-I: Adding /server-home/netbin/amber11/dat/leap/prep to search path.
-I: Adding /server-home/netbin/amber11/dat/leap/lib to search path.
-I: Adding /server-home/netbin/amber11/dat/leap/parm to search path.
-I: Adding /server-home/netbin/amber11/dat/leap/cmd to search path.
-f: Source build.leaprc.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./build.leaprc
----- Source: /server-home/netbin/amber11/dat/leap/cmd/leaprc.ff99SB
----- Source of /server-home/netbin/amber11/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /server-home/netbin/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /server-home/netbin/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /server-home/netbin/amber11/dat/leap/lib/all_nucleic94.lib
Loading library: /server-home/netbin/amber11/dat/leap/lib/all_amino94.lib
Loading library: /server-home/netbin/amber11/dat/leap/lib/all_aminoct94.lib
Loading library: /server-home/netbin/amber11/dat/leap/lib/all_aminont94.lib
Loading library: /server-home/netbin/amber11/dat/leap/lib/ions94.lib
Loading library: /server-home/netbin/amber11/dat/leap/lib/solvents.lib
Loading Prep file: /server-home/netbin/amber11/dat/leap/prep/chcl3.in
 WARNING - 1 of 8 atoms missing charges on atoms lines: chloroform
Loading parameters: /server-home/netbin/amber11/dat/leap/parm/frcmod.chcl3
Reading force field modification type file (frcmod)
Reading title:
 chloroform frcmod file
ACE       ALA       ARG       ASH       ASN       ASP       CALA      CARG      
CASN      CASP      CCYS      CCYX      CGLN      CGLU      CGLY      CHCL3BOX  
CHID      CHIE      CHIP      CHIS      CILE      CIO       CL3       CLEU      
CLYS      CMET      CPHE      CPRO      CSER      CTHR      CTRP      CTYR      
CVAL      CYM       CYS       CYX       Cl-       Cs+       DA        DA3       
DA5       DAN       DC        DC3       DC4       DC5       DCN       DG        
DG3       DG5       DGN       DT        DT3       DT5       DTN       GLH       
GLN       GLU       GLY       HID       HIE       HIP       HIS       HOH       
IB        ILE       K+        LEU       LYN       LYS       Li+       MEOHBOX   
MET       MG2       NALA      NARG      NASN      NASP      NCYS      NCYX      
NGLN      NGLU      NGLY      NHE       NHID      NHIE      NHIP      NHIS      
NILE      NLEU      NLYS      NMABOX    NME       NMET      NPHE      NPRO      
NSER      NTHR      NTRP      NTYR      NVAL      Na+       PHE       PL3       
POL3BOX   PRO       QSPCFWBOX RA        RA3       RA5       RAN       RC        
RC3       RC5       RCN       RG        RG3       RG5       RGN       RU        
RU3       RU5       RUN       Rb+       SER       SPC       SPCBOX    SPCFWBOX  
SPF       SPG       T4E       THR       TIP3PBOX  TIP3PFBOX TIP4PBOX  TIP4PEWBOX
TP3       TP4       TP5       TPF       TRP       TYR       VAL       WAT       
frcmod99SBparm99    
  Solute vdw bounding box:              11.957 16.870 7.236
  Total bounding box for atom centers:  27.957 32.870 23.236
  Solvent unit box:                     18.774 18.774 18.774
  Total vdw box size:                   31.398 35.779 26.192 angstroms.
  Volume: 29423.520 A^3 
  Total mass 10735.616 amu,  Density 0.606 g/cc
  Added 580 residues.
Solvent has no box, so preparing by making box including vdw
(Use 'setBox centers' first if box was pre-equilibrated)
  Solute vdw bounding box:              31.398 35.779 26.192
  Total bounding box for atom centers:  81.398 85.779 76.192
  Solvent unit box:                     4.790 5.866 6.286
  Total vdw box size:                   81.817 88.870 69.144 angstroms.
  Volume: 502750.092 A^3 
  Total mass 318705.056 amu,  Density 1.053 g/cc
  Added 2580 residues.
  Solute vdw bounding box:              81.817 88.870 69.144
  Total bounding box for atom centers:  87.817 94.870 75.144
  Solvent unit box:                     18.774 18.774 18.774
  Total vdw box size:                   91.323 97.992 78.086 angstroms.
  Volume: 698790.346 A^3 
  Total mass 361637.184 amu,  Density 0.859 g/cc
  Added 2383 residues.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 8 improper torsions applied
Building H-Bond parameters.
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	2963
  )
 (no restraints)
	Quit