-I: Adding /usr/local/amber14/dat/leap/prep to search path. -I: Adding /usr/local/amber14/dat/leap/lib to search path. -I: Adding /usr/local/amber14/dat/leap/parm to search path. -I: Adding /usr/local/amber14/dat/leap/cmd to search path. -s: Ignoring startup file: leaprc -f: Source tleap.in. Welcome to LEaP! Sourcing: ./tleap.in ----- Source: /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB ----- Source of /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB done Log file: ./leap.log Loading parameters: /usr/local/amber14/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /usr/local/amber14/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /usr/local/amber14/dat/leap/lib/amino12.lib Loading library: /usr/local/amber14/dat/leap/lib/aminoct12.lib Loading library: /usr/local/amber14/dat/leap/lib/aminont12.lib Loading library: /usr/local/amber14/dat/leap/lib/nucleic12.lib Loading library: /usr/local/amber14/dat/leap/lib/atomic_ions.lib Loading library: /usr/local/amber14/dat/leap/lib/solvents.lib ----- Source: /usr/local/amber14/dat/leap/cmd/leaprc.parmbsc0_chiOL4_ezOL1 ----- Source of /usr/local/amber14/dat/leap/cmd/leaprc.parmbsc0_chiOL4_ezOL1 done ----- Source: /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB ----- Source of /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB done Log file: ./leap.log Loading parameters: /usr/local/amber14/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /usr/local/amber14/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /usr/local/amber14/dat/leap/lib/amino12.lib Loading library: /usr/local/amber14/dat/leap/lib/aminoct12.lib Loading library: /usr/local/amber14/dat/leap/lib/aminont12.lib Loading library: /usr/local/amber14/dat/leap/lib/nucleic12.lib Loading library: /usr/local/amber14/dat/leap/lib/atomic_ions.lib Loading library: /usr/local/amber14/dat/leap/lib/solvents.lib Substituting map 0HYP -> NHYP for 0HYP -> NHYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS Substituting map 0G -> G5 for 0G -> G5 Substituting map 1G -> G3 for 1G -> G3 Substituting map 0A -> A5 for 0A -> A5 Substituting map 1A -> A3 for 1A -> A3 Substituting map 0C -> C5 for 0C -> C5 Substituting map 1C -> C3 for 1C -> C3 Substituting map 0U -> U5 for 0U -> U5 Substituting map 1U -> U3 for 1U -> U3 Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map 0RA5 -> A5 for 0RA5 -> A5 Substituting map 1RA3 -> A3 for 1RA3 -> A3 Substituting map RA -> A for RA -> A Substituting map 0RC5 -> C5 for 0RC5 -> C5 Substituting map 1RC3 -> C3 for 1RC3 -> C3 Substituting map RC -> C for RC -> C Substituting map 0RG5 -> G5 for 0RG5 -> G5 Substituting map 1RG3 -> G3 for 1RG3 -> G3 Substituting map RG -> G for RG -> G Substituting map 0RU5 -> U5 for 0RU5 -> U5 Substituting map 1RU3 -> U3 for 1RU3 -> U3 Substituting map RU -> U for RU -> U Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map O2* -> O2' for O2* -> O2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2' for H2*1 -> H2' Substituting map H2*2 -> H2'' for H2*2 -> H2'' Substituting map H2'1 -> H2' for H2'1 -> H2' Substituting map H2'2 -> H2'' for H2'2 -> H2'' Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5' for H5*1 -> H5' Substituting map H5*2 -> H5'' for H5*2 -> H5'' Substituting map H5'1 -> H5' for H5'1 -> H5' Substituting map H5'2 -> H5'' for H5'2 -> H5'' Substituting map HO'2 -> HO2' for HO'2 -> HO2' Substituting map H5T -> HO5' for H5T -> HO5' Substituting map H3T -> HO3' for H3T -> HO3' Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> OP1 for OA -> OP1 Substituting map OB -> OP2 for OB -> OP2 Substituting map O1P -> OP1 for O1P -> OP1 Substituting map O2P -> OP2 for O2P -> OP2 Substituting map H2*1 -> H2'1 for H2*1 -> H2' Substituting map H2*2 -> H2'2 for H2*2 -> H2'' Loading Prep file: /usr/local/amber14/dat/leap/prep/dna_nuc94-bsc0_chiOl4-ezOL1.in Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-GUANOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - OH group and 3' - OH group Loading parameters: /usr/local/amber14/dat/leap/parm/frcmod.parmbsc0_ezOL1 Reading force field modification type file (frcmod) Reading title: original Loading parameters: /usr/local/amber14/dat/leap/parm/frcmod.chiOL4 Reading force field modification type file (frcmod) Reading title: Original parameter file Loading parameters: /usr/local/amber14/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) Loading PDB file: ./cMYC121G4_noH.pdb -- residue 10: duplicate [ C2] atoms (total 2) -- residue 10: duplicate [ C4] atoms (total 2) -- residue 10: duplicate [ C5] atoms (total 2) -- residue 10: duplicate [ C6] atoms (total 2) -- residue 10: duplicate [ N1] atoms (total 2) -- residue 10: duplicate [ N3] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Created a new atom named: P within residue: .R Created a new atom named: OP1 within residue: .R Created a new atom named: OP2 within residue: .R Created a new atom named: OP3 within residue: .R Created a new atom named: N9 within residue: .R
Created a new atom named: N7 within residue: .R
Created a new atom named: C8 within residue: .R
Created a new atom named: N6 within residue: .R
total atoms in file: 522 Leap added 273 missing atoms according to residue templates: 273 H / lone pairs The file contained 8 atoms not in residue templates Checking 'mol'.... WARNING: There is a bond of 5.891966 angstroms between: ------- .R.A and .R.A

