log started: Wed May  3 19:25:18 2017

Log file: ./leap.log
>> #
>> # ----- NOTE: this is designed for PDB format 3!
>> #        Uses ff99bsc0+OL15 for DNA
>> #                (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
>> #                (bsc0): Perez et al. Biophys J. 92: 3817, 2007
>> #                (OL15): Zgarbova et al. JCTC 11: 5723, 2015
>> #	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" }
>> 	{ "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" }
>> }
>> #
>> #	Define the PDB name map for the nucleic acids
>> #
>> addPdbResMap {
>>   { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
>>   { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
>>   { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
>>   { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
>> #  some really old Amber residue names, assuming DNA:
>>   { 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" }
>> 
>> }
>> 
>> #  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''" }
>>   { "'H2'" "H2''" }
>>   { "H3*" "H3'" }
>>   { "H4*" "H4'" }
>>   { "H5*1" "H5'" }
>>   { "H5*2" "H5''" }
>>   { "H5'1" "H5'" }
>>   { "H5'2" "H5''" }
>>   { "'H5'" "H5''" }
>>   { "HO'2" "HO2'" }
>>   { "H5T"  "HO5'" }
>>   { "H3T"  "HO3'" }
>>   { "O1'" "O4'" }
>>   { "OA"  "OP1" }
>>   { "OB"  "OP2" }
>>   { "O1P" "OP1" }
>>   { "O2P" "OP2" }
>> }
>> 
>> #
>> # Load the OL15 force field for DNA
>> # 
>> 
>> addAtomTypes {
>>     { "CJ"  "C" "sp3" }
>>     { "C1"  "C" "sp2" }
>>     { "C2"  "C" "sp2" }
>>     { "C7"  "C" "sp3" }
>> }
>> 
>> loadoff DNA.OL15.lib 
Loading library: //home/luna.kuleuven.be/u0111760/amber/amber16/dat/leap/lib/DNA.OL15.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
>> parm10 = loadamberparams parm10.dat
Loading parameters: //home/luna.kuleuven.be/u0111760/amber/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> loadamberparams frcmod.DNA.OL15
Loading parameters: //home/luna.kuleuven.be/u0111760/amber/amber16/dat/leap/parm/frcmod.DNA.OL15
Reading force field modification type file (frcmod)
Reading title:
OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see http://ffol.upol.cz
> 
> 
> foo = sequence {DT5 DT DT3}
Sequence: DT5
Sequence: DT
Joining DT5 - DT
Sequence: DT3
Joining DT - DT3
> 
> savePdb foo TTT.pdb
Writing pdb file: TTT.pdb
> saveAmberParm foo TTT.prmtop TTT.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
For atom: .R<DT5 1>.A<HO5' 1> Could not find vdW (or other) parameters for type: HO
For atom: .R<DT5 1>.A<O5' 2> Could not find vdW (or other) parameters for type: OH
For atom: .R<DT5 1>.A<H5' 4> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT5 1>.A<H5'' 5> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT5 1>.A<C4' 6> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT5 1>.A<H4' 7> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT5 1>.A<O4' 8> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT5 1>.A<C1' 9> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT5 1>.A<H1' 10> Could not find vdW (or other) parameters for type: H2
For atom: .R<DT5 1>.A<N1 11> Could not find vdW (or other) parameters for type: N*
For atom: .R<DT5 1>.A<C6 12> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT5 1>.A<H6 13> Could not find vdW (or other) parameters for type: H4
For atom: .R<DT5 1>.A<C5 14> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT5 1>.A<C7 15> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT5 1>.A<H71 16> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT5 1>.A<H72 17> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT5 1>.A<H73 18> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT5 1>.A<C4 19> Could not find vdW (or other) parameters for type: C
For atom: .R<DT5 1>.A<O4 20> Could not find vdW (or other) parameters for type: O
For atom: .R<DT5 1>.A<N3 21> Could not find vdW (or other) parameters for type: NA
For atom: .R<DT5 1>.A<H3 22> Could not find vdW (or other) parameters for type: H
For atom: .R<DT5 1>.A<C2 23> Could not find vdW (or other) parameters for type: C
For atom: .R<DT5 1>.A<O2 24> Could not find vdW (or other) parameters for type: O
For atom: .R<DT5 1>.A<H3' 26> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT5 1>.A<C2' 27> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT5 1>.A<H2' 28> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT5 1>.A<H2'' 29> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT5 1>.A<O3' 30> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT 2>.A<P 1> Could not find vdW (or other) parameters for type: P
