log started: Mon Apr 24 21:10:28 2017

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #
>> #	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" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "C8"  "C" "sp3" }
>> 	{ "2C"  "C" "sp3" }
>> 	{ "3C"  "C" "sp3" }
>> 	{ "CH"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "C"   "C" "sp2" }
>> 	{ "CO"   "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" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CJ"  "C" "sp2" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CA"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "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" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /home/kim/Amber/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /home/kim/Amber/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
>> #
>> #	Load main chain and terminating amino acid libraries
>> #
>> loadOff amino12.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/amino12.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: HYP
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 aminoct12.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/aminoct12.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: CHYP
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 aminont12.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/aminont12.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
>> 
>> #
>> #	Define the PDB name map for the amino acids
>> #
>> addPdbResMap {
>>   { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
>>   { 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" }
>> }
>> 
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
> 
> source leaprc.RNA.OL3
----- Source: /home/kim/Amber/amber16/dat/leap/cmd/leaprc.RNA.OL3
----- Source of /home/kim/Amber/amber16/dat/leap/cmd/leaprc.RNA.OL3 done
>> logFile leap.log
log started: Mon Apr 24 21:10:29 2017

Log file: ./leap.log
>> # ----- NOTE: this is designed for PDB format 3!
>> #       Uses ff99bsc0_chiOL3 for RNA
>> #       	(ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
>> #       	(bsc0): Perez et al. Biophys J. 92: 3817, 2007
>> #       	(chiOL3): Zgarbova et al. JCTC 7: 2886, 2011
>> #           (note: all of the above are in parm10.dat, loaded below)
>> #
>> #	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" }
>> 	{ "HZ"  "H" "sp3" }
>> 	{ "OH"  "O" "sp3" }
>> 	{ "OS"  "O" "sp3" }
>> 	{ "O"   "O" "sp2" }
>> 	{ "O2"  "O" "sp2" }
>> 	{ "OP"  "O" "sp2" }
>> 	{ "OW"  "O" "sp3" }
>> 	{ "CT"  "C" "sp3" }
>> 	{ "CX"  "C" "sp3" }
>> 	{ "CS"  "C" "sp2" }
>> 	{ "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" }
>> 	{ "C5"  "C" "sp2" }
>> 	{ "C4"  "C" "sp2" }
>> 	{ "CP"  "C" "sp2" }
>> 	{ "CI"  "C" "sp3" }
>> 	{ "CW"  "C" "sp2" }
>> 	{ "CV"  "C" "sp2" }
>> 	{ "CR"  "C" "sp2" }
>> 	{ "CY"  "C" "sp2" }
>> 	{ "C0"  "Ca" "sp3" }
>> 	{ "MG"  "Mg" "sp3" }
>> 	{ "N"   "N" "sp2" }
>> 	{ "NA"  "N" "sp2" }
>> 	{ "N2"  "N" "sp2" }
>> 	{ "N*"  "N" "sp2" }
>> 	{ "NB"  "N" "sp2" }
>> 	{ "NC"  "N" "sp2" }
>> 	{ "NT"  "N" "sp3" }
>> 	{ "NY"  "N" "sp2" }
>> 	{ "N3"  "N" "sp3" }
>> 	{ "S"   "S" "sp3" }
>> 	{ "SH"  "S" "sp3" }
>> 	{ "P"   "P" "sp3" }
>> 	{ "LP"  ""  "sp3" }
>> 	{ "EP"  ""  "sp3" }
>> 	{ "F"   "F" "sp3" }
>> 	{ "Cl"  "Cl" "sp3" }
>> 	{ "Br"  "Br" "sp3" }
>> 	{ "I"   "I"  "sp3" }
>> }
