log started: Fri Jan 12 17:41:07 2007

Log file: ./leap.log

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> # ----- leaprc for loading the parm99 additive force field, no lone pairs
> #       assumes that any unspecified nucleic acids are DNA 
> #
> #	load atom type hybridizations
> #
> addAtomTypes {
> 	{ "H"   "H" "sp3" }
> 	{ "HO"  "H" "sp3" }

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> }
> #
> #	Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat

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> loadOff solvents.lib
Loading library: /home/yohsukeh/amber7/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: SPC
Loading: TIP4PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: WATBOX216
> HOH = TP3
> WAT = TP3
> 
> #
> #	Define the PDB name map for the amino acids and DNA.
> #
> addPdbResMap {
>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }

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>> #
>> #	TIP5P water
>> #
>> 
>> h1 = createAtom  H1   HW  0.2410
>> h2 = createAtom  H2   HW  0.2410
>> o  = createAtom  O    OW  0.0
>> ep1 = createAtom  EP1  EP  -0.241
>> ep2 = createAtom  EP2  EP  -0.241
>> 
>> set h1   element   H
>> set h2   element   H
>> set o   element   O
>> set ep1  element   Lp
>> set ep2  element   Lp
>> 
>> r = createResidue  TI5
>> add r h1
>> add r h2
>> add r o
>> add r ep1
>> add r ep2
>> 
>> bond h1  o
>> bond h2  o
>> bond h1  h2
>> bond ep1 o
>> bond ep2 o
>> 
>> TI5 = createUnit  TI5
>> 
>> add TI5  r
>> set TI5.1   restype   solvent
>> set TI5.1   imagingAtom  TI5.1.O
>> 
>> zMatrix TI5  {
>> 	{  H1  O 0.9572 }
>> 	{  H2  O  H1 0.9572 104.52 }
>> 	{  EP1 O  H1  H2  0.70  109.47  -90. }
>> 	{  EP2 O  H1  H2  0.70  109.47   90. }
>> }
>> 
> 
> loadamberparams parm99EP.dat
Loading parameters: /home/yohsukeh/amber7/dat/leap/parm/parm99EP.dat
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: EP)
> loadamberparams frcmod.tip5p
Loading parameters: /home/yohsukeh/amber7/dat/leap/parm/frcmod.tip5p
Reading force field mod type file (frcmod)
> model = TP5
> 
> solvatebox model TP5 20
Solvent has no box, so preparing by making box including vdw
(Use 'setBox centers' first if box was pre-equilibrated)
 (using default radius 1.500000 for EP2)
 (using default radius 1.500000 for EP1)
 (using default radius 1.500000 for EP1)
 (using default radius 1.500000 for EP2)
  Solute vdw bounding box:              3.708 3.678 4.320
  Total bounding box for atom centers:  43.708 43.678 44.320
  Solvent unit box:                     3.708 3.678 4.320
The number of boxes:  x=12  y=12  z=11
Adding box at: x=0  y=0  z=0
Center of solvent box is: 20.395100, 20.226948, 21.599710
Adding box at: x=0  y=0  z=1
Center of solvent box is: 20.395100, 20.226948, 17.279768

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  Total vdw box size:                   44.498 44.132 38.879 angstroms.
  Volume: 76350.827 A^3 
  Total mass 31052.688 amu,  Density 0.675 g/cc
  Added 1292 residues.
> edit model 
Table Editor: Check table...
Table Editor: There are no mistakes in the table.
Table Editor: Table has been 'saved' back to the program.
> saveamberparmpert model parmpert.top parmpert.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 0 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

	WAT	1293
  )
 (no restraints)