log started: Thu Apr 1 17:52:48 2010
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the Cornell et al. topology and
>> # parm96.dat for proteins
>> # 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" }
>> # glycam
>> { "OG" "O" "sp3" }
>> { "OL" "O" "sp3" }
>> { "AC" "C" "sp3" }
>> { "EC" "C" "sp3" }
>> }
>> #
>> # Load the main parameter set.
>> #
>> parm96 = loadamberparams parm96.dat
Loading parameters: /Users/jchodera/local/src/amber10/dat/leap/parm/parm96.dat
Reading title:
PARM96 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
(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: IB)
>> #
>> # Load DNA/RNA libraries
>> #
>> loadOff all_nucleic94.lib
Loading library: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/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: /Users/jchodera/local/src/amber10/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> 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
>
>
> # Create a container with a single sodium ion.
> system = sequence { Na+ }
Sequence: Na+
>
> # Solvate in water box.
> solvateBox system TIP3PBOX 10.0 iso
Solute vdw bounding box: 3.736 3.736 3.736
Total bounding box for atom centers: 23.736 23.736 23.736
(box expansion for 'iso' is 0.0%)
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: 19610.991 A^3
Total mass 6851.054 amu, Density 0.580 g/cc
Added 379 residues.
>
> # Check sytem.
> check system
Checking 'system'....
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
Checking parameters for unit 'system'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
>
> # Write parameters.
> saveAmberParm system system.prmtop system.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000000 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 0 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 379
)
(no restraints)
>
> # Exit
> quit
Quit