log started: Tue Apr  7 20:50:00 2009

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/apps/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> 
> mol = loadpdb wWater.pdb
Loading PDB file: ./wWater.pdb
Enter zPdbReadScan from call depth  0.
Warning: name change in pdb file residue 1 ;
 this residue is split into UNK and AGT.
1 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
-- residue 1: duplicate [ C] atoms (total 22)
-- residue 1: duplicate [ H] atoms (total 16)
-- residue 1: duplicate [ O] atoms (total 2)
-- residue 2: duplicate [ H] atoms (total 2)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: UNK, Terminal/last, was not found in name map.)
Unknown residue: UNK   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
(Residue 1: AGT, Terminal/last, was not found in name map.)
Unknown residue: AGT   number: 1   type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: UNK sequence: 1
Created a new atom named: C within residue: .R<UNK 1>
Created a new atom named: H within residue: .R<UNK 1>
Created a new atom named: O within residue: .R<UNK 1>
Creating new UNIT for residue: AGT sequence: 2
Created a new atom named: H within residue: .R<AGT 2>
Created a new atom named: O within residue: .R<AGT 2>
  total atoms in file: 43
  The file contained 5 atoms not in residue templates
> loadamberprep just_water.prepi
Loading Prep file: ./just_water.prepi
Loaded UNIT: AGT
> loadamberparams just_water.frcmod
Loading parameters: ./just_water.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> check UNK
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
> check AGT
Checking 'AGT'....
Checking parameters for unit 'AGT'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> loadamberprep no_charge.prepi
Loading Prep file: ./no_charge.prepi
Loaded UNIT: UNK
> loadamberparams no_charge.frcmod
Loading parameters: ./no_charge.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> check UNK
Checking 'UNK'....
Checking parameters for unit 'UNK'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> check AGT
Checking 'AGT'....
Checking parameters for unit 'AGT'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> var = combine UNK AGT
combine: Improper number of arguments!
usage:  <variable> = combine <LIST>
> var = combine { UNK AGT }
  Sequence: UNK
  Sequence: AGT
> check var
Checking 'var'....
Warning: Close contact of 1.998561 angstroms between .R<UNK 1>.A<C6 14> and .R<AGT 2>.A<O 1>
Warning: Close contact of 1.535359 angstroms between .R<UNK 1>.A<H1 4> and .R<AGT 2>.A<H1 3>
Warning: Close contact of 0.497750 angstroms between .R<UNK 1>.A<C 3> and .R<AGT 2>.A<H1 3>
Warning: Close contact of 1.965604 angstroms between .R<UNK 1>.A<C 3> and .R<AGT 2>.A<O 1>
Warning: Close contact of 0.265215 angstroms between .R<UNK 1>.A<H 2> and .R<AGT 2>.A<H 2>
Warning: Close contact of 1.179396 angstroms between .R<UNK 1>.A<H 2> and .R<AGT 2>.A<O 1>
Warning: Close contact of 0.917764 angstroms between .R<UNK 1>.A<C1 1> and .R<AGT 2>.A<H1 3>
Warning: Close contact of 0.917764 angstroms between .R<UNK 1>.A<C1 1> and .R<AGT 2>.A<H 2>
Warning: Close contact of 0.000000 angstroms between .R<UNK 1>.A<C1 1> and .R<AGT 2>.A<O 1>
Checking parameters for unit 'var'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 9
Unit is OK.