>> #
>> #	Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Skipping parm10.dat: already loaded
>> #
>> #	Load main chain and terminating nucleic acids
>> #
>> 
>> loadOff RNA.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/RNA.lib
Loading: A
Loading: A3
Loading: A5
Loading: AN
Loading: C
Loading: C3
Loading: C5
Loading: CN
Loading: G
Loading: G3
Loading: G5
Loading: GN
Loading: OHE
Loading: U
Loading: U3
Loading: U5
Loading: UN
>> 
>> #
>> #	Define the PDB name map for the nucleic acids
>> #
>> addPdbResMap {
>>   { 0 "G" "G5"  } { 1 "G" "G3"  } 
>>   { 0 "A" "A5"  } { 1 "A" "A3"  } 
>>   { 0 "C" "C5"  } { 1 "C" "C3"  } 
>>   { 0 "U" "U5"  } { 1 "U" "U3"  } 
>> #  some old Amber residue names for RNA:
>>   { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
>>   { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
>>   { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
>>   { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
>> #  uncomment out the following if you have this old style RNA files:
>> # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
>> # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
>> # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
>> # { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
>> 
>> }
>> 
>> #  try to be good about reading in really old atom names as well:
>> addPdbAtomMap {
>>   { "O5*" "O5'" }
>>   { "C5*" "C5'" }
>>   { "C4*" "C4'" }
>>   { "O4*" "O4'" }
>>   { "C3*" "C3'" }
>>   { "O3*" "O3'" }
>>   { "C2*" "C2'" }
>>   { "O2*" "O2'" }
>>   { "C1*" "C1'" }
>>   { "C5M" "C7"  }
>>   { "H1*" "H1'" }
>>   { "H2*1" "H2'" }
>>   { "H2*2" "H2''" }
>>   { "H2'1" "H2'" }
>>   { "H2'2" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
> 
> source leaprc.water.tip3p
----- Source: /home/kim/Amber/amber16/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/kim/Amber/amber16/dat/leap/cmd/leaprc.water.tip3p done
>> #
>> #       Load water and ions for TIP3P + Joung-Chetham monovalent ions
>> #       + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
>> #
>> addAtomTypes {
>> 	{ "F-"   "F" "sp3" }
>> 	{ "Cl-"  "Cl" "sp3" }
>> 	{ "Br-"  "Br" "sp3" }
>> 	{ "I-"   "I"  "sp3" }
>> 	{ "Li+"  "Li"  "sp3" }
>> 	{ "Na+"  "Na"  "sp3" }
>> 	{ "K+"  "K"  "sp3" }
>> 	{ "Rb+"  "Rb"  "sp3" }
>> 	{ "Cs+"  "Cs"  "sp3" }
>> 	{ "Mg+"  "Mg"  "sp3" }
>>     { "Tl+"  "Tl"  "sp3" }
>>     { "Cu+"  "Cu"  "sp3" }
>>     { "Ag+"  "Ag"  "sp3" }
>>     { "Be2+" "Be"  "sp3" }
>>     { "Cu2+" "Cu"  "sp3" }
>>     { "Ni2+" "Ni"  "sp3" }
>>     { "Pt2+" "Pt"  "sp3" }
>>     { "Zn2+" "Zn"  "sp3" }
>>     { "Co2+" "Co"  "sp3" }
>>     { "Pd2+" "Pd"  "sp3" }
>>     { "Ag2+" "Ag"  "sp3" }
>>     { "Cr2+" "Cr"  "sp3" }
>>     { "Fe2+" "Fe"  "sp3" }
>>     { "Mg2+" "Mg"  "sp3" }
>>     { "V2+"  "V"   "sp3" }
>>     { "Mn2+" "Mn"  "sp3" }
>>     { "Hg2+" "Hg"  "sp3" }
>>     { "Cd2+" "Cd"  "sp3" }
>>     { "Yb2+" "Yb"  "sp3" }
>>     { "Ca2+" "Ca"  "sp3" }
>>     { "Sn2+" "Sn"  "sp3" }
>>     { "Pb2+" "Pb"  "sp3" }
>>     { "Eu2+" "Eu"  "sp3" }
>>     { "Sr2+" "Sr"  "sp3" }
>>     { "Sm2+" "Sm"  "sp3" }
>>     { "Ba2+" "Ba"  "sp3" }
>>     { "Ra2+" "Ra"  "sp3" }
>>     { "Al3+" "Al"  "sp3" }
>>     { "Fe3+" "Fe"  "sp3" }
>>     { "Cr3+" "Cr"  "sp3" }
>>     { "In3+" "In"  "sp3" }
>>     { "Tl3+" "Tl"  "sp3" }
>>     { "Y3+"  "Y"   "sp3" }