For atom: .R<DT 2>.A<OP1 2> Could not find vdW (or other) parameters for type: O2
For atom: .R<DT 2>.A<OP2 3> Could not find vdW (or other) parameters for type: O2
For atom: .R<DT 2>.A<O5' 4> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT 2>.A<H5' 6> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT 2>.A<H5'' 7> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT 2>.A<C4' 8> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT 2>.A<H4' 9> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT 2>.A<O4' 10> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT 2>.A<C1' 11> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT 2>.A<H1' 12> Could not find vdW (or other) parameters for type: H2
For atom: .R<DT 2>.A<N1 13> Could not find vdW (or other) parameters for type: N*
For atom: .R<DT 2>.A<C6 14> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT 2>.A<H6 15> Could not find vdW (or other) parameters for type: H4
For atom: .R<DT 2>.A<C5 16> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT 2>.A<C7 17> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT 2>.A<H71 18> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT 2>.A<H72 19> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT 2>.A<H73 20> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT 2>.A<C4 21> Could not find vdW (or other) parameters for type: C
For atom: .R<DT 2>.A<O4 22> Could not find vdW (or other) parameters for type: O
For atom: .R<DT 2>.A<N3 23> Could not find vdW (or other) parameters for type: NA
For atom: .R<DT 2>.A<H3 24> Could not find vdW (or other) parameters for type: H
For atom: .R<DT 2>.A<C2 25> Could not find vdW (or other) parameters for type: C
For atom: .R<DT 2>.A<O2 26> Could not find vdW (or other) parameters for type: O
For atom: .R<DT 2>.A<H3' 28> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT 2>.A<C2' 29> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT 2>.A<H2' 30> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT 2>.A<H2'' 31> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT 2>.A<O3' 32> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT3 3>.A<P 1> Could not find vdW (or other) parameters for type: P
For atom: .R<DT3 3>.A<OP1 2> Could not find vdW (or other) parameters for type: O2
For atom: .R<DT3 3>.A<OP2 3> Could not find vdW (or other) parameters for type: O2
For atom: .R<DT3 3>.A<O5' 4> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT3 3>.A<H5' 6> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT3 3>.A<H5'' 7> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT3 3>.A<C4' 8> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT3 3>.A<H4' 9> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT3 3>.A<O4' 10> Could not find vdW (or other) parameters for type: OS
For atom: .R<DT3 3>.A<C1' 11> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT3 3>.A<H1' 12> Could not find vdW (or other) parameters for type: H2
For atom: .R<DT3 3>.A<N1 13> Could not find vdW (or other) parameters for type: N*
For atom: .R<DT3 3>.A<C6 14> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT3 3>.A<H6 15> Could not find vdW (or other) parameters for type: H4
For atom: .R<DT3 3>.A<C5 16> Could not find vdW (or other) parameters for type: CM
For atom: .R<DT3 3>.A<C7 17> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT3 3>.A<H71 18> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT3 3>.A<H72 19> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT3 3>.A<H73 20> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT3 3>.A<C4 21> Could not find vdW (or other) parameters for type: C
For atom: .R<DT3 3>.A<O4 22> Could not find vdW (or other) parameters for type: O
For atom: .R<DT3 3>.A<N3 23> Could not find vdW (or other) parameters for type: NA
For atom: .R<DT3 3>.A<H3 24> Could not find vdW (or other) parameters for type: H
For atom: .R<DT3 3>.A<C2 25> Could not find vdW (or other) parameters for type: C
For atom: .R<DT3 3>.A<O2 26> Could not find vdW (or other) parameters for type: O
For atom: .R<DT3 3>.A<H3' 28> Could not find vdW (or other) parameters for type: H1
For atom: .R<DT3 3>.A<C2' 29> Could not find vdW (or other) parameters for type: CT
For atom: .R<DT3 3>.A<H2' 30> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT3 3>.A<H2'' 31> Could not find vdW (or other) parameters for type: HC
For atom: .R<DT3 3>.A<O3' 32> Could not find vdW (or other) parameters for type: OH
For atom: .R<DT3 3>.A<HO3' 33> Could not find vdW (or other) parameters for type: HO
Parameter file was not saved.
> quit 
	Quit