log started: Wed Jun 18 19:42:41 2008

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> #       This file is mostly for use with Antechamber
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "h1"  "H" "sp3" }
>> 	{ "h2"  "H" "sp3" }
>> 	{ "h3"  "H" "sp3" }
>> 	{ "h4"  "H" "sp3" }
>> 	{ "h5"  "H" "sp3" }
>> 	{ "ha"  "H" "sp3" }
>> 	{ "hc"  "H" "sp3" }
>> 	{ "hn"  "H" "sp3" }
>> 	{ "ho"  "H" "sp3" }
>> 	{ "hp"  "H" "sp3" }
>> 	{ "hs"  "H" "sp3" }
>> 	{ "hw"  "H" "sp3" }
>> 	{ "hx"  "H" "sp3" }
>> 	{ "o"  "O" "sp2" }
>> 	{ "o2"  "O" "sp2" }
>> 	{ "oh"  "O" "sp3" }
>> 	{ "os"  "O" "sp3" }
>> 	{ "ow"  "O" "sp3" }
>> 	{ "c"  "C" "sp2" }
>> 	{ "c1"  "C" "sp2" }
>> 	{ "c2"  "C" "sp2" }
>> 	{ "c3"  "C" "sp3" }
>> 	{ "ca"  "C" "sp2" }
>> 	{ "cc"  "C" "sp2" }
>> 	{ "cd"  "C" "sp2" }
>> 	{ "ce"  "C" "sp2" }
>> 	{ "cf"  "C" "sp2" }
>> 	{ "cg"  "C" "sp2" }
>> 	{ "ch"  "C" "sp2" }
>> 	{ "cp"  "C" "sp2" }
>> 	{ "cq"  "C" "sp2" }
>> 	{ "cu"  "C" "sp2" }
>> 	{ "cv"  "C" "sp2" }
>> 	{ "cx"  "C" "sp2" }
>> 	{ "cy"  "C" "sp2" }
>> 	{ "n"   "N" "sp2" }
>> 	{ "n1"  "N" "sp2" }
>> 	{ "n2"  "N" "sp2" }
>> 	{ "n3"  "N" "sp3" }
>> 	{ "n4"  "N" "sp3" }
>> 	{ "na"  "N" "sp2" }
>> 	{ "nb"  "N" "sp2" }
>> 	{ "nc"  "N" "sp2" }
>> 	{ "nd"  "N" "sp2" }
>> 	{ "ne"  "N" "sp2" }
>> 	{ "nf"  "N" "sp2" }
>> 	{ "nh"  "N" "sp2" }
>> 	{ "no"  "N" "sp2" }
>> 	{ "s"   "S" "sp2" }
>> 	{ "s2"   "S" "sp2" }
>> 	{ "s3"   "S" "sp3" }
>> 	{ "s4"   "S" "sp3" }
>> 	{ "s6"   "S" "sp3" }
>> 	{ "sh"   "S" "sp3" }
>> 	{ "ss"   "S" "sp3" }
>> 	{ "sx"   "S" "sp3" }
>> 	{ "sy"   "S" "sp3" }
>> 	{ "p2"   "P" "sp2" }
>> 	{ "p3"   "P" "sp3" }
>> 	{ "p4"   "P" "sp3" }
>> 	{ "p5"   "P" "sp3" }
>> 	{ "pb"   "P" "sp3" }
>> 	{ "pd"   "P" "sp3" }
>> 	{ "px"   "P" "sp3" }
>> 	{ "py"   "P" "sp3" }
>> 	{ "f"   "F" "sp3" }
>> 	{ "cl"  "Cl" "sp3" }
>> 	{ "br"  "Br" "sp3" }
>> 	{ "i"   "I"  "sp3" }
>> }
>> #
>> #	Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /usr/local/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> 
> source leaprc.ff99
----- Source: /usr/local/amber9/dat/leap/cmd/leaprc.ff99
----- Source of /usr/local/amber9/dat/leap/cmd/leaprc.ff99 done
>> logFile leap.log
log started: Wed Jun 18 19:42:45 2008