>>     { "La3+" "La"  "sp3" }
>>     { "Ce3+" "Ce"  "sp3" }
>>     { "Pr3+" "Pr"  "sp3" }
>>     { "Nd3+" "Nd"  "sp3" }
>>     { "Sm3+" "Sm"  "sp3" }
>>     { "Eu3+" "Eu"  "sp3" }
>>     { "Gd3+" "Gd"  "sp3" }
>>     { "Tb3+" "Tb"  "sp3" }
>>     { "Dy3+" "Dy"  "sp3" }
>>     { "Er3+" "Er"  "sp3" }
>>     { "Tm3+" "Tm"  "sp3" }
>>     { "Lu3+" "Lu"  "sp3" }
>>     { "Hf4+" "Hf"  "sp3" }
>>     { "Zr4+" "Zr"  "sp3" }
>>     { "Ce4+" "Ce"  "sp3" }
>>     { "U4+"  "U"   "sp3" }
>>     { "Pu4+" "Pu"  "sp3" }
>>     { "Th4+" "Th"  "sp3" }
>> }
>> loadOff atomic_ions.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /home/kim/Amber/amber16/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OPC
Loading: OPCBOX
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: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /home/kim/Amber/amber16/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip3p
Loading parameters: /home/kim/Amber/amber16/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
>> 
> 
> 
> 
> RNA = loadpdb pdb2mvy_noH.pdb
Loading PDB file: ./pdb2mvy_noH.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
Mapped residue G, term: Terminal/beginning, seq. number: 0 to: G5.
(Residue 1: G, Nonterminal, was not found in name map.)
(Residue 2: A, Nonterminal, was not found in name map.)
(Residue 3: C, Nonterminal, was not found in name map.)
(Residue 4: U, Nonterminal, was not found in name map.)
(Residue 5: A, Nonterminal, was not found in name map.)
(Residue 6: G, Nonterminal, was not found in name map.)
(Residue 7: U, Nonterminal, was not found in name map.)
(Residue 8: C, Nonterminal, was not found in name map.)
Mapped residue C, term: Terminal/last, seq. number: 9 to: C3.
Joining G5 - G
Joining G - A
Joining A - C
Joining C - U
Joining U - A
Joining A - G
Joining G - U
Joining U - C
Joining C - C3
  total atoms in file: 210
  Leap added 110 missing atoms according to residue templates:
       110 H / lone pairs
> 
> saveamberparm RNA pdb2mvy.prmtop pdb2mvy.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -9.000000 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.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 total 58 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> savepdb RNA pdb2mvy_tleap.pdb
Writing pdb file: pdb2mvy_tleap.pdb
> 
> solvateOct RNA TIP3PBOX 12
Scaling up box by a factor of 1.339679 to meet diagonal cut criterion
  Solute vdw bounding box:              24.944 16.201 36.278
  Total bounding box for atom centers:  68.430 68.430 68.430
      (box expansion for 'iso' is  69.6%)
  Solvent unit box:                     18.774 18.774 18.774
The number of boxes:  x= 4  y= 4  z= 4
Adding box at: x=0  y=0  z=0
Center of solvent box is: 28.161524, 28.161524, 28.161524
Adding box at: x=0  y=0  z=1
Center of solvent box is: 28.161524, 28.161524, 9.387175
Adding box at: x=0  y=0  z=2
Center of solvent box is: 28.161524, 28.161524, -9.387175
Adding box at: x=0  y=0  z=3
Center of solvent box is: 28.161524, 28.161524, -28.161524
Adding box at: x=0  y=1  z=0
Center of solvent box is: 28.161524, 9.387175, 28.161524
Adding box at: x=0  y=1  z=1
Center of solvent box is: 28.161524, 9.387175, 9.387175
Adding box at: x=0  y=1  z=2
Center of solvent box is: 28.161524, 9.387175, -9.387175
Adding box at: x=0  y=1  z=3
Center of solvent box is: 28.161524, 9.387175, -28.161524
