-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: ../../../../../scripts/leaprc.ff99bsc0 ----- Source of ../../../../../scripts/leaprc.ff99bsc0 done Log file: ./leap.log Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.parmbsc0 Reading force field modification type file (frcmod) Reading title: modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/ Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_nucleic94.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_amino94.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminoct94.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminont94.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/DNA_CI.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/ions94.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/RNA_CI.lib Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/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: ../../../../../scripts/frcmod.ff99Chen-Garcia Reading force field modification type file (frcmod) Reading title: glycosdic bond torsion modifications to parm99 from Chen and Garcia (PNAS, 2013, 110, 16820) Loading PDB file: ./init.pdb total atoms in file: 67 Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.127157 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. Solute vdw bounding box: 9.654 20.646 11.915 Total bounding box for atom centers: 33.806 33.806 33.806 (box expansion for 'iso' is 99.8%) Solvent unit box: 18.774 18.774 18.774 Volume: 49828.855 A^3 Total mass 20246.886 amu, Density 0.675 g/cc Added 1089 residues. 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Grid extends from solute vdw + 1.87 to 7.97 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 (5.56, -0.13, 2.85). 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 + 5.49 to 11.59 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 (1.32, -1.81, -7.58). (Replacing solvent molecule) Placed Cl- in m at (4.31, -3.83, -8.04). (Replacing solvent molecule) Placed Na+ in m at (9.75, -5.50, -9.10). (Replacing solvent molecule) Placed Cl- in m at (1.98, 1.84, -14.74). (Replacing solvent molecule) Placed Na+ in m at (-2.60, 1.02, -15.23). (Replacing solvent molecule) Placed Cl- in m at (-3.07, -0.83, -11.67). (Replacing solvent molecule) Placed Na+ in m at (1.25, -4.29, -13.85). (Replacing solvent molecule) Placed Cl- in m at (13.39, -4.01, -4.12). (Replacing solvent molecule) Placed Na+ in m at (13.96, -7.49, -2.97). (Replacing solvent molecule) Placed Cl- in m at (11.95, -11.10, -1.25). 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