-I: Adding /home/jkalliau/prgm/amber16/dat/leap/prep to search path. -I: Adding /home/jkalliau/prgm/amber16/dat/leap/lib to search path. -I: Adding /home/jkalliau/prgm/amber16/dat/leap/parm to search path. -I: Adding /home/jkalliau/prgm/amber16/dat/leap/cmd to search path. -f: Source LeapVorbereitung.leap. Welcome to LEaP! (no leaprc in search path) Sourcing: ./LeapVorbereitung.leap ----- Source: /home/jkalliau/prgm/amber16/dat/leap/cmd/leaprc.DNA.bsc1 ----- Source of /home/jkalliau/prgm/amber16/dat/leap/cmd/leaprc.DNA.bsc1 done Log file: ./leap.log Loading parameters: /home/jkalliau/prgm/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading library: /home/jkalliau/prgm/amber16/dat/leap/lib/parmBSC1.lib Loading parameters: /home/jkalliau/prgm/amber16/dat/leap/parm/frcmod.parmbsc1 Reading force field modification type file (frcmod) Reading title: Parmbsc1 force-field for DNA ----- Source: /home/jkalliau/prgm/amber16/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/jkalliau/prgm/amber16/dat/leap/cmd/leaprc.water.tip3p done Loading library: /home/jkalliau/prgm/amber16/dat/leap/lib/atomic_ions.lib Loading library: /home/jkalliau/prgm/amber16/dat/leap/lib/solvents.lib Loading parameters: /home/jkalliau/prgm/amber16/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for SPC/E water Loading parameters: /home/jkalliau/prgm/amber16/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: /home/jkalliau/prgm/amber16/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) Loading PDB file: ./nuc10.pdb Created a new atom named: P within residue: .R Created a new atom named: OP1 within residue: .R Created a new atom named: OP2 within residue: .R Created a new atom named: P within residue: .R Created a new atom named: OP1 within residue: .R Created a new atom named: OP2 within residue: .R total atoms in file: 640 Leap added 4 missing atoms according to residue templates: 4 H / lone pairs The file contained 6 atoms not in residue templates 18 Na+ ions required to neutralize. Adding 18 counter ions to "nuc10" using 1A grid Used default radius 1.50 for 6 atoms Grid extends from solute vdw + 3.65 to 9.75 Resolution: 1.00 Angstrom. grid build: 0 sec (no solvent present) Calculating grid charges charges: 0 sec Placed Na+ in nuc10 at (6.44, 3.95, 18.17). Placed Na+ in nuc10 at (-1.56, 7.95, 24.17). Placed Na+ in nuc10 at (-10.56, -6.05, 20.17). Placed Na+ in nuc10 at (7.44, -9.05, 17.17). Placed Na+ in nuc10 at (-10.56, 5.95, 14.17). Placed Na+ in nuc10 at (10.44, -4.05, 10.17). Placed Na+ in nuc10 at (-10.56, 3.95, 27.17). Placed Na+ in nuc10 at (-1.56, -12.05, 24.17). Placed Na+ in nuc10 at (-11.56, -4.05, 7.17). Placed Na+ in nuc10 at (5.44, 12.95, 14.17). Placed Na+ in nuc10 at (13.44, 1.95, 25.17). Placed Na+ in nuc10 at (-7.56, -8.05, 34.17). Placed Na+ in nuc10 at (-5.56, -10.05, 10.17). Placed Na+ in nuc10 at (-5.56, 10.95, 10.17). Placed Na+ in nuc10 at (11.44, 7.95, 32.17). Placed Na+ in nuc10 at (10.44, 8.95, 8.17). Placed Na+ in nuc10 at (9.44, -9.05, 27.17). Placed Na+ in nuc10 at (-11.56, 3.95, 3.17). Done adding ions. (using default radius 1.500000 for P) (using default radius 1.500000 for OP1) (using default radius 1.500000 for OP2) (using default radius 1.500000 for P) (using default radius 1.500000 for OP1) (using default radius 1.500000 for OP2) Box dimensions: 27.738000 27.738000 40.099000 Checking Unit. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. Quit