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test_all_lib.log
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/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/amino19.lib
Success: ALA
Setting C=[N+]: CZ - NE
Success: ARG
Success: ASH
Success: ASN
Success: ASP
Success: CYM
Success: CYS
Success: CYX
Success: GLH
Success: GLN
Success: GLU
Success: GLY
HID Leaf Nodes [10, 7]
HID: New Longest Valid Path Found: [10, 12, 13, 7]
HID path [10, 12, 13, 7]
Found path: CE1-NE2-CD2-CG
Setting double bond: CE1 = NE2
Setting double bond: CD2 = CG
Success: HID
HIE Leaf Nodes [9, 13]
HIE: New Longest Valid Path Found: [9, 8, 7, 13]
HIE path [9, 8, 7, 13]
Found path: CE1-ND1-CG-CD2
Setting double bond: ND1 = CE1
Setting double bond: CD2 = CG
Success: HIE
HIP Leaf Nodes [14, 7]
HIP: New Longest Valid Path Found: [14, 7]
HIP path [14, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: HIP
Success: HYP
Success: ILE
Success: LEU
Success: LYN
Success: LYS
Success: MET
PHE Leaf Nodes []
PHE: New Longest Valid Path Found: [8, 7, 16, 14, 12, 10]
PHE path [8, 7, 16, 14, 12, 10]
Found path: CD1-CG-CD2-CE2-CZ-CE1
Setting double bond: CD1 = CG
Setting double bond: CD2 = CE2
Setting double bond: CE1 = CZ
Success: PHE
Success: PRO
Success: SER
Success: THR
TRP Leaf Nodes [8]
TRP: New Longest Valid Path Found: [19, 17, 15, 13, 12, 21, 7, 8]
TRP path [19, 17, 15, 13, 12, 21, 7, 8]
Found path: CE3-CZ3-CH2-CZ2-CE2-CD2-CG-CD1
Setting double bond: CZ3 = CE3
Setting double bond: CZ2 = CH2
Setting double bond: CE2 = CD2
Setting double bond: CD1 = CG
Success: TRP
TYR Leaf Nodes []
TYR: New Longest Valid Path Found: [17, 7, 8, 10, 12, 15]
TYR path [17, 7, 8, 10, 12, 15]
Found path: CD2-CG-CD1-CE1-CZ-CE2
Setting double bond: CD2 = CG
Setting double bond: CD1 = CE1
Setting double bond: CZ = CE2
Success: TYR
Success: VAL
amino19.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/amino19ipq_0.9.lib
Success: ALA
Setting C=[N+]: CZ - NE
Success: ARG
Success: ASH
Success: ASN
Success: ASP
Success: CYM
Success: CYS
Success: CYX
Success: GLH
Success: GLN
Success: GLU
Success: GLY
HID Leaf Nodes [10, 7]
HID: New Longest Valid Path Found: [10, 12, 13, 7]
HID path [10, 12, 13, 7]
Found path: CE1-NE2-CD2-CG
Setting double bond: CE1 = NE2
Setting double bond: CD2 = CG
Success: HID
HIE Leaf Nodes [13, 9]
HIE: New Longest Valid Path Found: [13, 7, 8, 9]
HIE path [13, 7, 8, 9]
Found path: CD2-CG-ND1-CE1
Setting double bond: CD2 = CG
Setting double bond: ND1 = CE1
Success: HIE
HIP Leaf Nodes [14, 7]
HIP: New Longest Valid Path Found: [14, 7]
HIP path [14, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: HIP
Success: ILE
Success: LEU
Success: LYN
Success: LYS
Success: MET
Success: MTB
Success: NLE
