tleap.log

-I: Adding /Users/david/bin/amber14/dat/leap/prep to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/lib to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/parm to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source tleapIn.

Welcome to LEaP!
Sourcing: ./tleapIn
----- Source: /Users/david/bin/amber14/dat/leap/cmd/leaprc.ff12SB
----- Source of /Users/david/bin/amber14/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /Users/david/bin/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /Users/david/bin/amber14/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /Users/david/bin/amber14/dat/leap/lib/amino12.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/aminoct12.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/aminont12.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/nucleic12.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/solvents.lib
----- Source: /Users/david/bin/amber14/dat/leap/cmd/leaprc.GLYCAM_06h
----- Source of /Users/david/bin/amber14/dat/leap/cmd/leaprc.GLYCAM_06h done
Loading parameters: /Users/david/bin/amber14/dat/leap/parm/GLYCAM_06h.dat
Reading title:
GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
Loading Prep file: /Users/david/bin/amber14/dat/leap/prep/GLYCAM_06h.prep
Loading library: /Users/david/bin/amber14/dat/leap/lib/GLYCAM_amino_06h.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/GLYCAM_aminoct_06h.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/GLYCAM_aminont_06h.lib
Substituting map 0HYP -> NHYP  for  0HYP -> HYP
Substituting map 1HYP -> CHYP  for  1HYP -> CHYP
Loading library: /Users/david/bin/amber14/dat/leap/lib/solvents.lib
Loading library: /Users/david/bin/amber14/dat/leap/lib/atomic_ions.lib
Loading parameters: /Users/david/bin/amber14/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: /Users/david/bin/amber14/dat/leap/parm/GLYCAM_06h.dat
Reading title:
GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
Loading library: /Users/david/ProteinModellingTK/Sugars/SIA26GAL14NAG_OME_resp.lib
Loading Prep file: /Users/david/ProteinModellingTK/Sugars/SIA26GAL14NAG_OME_resp.prepin
Using H(N)-modified Bondi radii
Loading PDB file: ./rec_4amb.pdb
  total atoms in file: 1963
  Leap added 1916 missing atoms according to residue templates:
       1916 H / lone pairs
Loading PDB file: ./lig.pdb
  total atoms in file: 90
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
/Users/david/bin/amber14/bin/tleap: line 17: 60322 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*