-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-full.in. Welcome to LEaP! Sourcing: ./buildit-full.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 library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) Loading PDB file: ./init.pdb total atoms in file: 59 Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.309643 angstroms between .R.A and .R.A Warning: Close contact of 1.131155 angstroms between .R.A and .R.A Warning: Close contact of 1.307451 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 4 Unit is OK. Solute vdw bounding box: 10.890 12.651 9.670 Total bounding box for atom centers: 33.591 33.591 33.591 (box expansion for 'iso' is 15.8%) Solvent unit box: 18.865 18.478 19.006 Volume: 48622.506 A^3 Total mass 20114.742 amu, Density 0.687 g/cc Added 1086 residues. 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Grid extends from solute vdw + 1.23 to 7.33 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 (-5.41, -1.68, -6.45). Done adding ions. Adding 10 counter ions to "m" using 1A grid Grid extends from solute vdw + 6.14 to 12.24 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 (-6.06, -7.45, 6.96). (Replacing solvent molecule) Placed Cl- in m at (-9.46, -8.17, 9.23). (Replacing solvent molecule) Placed Na+ in m at (-13.16, -4.98, 7.49). (Replacing solvent molecule) Placed Cl- in m at (-10.11, -6.16, 5.19). (Replacing solvent molecule) Placed Na+ in m at (-8.69, -10.22, 4.80). (Replacing solvent molecule) Placed Cl- in m at (-4.88, -10.07, 4.35). (Replacing solvent molecule) Placed Na+ in m at (-1.51, -11.50, 4.05). (Replacing solvent molecule) Placed Cl- in m at (-1.83, -16.44, 3.33). (Replacing solvent molecule) Placed Na+ in m at (-0.98, -14.13, -0.77). (Replacing solvent molecule) Placed Cl- in m at (2.65, -12.98, 0.45). Done adding ions. Checking Unit. -- ignoring the warnings. 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. (no restraints) Quit