WARNING: The unperturbed charge of the unit: -23.000000 is not zero. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R

.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. Warning: Close contact of 0.818434 angstroms between .R.A and .R.A

Warning: Close contact of 1.482293 angstroms between .R.A

and .R.A Warning: Close contact of 1.485337 angstroms between .R.A

and .R.A Warning: Close contact of 1.214984 angstroms between .R

.A and .R
.A Warning: Close contact of 1.272457 angstroms between .R
.A and .R
.A Warning: Close contact of 1.465421 angstroms between .R.A and .R.A

Warning: Close contact of 1.396379 angstroms between .R.A and .R.A Warning: Close contact of 1.422230 angstroms between .R
.A and .R
.A Warning: Close contact of 1.233784 angstroms between .R
.A and .R
.A Warning: Close contact of 1.087795 angstroms between .R
.A and .R
.A Warning: Close contact of 0.462036 angstroms between .R
.A and .R
.A Warning: Close contact of 1.290916 angstroms between .R
.A and .R
.A Warning: Close contact of 1.194655 angstroms between .R
.A
and .R
.A Warning: Close contact of 1.431015 angstroms between .R
.A and .R
.A Warning: Close contact of 1.400589 angstroms between .R
.A and .R
.A Warning: Close contact of 0.114769 angstroms between .R
.A and .R
.A Warning: Close contact of 0.109991 angstroms between .R
.A and .R
.A Warning: Close contact of 1.315453 angstroms between .R
.A and .R
.A Warning: Close contact of 1.460451 angstroms between .R
.A and .R
.A Warning: Close contact of 1.379355 angstroms between .R
.A and .R
.A Warning: Close contact of 1.321065 angstroms between .R
.A and .R
.A Warning: Close contact of 1.413788 angstroms between .R.A and .R.A Warning: Close contact of 0.967387 angstroms between .R.A and .R.A Warning: Close contact of 1.100319 angstroms between .R.A and .R.A Warning: Close contact of 1.131973 angstroms between .R.A and .R.A Warning: Close contact of 0.393705 angstroms between .R.A and .R.A Warning: Close contact of 1.306659 angstroms between .R.A and .R.A Warning: Close contact of 1.474850 angstroms between .R.A and .R.A Warning: Close contact of 0.949723 angstroms between .R.A and .R.A Warning: Close contact of 1.306360 angstroms between .R.A and .R.A Warning: Close contact of 0.836268 angstroms between .R.A and .R.A Warning: Close contact of 1.033024 angstroms between .R.A and .R.A Warning: Close contact of 1.497796 angstroms between .R.A and .R.A Warning: Close contact of 1.361060 angstroms between .R.A and .R.A Warning: Close contact of 0.480322 angstroms between .R.A and .R.A Warning: Close contact of 1.104714 angstroms between .R.A and .R.A Warning: Close contact of 0.707878 angstroms between .R.A and .R.A Warning: Close contact of 1.439463 angstroms between .R.A and .R.A Warning: Close contact of 1.158659 angstroms between .R.A and .R.A Warning: Close contact of 0.904453 angstroms between .R.A and .R.A Warning: Close contact of 0.561235 angstroms between .R.A and .R.A Warning: Close contact of 0.761339 angstroms between .R.A and .R.A Warning: Close contact of 1.256011 angstroms between .R.A and .R.A Warning: Close contact of 1.483587 angstroms between .R.A and .R.A Warning: Close contact of 0.676733 angstroms between .R.A and .R.A Warning: Close contact of 0.611242 angstroms between .R.A and .R.A Warning: Close contact of 1.189430 angstroms between .R.A and .R.A Warning: Close contact of 0.632057 angstroms between .R.A and .R.A Warning: Close contact of 0.872879 angstroms between .R.A and .R.A Warning: Close contact of 0.992257 angstroms between .R.A and .R.A Warning: Close contact of 0.517912 angstroms between .R.A and .R.A Warning: Close contact of 1.446491 angstroms between .R.A and .R.A Warning: Close contact of 0.457975 angstroms between .R.A

