-I: Adding /home/onufriev/amber7/dat/leap/prep to search path.
-I: Adding /home/onufriev/amber7/dat/leap/lib to search path.
-I: Adding /home/onufriev/amber7/dat/leap/parm to search path.
-I: Adding /home/onufriev/amber7/dat/leap/cmd to search path.
-f: Source leap.scrpt.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leap.scrpt
----- Source: /home/onufriev/amber7/dat/leap/cmd/leaprc.ff99
----- Source of /home/onufriev/amber7/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /home/onufriev/amber7/dat/leap/parm/parm99.dat
Loading library: /home/onufriev/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /home/onufriev/amber7/dat/leap/lib/all_amino94.lib
Loading library: /home/onufriev/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /home/onufriev/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /home/onufriev/amber7/dat/leap/lib/ions94.lib
Loading library: /home/onufriev/amber7/dat/leap/lib/solvents.lib
Loading PDB file: ./trx.pdb
  total atoms in file: 822
  Leap added 832 missing atoms according to residue templates:
       832 H / lone pairs
Checking Unit.
WARNING: The unperturbed charge of the unit: -4.000000 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.
 total 303 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	CALA	1
	NSER	1
  )
 (no restraints)
	Quit