-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 1.131155 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: 3 Unit is OK. Solute vdw bounding box: 12.265 11.150 10.292 Total bounding box for atom centers: 33.645 33.645 33.645 (box expansion for 'iso' is 9.9%) 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 (-5.98, 4.85, -2.80). 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 (-0.14, -3.24, 9.75). (Replacing solvent molecule) Placed Cl- in m at (2.85, -0.93, 8.58). (Replacing solvent molecule) Placed Na+ in m at (8.07, 1.13, 7.86). (Replacing solvent molecule) Placed Cl- in m at (-0.46, 0.47, 14.00). (Replacing solvent molecule) Placed Na+ in m at (3.98, 1.37, 9.85). (Replacing solvent molecule) Placed Cl- in m at (8.42, 0.74, 10.66). (Replacing solvent molecule) Placed Na+ in m at (1.80, 4.34, 13.61). (Replacing solvent molecule) Placed Cl- in m at (4.87, 5.75, 10.61). (Replacing solvent molecule) Placed Na+ in m at (7.00, 4.40, 11.69). (Replacing solvent molecule) Placed Cl- in m at (3.61, 1.92, 13.32). 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