PHE Leaf Nodes []
PHE: New Longest Valid Path Found: [10, 8, 7, 16, 14, 12]
PHE path [10, 8, 7, 16, 14, 12]
Found path: CE1-CD1-CG-CD2-CE2-CZ
Setting double bond: CD1 = CE1
Setting double bond: CD2 = CG
Setting double bond: CZ = CE2
Success: PHE
Success: PRO
Success: SER
Success: THR
TRP Leaf Nodes [8]
TRP: New Longest Valid Path Found: [19, 17, 15, 13, 12, 21, 7, 8]
TRP path [19, 17, 15, 13, 12, 21, 7, 8]
Found path: CE3-CZ3-CH2-CZ2-CE2-CD2-CG-CD1
Setting double bond: CZ3 = CE3
Setting double bond: CZ2 = CH2
Setting double bond: CE2 = CD2
Setting double bond: CD1 = CG
Success: TRP
TYR Leaf Nodes []
TYR: New Longest Valid Path Found: [17, 7, 8, 10, 12, 15]
TYR path [17, 7, 8, 10, 12, 15]
Found path: CD2-CG-CD1-CE1-CZ-CE2
Setting double bond: CD2 = CG
Setting double bond: CD1 = CE1
Setting double bond: CZ = CE2
Success: TYR
Success: VAL
amino19ipq_0.9.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminoct19ipq_0.9.lib
Success: CALA
Setting C=[N+]: CZ - NE
Success: CARG
Success: CASH
Success: CASN
Success: CASP
Success: CCYM
Success: CCYS
Success: CCYX
Success: CGLH
Success: CGLN
Success: CGLU
Success: CGLY
CHID Leaf Nodes [10, 7]
CHID: New Longest Valid Path Found: [10, 12, 13, 7]
CHID path [10, 12, 13, 7]
Found path: CE1-NE2-CD2-CG
Setting double bond: CE1 = NE2
Setting double bond: CD2 = CG
Success: CHID
CHIE Leaf Nodes [13, 9]
CHIE: New Longest Valid Path Found: [13, 7, 8, 9]
CHIE path [13, 7, 8, 9]
Found path: CD2-CG-ND1-CE1
Setting double bond: CD2 = CG
Setting double bond: ND1 = CE1
Success: CHIE
CHIP Leaf Nodes [14, 7]
CHIP: New Longest Valid Path Found: [14, 7]
CHIP path [14, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: CHIP
Success: CILE
Success: CLEU
Success: CLYN
Success: CLYS
Success: CMET
Success: CNLE
CPHE Leaf Nodes []
CPHE: New Longest Valid Path Found: [12, 10, 8, 7, 16, 14]
CPHE path [12, 10, 8, 7, 16, 14]
Found path: CZ-CE1-CD1-CG-CD2-CE2
Setting double bond: CE1 = CZ
Setting double bond: CD1 = CG
Setting double bond: CD2 = CE2
Success: CPHE
Success: CPRO
Success: CSER
Success: CTHR
CTRP Leaf Nodes [8]
CTRP: New Longest Valid Path Found: [8, 7, 21, 12, 13, 15, 17, 19]
CTRP path [8, 7, 21, 12, 13, 15, 17, 19]
Found path: CD1-CG-CD2-CE2-CZ2-CH2-CZ3-CE3
Setting double bond: CD1 = CG
Setting double bond: CE2 = CD2
Setting double bond: CZ2 = CH2
Setting double bond: CZ3 = CE3
Success: CTRP
CTYR Leaf Nodes []
CTYR: New Longest Valid Path Found: [17, 7, 8, 10, 12, 15]
CTYR path [17, 7, 8, 10, 12, 15]
Found path: CD2-CG-CD1-CE1-CZ-CE2
Setting double bond: CD2 = CG
Setting double bond: CD1 = CE1
Setting double bond: CZ = CE2
Success: CTYR
Success: CVAL
Success: NHE
Success: NME
aminoct19ipq_0.9.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminont19ipq_0.9.lib