Adding box at: x=0  y=2  z=0
Center of solvent box is: 28.161524, -9.387175, 28.161524
Adding box at: x=0  y=2  z=1
Center of solvent box is: 28.161524, -9.387175, 9.387175
Adding box at: x=0  y=2  z=2
Center of solvent box is: 28.161524, -9.387175, -9.387175
Adding box at: x=0  y=2  z=3
Center of solvent box is: 28.161524, -9.387175, -28.161524
Adding box at: x=0  y=3  z=0
Center of solvent box is: 28.161524, -28.161524, 28.161524
Adding box at: x=0  y=3  z=1
Center of solvent box is: 28.161524, -28.161524, 9.387175
Adding box at: x=0  y=3  z=2
Center of solvent box is: 28.161524, -28.161524, -9.387175
Adding box at: x=0  y=3  z=3
Center of solvent box is: 28.161524, -28.161524, -28.161524
Adding box at: x=1  y=0  z=0
Center of solvent box is: 9.387175, 28.161524, 28.161524
Adding box at: x=1  y=0  z=1
Center of solvent box is: 9.387175, 28.161524, 9.387175
Adding box at: x=1  y=0  z=2
Center of solvent box is: 9.387175, 28.161524, -9.387175
Adding box at: x=1  y=0  z=3
Center of solvent box is: 9.387175, 28.161524, -28.161524
Adding box at: x=1  y=1  z=0
Center of solvent box is: 9.387175, 9.387175, 28.161524
Adding box at: x=1  y=1  z=1
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=1  y=1  z=2
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=1  y=1  z=3
Center of solvent box is: 9.387175, 9.387175, -28.161524
Adding box at: x=1  y=2  z=0
Center of solvent box is: 9.387175, -9.387175, 28.161524
Adding box at: x=1  y=2  z=1
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=1  y=2  z=2
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1  y=2  z=3
Center of solvent box is: 9.387175, -9.387175, -28.161524
Adding box at: x=1  y=3  z=0
Center of solvent box is: 9.387175, -28.161524, 28.161524
Adding box at: x=1  y=3  z=1
Center of solvent box is: 9.387175, -28.161524, 9.387175
Adding box at: x=1  y=3  z=2
Center of solvent box is: 9.387175, -28.161524, -9.387175
Adding box at: x=1  y=3  z=3
Center of solvent box is: 9.387175, -28.161524, -28.161524
Adding box at: x=2  y=0  z=0
Center of solvent box is: -9.387175, 28.161524, 28.161524
Adding box at: x=2  y=0  z=1
Center of solvent box is: -9.387175, 28.161524, 9.387175
Adding box at: x=2  y=0  z=2
Center of solvent box is: -9.387175, 28.161524, -9.387175
Adding box at: x=2  y=0  z=3
Center of solvent box is: -9.387175, 28.161524, -28.161524
Adding box at: x=2  y=1  z=0
Center of solvent box is: -9.387175, 9.387175, 28.161524
Adding box at: x=2  y=1  z=1
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=2  y=1  z=2
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=2  y=1  z=3
Center of solvent box is: -9.387175, 9.387175, -28.161524
Adding box at: x=2  y=2  z=0
Center of solvent box is: -9.387175, -9.387175, 28.161524
Adding box at: x=2  y=2  z=1
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=2  y=2  z=2
Center of solvent box is: -9.387175, -9.387175, -9.387175
Adding box at: x=2  y=2  z=3
Center of solvent box is: -9.387175, -9.387175, -28.161524
Adding box at: x=2  y=3  z=0
Center of solvent box is: -9.387175, -28.161524, 28.161524
Adding box at: x=2  y=3  z=1
Center of solvent box is: -9.387175, -28.161524, 9.387175
Adding box at: x=2  y=3  z=2
Center of solvent box is: -9.387175, -28.161524, -9.387175
Adding box at: x=2  y=3  z=3
Center of solvent box is: -9.387175, -28.161524, -28.161524