> saveamberparm var brwWater.inpcrd brwWater.prmtop
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <UNK 1>:  C6   C    C1   H   
 <UNK 1>:  C1   C2   C    H1  
 <UNK 1>:  C3   C4   C2   C   
 <UNK 1>:  C5   C2   C4   H5  
 <UNK 1>:  C4   C6   C5   H6  
 <UNK 1>:  C7   C5   C6   C1  
 <UNK 1>:  C8   C10  C9   O   
 <UNK 1>:  C9   C11  C10  H8  
 <UNK 1>:  C10  C12  C11  H7  
 <UNK 1>:  C13  C11  C12  O1  
 <UNK 1>:  C14  C16  C15  C21 
 <UNK 1>:  C15  C17  C16  H9  
 <UNK 1>:  C16  C18  C17  H10 
 <UNK 1>:  C19  C17  C18  C20 
 <UNK 1>:  C18  C21  C20  H14 
 <UNK 1>:  C15  C20  C21  H15 
 total 16 improper torsions applied
 16 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> saveamberparm var brwWater.prmtop brwWater.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <UNK 1>:  C6   C    C1   H   
 <UNK 1>:  C1   C2   C    H1  
 <UNK 1>:  C3   C4   C2   C   
 <UNK 1>:  C5   C2   C4   H5  
 <UNK 1>:  C4   C6   C5   H6  
 <UNK 1>:  C7   C5   C6   C1  
 <UNK 1>:  C8   C10  C9   O   
 <UNK 1>:  C9   C11  C10  H8  
 <UNK 1>:  C10  C12  C11  H7  
 <UNK 1>:  C13  C11  C12  O1  
 <UNK 1>:  C14  C16  C15  C21 
 <UNK 1>:  C15  C17  C16  H9  
 <UNK 1>:  C16  C18  C17  H10 
 <UNK 1>:  C19  C17  C18  C20 
 <UNK 1>:  C18  C21  C20  H14 
 <UNK 1>:  C15  C20  C21  H15 
 total 16 improper torsions applied
 16 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit
log started: Tue Apr  7 21:00:33 2009

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/apps/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> 
> mol = loadpdb wWater.pdb
Loading PDB file: ./wWater.pdb
Enter zPdbReadScan from call depth  0.
Warning: name change in pdb file residue 1 ;
 this residue is split into UNK and AGT.
1 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
-- residue 1: duplicate [ C] atoms (total 22)
-- residue 1: duplicate [ H] atoms (total 16)
-- residue 1: duplicate [ O] atoms (total 2)
-- residue 2: duplicate [ H] atoms (total 2)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: UNK, Terminal/last, was not found in name map.)
Unknown residue: UNK   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
(Residue 1: AGT, Terminal/last, was not found in name map.)
Unknown residue: AGT   number: 1   type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: UNK sequence: 1
Created a new atom named: C within residue: .R<UNK 1>
Created a new atom named: H within residue: .R<UNK 1>
Created a new atom named: O within residue: .R<UNK 1>
Creating new UNIT for residue: AGT sequence: 2
Created a new atom named: H within residue: .R<AGT 2>
Created a new atom named: O within residue: .R<AGT 2>
  total atoms in file: 43
  The file contained 5 atoms not in residue templates
> VAR = combine { UNK AGT }
combine: UNK is type String
  expected UNIT
combine: AGT is type String
  expected UNIT
No UNITS, so no combine performed
> loadamberprep just_water.prepi
Loading Prep file: ./just_water.prepi
Loaded UNIT: AGT
> loadamberprep no_charge.prepi
Loading Prep file: ./no_charge.prepi
Loaded UNIT: UNK
> loadamberparams just_water.frcmod
Loading parameters: ./just_water.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberparams no_charge.frcmod
Loading parameters: ./no_charge.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> check UNK
Checking 'UNK'....
Checking parameters for unit 'UNK'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> check AGT
Checking 'AGT'....
Checking parameters for unit 'AGT'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> VAR = combine { UNK AGT }
  Sequence: UNK
  Sequence: AGT
> saveamberparm VAR test.prmtop test.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <UNK 1>:  C6   C    C1   H   
 <UNK 1>:  C1   C2   C    H1  
 <UNK 1>:  C3   C4   C2   C   
 <UNK 1>:  C5   C2   C4   H5  
 <UNK 1>:  C4   C6   C5   H6  
 <UNK 1>:  C7   C5   C6   C1  
 <UNK 1>:  C8   C10  C9   O   
 <UNK 1>:  C9   C11  C10  H8  
 <UNK 1>:  C10  C12  C11  H7  
 <UNK 1>:  C13  C11  C12  O1  
 <UNK 1>:  C14  C16  C15  C21 
 <UNK 1>:  C15  C17  C16  H9  
 <UNK 1>:  C16  C18  C17  H10 
 <UNK 1>:  C19  C17  C18  C20 
 <UNK 1>:  C18  C21  C20  H14 
 <UNK 1>:  C15  C20  C21  H15 
 total 16 improper torsions applied
 16 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit
	Quit