Success: ACE
Success: NALA
Setting C=[N+]: CZ - NE
Success: NARG
Success: NASH
Success: NASN
Success: NASP
Success: NCYM
Success: NCYS
Success: NCYX
Success: NGLH
Success: NGLN
Success: NGLU
Success: NGLY
NHID Leaf Nodes [12, 9]
NHID: New Longest Valid Path Found: [12, 14, 15, 9]
NHID path [12, 14, 15, 9]
Found path: CE1-NE2-CD2-CG
Setting double bond: CE1 = NE2
Setting double bond: CG = CD2
Success: NHID
NHIE Leaf Nodes [15, 11]
NHIE: New Longest Valid Path Found: [15, 9, 10, 11]
NHIE path [15, 9, 10, 11]
Found path: CD2-CG-ND1-CE1
Setting double bond: CG = CD2
Setting double bond: ND1 = CE1
Success: NHIE
NHIP Leaf Nodes [16, 9]
NHIP: New Longest Valid Path Found: [16, 9]
NHIP path [16, 9]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: NHIP
Success: NILE
Success: NLEU
Success: NLYS
Success: NMET
Success: NNLE
NPHE Leaf Nodes []
NPHE: New Longest Valid Path Found: [9, 10, 12, 14, 16, 18]
NPHE path [9, 10, 12, 14, 16, 18]
Found path: CG-CD1-CE1-CZ-CE2-CD2
Setting double bond: CG = CD1
Setting double bond: CE1 = CZ
Setting double bond: CE2 = CD2
Success: NPHE
Success: NPRO
Success: NSER
Success: NTHR
NTRP Leaf Nodes [10]
NTRP: New Longest Valid Path Found: [14, 15, 17, 19, 21, 23, 9, 10]
NTRP path [14, 15, 17, 19, 21, 23, 9, 10]
Found path: CE2-CZ2-CH2-CZ3-CE3-CD2-CG-CD1
Setting double bond: CE2 = CZ2
Setting double bond: CH2 = CZ3
Setting double bond: CE3 = CD2
Setting double bond: CG = CD1
Success: NTRP
NTYR Leaf Nodes []
NTYR: New Longest Valid Path Found: [12, 10, 9, 19, 17, 14]
NTYR path [12, 10, 9, 19, 17, 14]
Found path: CE1-CD1-CG-CD2-CE2-CZ
Setting double bond: CD1 = CE1
Setting double bond: CG = CD2
Setting double bond: CE2 = CZ
Success: NTYR
Success: NVAL
aminont19ipq_0.9.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/phosaa19SB.lib
Success: S1P
Success: SEP
Success: T1P
Success: TPO
Y1P Leaf Nodes []
Y1P: New Longest Valid Path Found: [8, 7, 15, 13, 12, 10]
Y1P path [8, 7, 15, 13, 12, 10]
Found path: CD1-CG-CD2-CE2-CZ-CE1
Setting double bond: CD1 = CG
Setting double bond: CE2 = CD2
Setting double bond: CE1 = CZ
Success: Y1P
PTR Leaf Nodes []
PTR: New Longest Valid Path Found: [13, 12, 10, 8, 7, 15]
PTR path [13, 12, 10, 8, 7, 15]
Found path: CE2-CZ-CE1-CD1-CG-CD2
Setting double bond: CZ = CE2
Setting double bond: CD1 = CE1
Setting double bond: CD2 = CG
Success: PTR
H1D Leaf Nodes [13, 7]
H1D: New Longest Valid Path Found: [13, 7]
H1D path [13, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: H1D
H2D Leaf Nodes [13, 7]
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:372: AmberWarning: residue table predicted 25, not 26 atoms for residue ALY
warnings.warn(
Molecule contains unexpected elements -> template for MSE will be None.
