-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: 63 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: 13.078 11.317 9.183 Total bounding box for atom centers: 33.658 33.658 33.658 (box expansion for 'iso' is 19.3%) Solvent unit box: 18.865 18.478 19.006 Volume: 48626.484 A^3 Total mass 20172.840 amu, Density 0.689 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 + 1.23 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 (-5.87, 3.93, -5.33). 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 + 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 (-6.21, 0.77, 10.29). (Replacing solvent molecule) Placed Cl- in m at (-7.71, -1.33, 13.76). (Replacing solvent molecule) Placed Na+ in m at (-5.64, -5.05, 12.83). (Replacing solvent molecule) Placed Cl- in m at (-2.73, -3.15, 11.09). (Replacing solvent molecule) Placed Na+ in m at (-0.14, -3.24, 9.75). (Replacing solvent molecule) Placed Cl- in m at (-0.83, -6.41, 12.29). (Replacing solvent molecule) Placed Na+ in m at (3.25, -8.48, 11.54). (Replacing solvent molecule) Placed Cl- in m at (7.29, -14.98, 0.14). (Replacing solvent molecule) Placed Na+ in m at (6.61, -13.59, -4.34). (Replacing solvent molecule) Placed Cl- in m at (4.42, -2.76, 10.04). 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 11 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