Log file: ./leap.log
>> #
>> # ----- 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" }
>> 	{ "HS"  "H" "sp3" }
>> 	{ "H1"  "H" "sp3" }
>> 	{ "H2"  "H" "sp3" }
>> 	{ "H3"  "H" "sp3" }
>> 	{ "H4"  "H" "sp3" }
>> 	{ "H5"  "H" "sp3" }
>> 	{ "HW"  "H" "sp3" }
>> 	{ "HC"  "H" "sp3" }
>> 	{ "HA"  "H" "sp3" }
>> 	{ "HP"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "C2"  "C" "sp3" }
>> 	{ "C3"  "C" "sp3" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "C*"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CB"  "C" "sp2" }
>> 	{ "CC"  "C" "sp2" }
>> 	{ "CN"  "C" "sp2" }
>> 	{ "CM"  "C" "sp2" }
>> 	{ "CK"  "C" "sp2" }
>> 	{ "CQ"  "C" "sp2" }
>> 	{ "CD"  "C" "sp2" }
>> 	{ "CE"  "C" "sp2" }
>> 	{ "CF"  "C" "sp2" }
>> 	{ "CG"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp2" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "C" "sp2" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NP"  "N" "sp2" }
>> 	{ "NQ"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "CL"  "Cl" "sp3" }
>> 	{ "BR"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> 	{ "FE"  "Fe" "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> # glycam
>> 	{ "OG"  "O" "sp3" }
>> 	{ "OL"  "O" "sp3" }
>> 	{ "AC"  "C" "sp3" }
>> 	{ "EC"  "C" "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm99 = loadamberparams parm99.dat
Loading parameters: /usr/local/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
(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: LP)
>> #
>> #	Load DNA/RNA libraries
>> #
>> loadOff all_nucleic94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: RA
Loading: RA3
Loading: RA5
Loading: RAN
Loading: RC
Loading: RC3
Loading: RC5
Loading: RCN
Loading: RG
Loading: RG3
Loading: RG5
Loading: RGN
Loading: RU
Loading: RU3
Loading: RU5
Loading: RUN
>> #
>> #	Load main chain and terminating 
>> #	amino acid libraries.
>> #
>> loadOff all_amino94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff all_aminoct94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff all_aminont94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>> 
>> loadOff ions94.lib
Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: MG2
Loading: Na+
Loading: Rb+
>> loadOff solvents.lib
Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: T4E
Loading: TIP3PBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
>> HOH = TP3
>> WAT = TP3
>> 
>> #
>> #	Define the PDB name map for the amino acids and DNA.
>> #
>> addPdbResMap {
>>   { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>>   { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>>   { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>>   { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>>   { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>>   { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>>   { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>>   { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>>   { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>>   { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>>   { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>>   { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>>   { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>>   { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>>   { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>>   { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>>   { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>>   { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>>   { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>>   { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>>   { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>>   { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>>   { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>>   { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>>   { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
>>   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
>>   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
>>   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
>>   { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
>>   { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
>>   { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
>>   { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
>>   { 0 "C5" "DC5" }
>>   { 0 "G5" "DG5" }
>>   { 0 "A5" "DA5" }
>>   { 0 "T5" "DT5" }
>>   { 1 "C3" "DC3" }
>>   { 1 "G3" "DG3" }
>>   { 1 "A3" "DA3" }
>>   { 1 "T3" "DT3" }
>> 
>> }
>> 
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'1" }
>>   { "H2*2" "H2'2" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'1" }
>>   { "H5*2" "H5'2" }
>> # old ff atom names -> new
>>   { "O1'" "O4'" }
>>   { "OA"  "O1P" }
>>   { "OB"  "O2P" }
>> }
>> 
>> 
>> #
>> # assumed that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> egta = loadmol2 EGTA.mol2
Loading Mol2 file: ./EGTA.mol2
Reading MOLECULE named UNK 
> ca = createatom Ca Ca 2
> set ca element Ca
> set ca type C0
> CAL = createresidue CAL
> add CAL ca
> add egta CAL
> set CAL.1 position { 3.184 19.282 7.942 }
> addions egta Na 0
addIons: Argument #2 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
 
	UNIT			_unit_
	UNIT			_ion1_
	NUMBER			_#ion1_
	UNIT			_ion2_
	NUMBER			_#ion2_
 
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added 
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.


> addions egta Na+ 0
2 Na+ ions required to neutralize.
Adding 2 counter ions to "egta" using 1A grid
Total solute charge:  -2.00  Max atom radius:   1.91
Grid extends from solute vdw + 1.87  to  7.78
Box:
   enclosing:  -8.10  7.46 -3.55   14.88 30.71 19.80
   sized:			      23.90 39.46 28.45
   edge:        32.00
Resolution:      1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 14.80% of box, grid points 4849
 (no solvent present)
Calculating grid charges
charges: 0 sec
Placed Na+ in egta at (-1.10, 18.46, 6.45).
Placed Na+ in egta at (5.90, 14.46, 5.45).

Done adding ions.
> check egta
Checking 'egta'....
Checking parameters for unit 'egta'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> solvateoct egta TIP3PBOX 8
Scaling up box by a factor of 1.218269 to meet diagonal cut criterion
  Solute vdw bounding box:              11.390 11.017 11.783
  Total bounding box for atom centers:  31.276 31.276 31.276
      (box expansion for 'iso' is   3.8%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 2  y= 2  z= 2
Adding box at: x=0  y=0  z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0  y=0  z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0  y=1  z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0  y=1  z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=0  z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1  y=0  z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1  y=1  z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
  Volume: 16810.932 A^3 (oct)
  Total mass 7704.812 amu,  Density 0.761 g/cc
  Added 402 residues.
> check egta
Checking 'egta'....
Checking parameters for unit 'egta'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveamberparm egta egta_counter.prmcrd egta_counter.prmtop
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 4 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

	UNK	1
	WAT	402
  )
 (no restraints)
> quit
	Quit