and .R.A

Warning: Close contact of 0.664619 angstroms between .R.A

and .R.A Warning: Close contact of 1.484409 angstroms between .R.A and .R.A Warning: Close contact of 1.424465 angstroms between .R.A and .R.A

Warning: Close contact of 0.532895 angstroms between .R.A and .R.A Warning: Close contact of 1.116945 angstroms between .R.A and .R.A Warning: Close contact of 0.864688 angstroms between .R.A and .R.A Warning: Close contact of 1.494688 angstroms between .R.A and .R.A Warning: Close contact of 1.434340 angstroms between .R.A and .R.A Warning: Close contact of 0.730841 angstroms between .R.A and .R.A Warning: Close contact of 1.312377 angstroms between .R.A and .R.A Warning: Close contact of 0.863107 angstroms between .R.A and .R.A Warning: Close contact of 1.270941 angstroms between .R.A and .R.A Warning: Close contact of 1.163524 angstroms between .R.A and .R.A Warning: Close contact of 1.379618 angstroms between .R.A and .R.A Warning: Close contact of 1.281662 angstroms between .R.A and .R.A Warning: Close contact of 1.165796 angstroms between .R.A and .R.A Warning: Close contact of 1.257844 angstroms between .R.A and .R.A Warning: Close contact of 0.847945 angstroms between .R.A and .R.A Warning: Close contact of 0.699010 angstroms between .R.A and .R.A Warning: Close contact of 0.836916 angstroms between .R.A and .R.A Warning: Close contact of 1.384061 angstroms between .R.A and .R.A Warning: Close contact of 0.736035 angstroms between .R.A and .R.A Warning: Close contact of 0.863914 angstroms between .R.A and .R.A Warning: Close contact of 0.666542 angstroms between .R.A and .R.A Warning: Close contact of 1.446997 angstroms between .R.A and .R.A Warning: Close contact of 0.633010 angstroms between .R.A and .R.A Warning: Close contact of 1.404790 angstroms between .R.A and .R.A Warning: Close contact of 1.041608 angstroms between .R.A and .R.A Warning: Close contact of 0.555242 angstroms between .R.A and .R.A Warning: Close contact of 1.186702 angstroms between .R.A and .R.A Warning: Close contact of 0.823621 angstroms between .R.A and .R.A Warning: Close contact of 1.212993 angstroms between .R.A and .R.A Warning: Close contact of 1.134753 angstroms between .R.A and .R.A Warning: Close contact of 0.685288 angstroms between .R.A and .R.A Warning: Close contact of 1.344350 angstroms between .R.A and .R.A Warning: Close contact of 0.724316 angstroms between .R.A and .R.A Warning: Close contact of 0.540351 angstroms between .R.A and .R.A Warning: Close contact of 1.391349 angstroms between .R.A and .R.A Warning: Close contact of 0.831996 angstroms between .R.A and .R.A Warning: Close contact of 1.202151 angstroms between .R.A and .R.A

Warning: Close contact of 0.801660 angstroms between .R.A and .R.A Warning: Close contact of 1.125915 angstroms between .R.A and .R.A Warning: Close contact of 1.030414 angstroms between .R.A

and .R.A Warning: Close contact of 0.560433 angstroms between .R.A

and .R.A

Warning: Close contact of 1.472762 angstroms between .R.A and .R.A Checking parameters for unit 'mol'. Checking for bond parameters. Checking for angle parameters. check: Errors: 8 Warnings: 100 Writing pdb file: cMYC121G4_leap.pdb