cl- in m at (-1.12, 10.96, 3.32). (Replacing solvent molecule) Placed Na+ in m at (0.79, 12.86, 2.83). (Replacing solvent molecule) Placed Cl- in m at (2.37, 12.33, -2.96). (Replacing solvent molecule) Placed Na+ in m at (4.78, 10.14, -3.58). (Replacing solvent molecule) Placed Cl- in m at (6.29, 11.70, -6.64). Done adding ions. Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 12 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 WAT 1075 ) (no restraints) Quit