Adding box at: x=3  y=0  z=0
Center of solvent box is: -28.161524, 28.161524, 28.161524
Adding box at: x=3  y=0  z=1
Center of solvent box is: -28.161524, 28.161524, 9.387175
Adding box at: x=3  y=0  z=2
Center of solvent box is: -28.161524, 28.161524, -9.387175
Adding box at: x=3  y=0  z=3
Center of solvent box is: -28.161524, 28.161524, -28.161524
Adding box at: x=3  y=1  z=0
Center of solvent box is: -28.161524, 9.387175, 28.161524
Adding box at: x=3  y=1  z=1
Center of solvent box is: -28.161524, 9.387175, 9.387175
Adding box at: x=3  y=1  z=2
Center of solvent box is: -28.161524, 9.387175, -9.387175
Adding box at: x=3  y=1  z=3
Center of solvent box is: -28.161524, 9.387175, -28.161524
Adding box at: x=3  y=2  z=0
Center of solvent box is: -28.161524, -9.387175, 28.161524
Adding box at: x=3  y=2  z=1
Center of solvent box is: -28.161524, -9.387175, 9.387175
Adding box at: x=3  y=2  z=2
Center of solvent box is: -28.161524, -9.387175, -9.387175
Adding box at: x=3  y=2  z=3
Center of solvent box is: -28.161524, -9.387175, -28.161524
Adding box at: x=3  y=3  z=0
Center of solvent box is: -28.161524, -28.161524, 28.161524
Adding box at: x=3  y=3  z=1
Center of solvent box is: -28.161524, -28.161524, 9.387175
Adding box at: x=3  y=3  z=2
Center of solvent box is: -28.161524, -28.161524, -9.387175
Adding box at: x=3  y=3  z=3
Center of solvent box is: -28.161524, -28.161524, -28.161524
  Volume: 167345.679 A^3 (oct)
  Total mass 89609.724 amu,  Density 0.889 g/cc
  Added 4799 residues.
> addIons RNA Cl- 0
addIons: 1st Ion & target are the same charge:
     can't neutralize.
> addIons RNA Na+ 0
9 Na+ ions required to neutralize.
Adding 9 counter ions to "RNA" using 1A grid
Total solute charge:  -9.00  Max atom radius:   2.10
Grid extends from solute vdw + 2.95  to  9.05
Box:
   enclosing:  -22.02 -22.99 -20.30   19.98 27.22 18.12
   sized:			      41.98 41.01 43.70
   edge:        64.00
Resolution:      1.00 Angstrom.
Tree depth: 6
grid build: 1 sec
Volume =  7.35% of box, grid points 19277
Solvent present: replacing closest with ion
	 when steric overlaps occur
Calculating grid charges
charges: 1 sec
(Replacing solvent molecule)
Placed Na+ in RNA at (-2.40, -0.10, 5.84).
(Replacing solvent molecule)
Placed Na+ in RNA at (11.79, 7.67, 3.47).
(Replacing solvent molecule)
Placed Na+ in RNA at (-8.88, -1.30, -7.66).
(Replacing solvent molecule)
Placed Na+ in RNA at (5.46, 1.54, 10.19).
(Replacing solvent molecule)
Placed Na+ in RNA at (-11.92, -1.08, 3.44).
(Replacing solvent molecule)
Placed Na+ in RNA at (10.91, 13.76, -5.83).
(Replacing solvent molecule)
Placed Na+ in RNA at (-6.45, -5.08, 11.20).
(Replacing solvent molecule)
Placed Na+ in RNA at (9.84, -4.61, 8.42).
(Replacing solvent molecule)
Placed Na+ in RNA at (-3.32, -9.99, -7.73).

Done adding ions.
> saveamberparm RNA pdb2mvy.sol.prmtop pdb2mvy.sol.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for  N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for  NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 total 58 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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	4790
  )
 (no restraints)
> savepdb RNA pdb2mvy_tleap.sol.pdb
Writing pdb file: pdb2mvy_tleap.sol.pdb
   printing CRYST1 record to PDB file with box info
> quit
	Quit