H2D: New Longest Valid Path Found: [13, 7]
H2D path [13, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: H2D
H1E Leaf Nodes [13, 7]
H1E: New Longest Valid Path Found: [13, 7]
H1E path [13, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: H1E
H2E Leaf Nodes [13, 7]
H2E: New Longest Valid Path Found: [13, 7]
H2E path [13, 7]
Found path: CD2-CG
Setting double bond: CD2 = CG
Setting C=[N+]: CE1 - ND1
Success: H2E
phosaa19SB.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/mod_amino19.lib
Success: ALY
AZF Leaf Nodes [18]
AZF: New Longest Valid Path Found: [18, 17, 12, 10, 8, 7, 15, 13]
AZF path [18, 17, 12, 10, 8, 7, 15, 13]
Found path: N2-N1-CZ-CE1-CD1-CG-CD2-CE2
Setting double bond: N1 = N2
Setting double bond: CE1 = CZ
Setting double bond: CD1 = CG
Setting double bond: CE2 = CD2
Success: AZF
CNX Leaf Nodes [33, 12]
CNX: New Longest Valid Path Found: [33, 12]
CNX path [33, 12]
Found path: C2-C3
Setting double bond: C2 = C3
Charging N+: N1
Success: CNX
CYF Leaf Nodes [17]
CYF: New Longest Valid Path Found: [13, 15, 7, 8, 10, 12, 17]
CYF path [13, 15, 7, 8, 10, 12, 17]
Found path: CE2-CD2-CG-CD1-CE1-CZ-C1
Setting double bond: CE2 = CD2
Setting double bond: CD1 = CG
Setting double bond: CE1 = CZ
Success: CYF
We have a problem... MSE
Num Failures: 1 Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/mod_amino19.lib
mod_amino19.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/RNA.lib
A Leaf Nodes [13]
A: New Longest Valid Path Found: [25, 24, 22, 21, 17, 16, 15, 13]
A path [25, 24, 22, 21, 17, 16, 15, 13]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: A
A3 Leaf Nodes [13]
A3: New Longest Valid Path Found: [13, 15, 16, 17, 21, 22, 24, 25]
A3 path [13, 15, 16, 17, 21, 22, 24, 25]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: C8 = N7
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: A3
A5 Leaf Nodes [11]
A5: New Longest Valid Path Found: [15, 19, 20, 22, 23, 14, 13, 11]
A5 path [15, 19, 20, 22, 23, 14, 13, 11]
Found path: C6-N1-C2-N3-C4-C5-N7-C8
Setting double bond: N1 = C6
Setting double bond: C2 = N3
Setting double bond: C5 = C4
Setting double bond: C8 = N7
Success: A5
AN Leaf Nodes [11]
AN: New Longest Valid Path Found: [23, 22, 20, 19, 15, 14, 13, 11]
AN path [23, 22, 20, 19, 15, 14, 13, 11]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: AN
C Leaf Nodes [13, 21]
C: New Longest Valid Path Found: [13, 15, 17, 21]
C path [13, 15, 17, 21]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: C4 = N3
Success: C
C3 Leaf Nodes [13, 21]
C3: New Longest Valid Path Found: [13, 15, 17, 21]
C3 path [13, 15, 17, 21]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: C4 = N3
Success: C3
C5 Leaf Nodes [19, 11]
C5: New Longest Valid Path Found: [19, 15, 13, 11]
C5 path [19, 15, 13, 11]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C6 = C5
Success: C5
CN Leaf Nodes [11, 19]
CN: New Longest Valid Path Found: [11, 13, 15, 19]
CN path [11, 13, 15, 19]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: N3 = C4
Success: CN
G Leaf Nodes [21, 13]
G: New Longest Valid Path Found: [21, 25, 26, 16, 15, 13]
G path [21, 25, 26, 16, 15, 13]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: N3 = C2
Setting double bond: C5 = C4
Setting double bond: C8 = N7
Success: G
G3 Leaf Nodes [13, 21]
G3: New Longest Valid Path Found: [13, 15, 16, 26, 25, 21]
G3 path [13, 15, 16, 26, 25, 21]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: G3
G5 Leaf Nodes [11, 19]
G5: New Longest Valid Path Found: [11, 13, 14, 24, 23, 19]
G5 path [11, 13, 14, 24, 23, 19]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C4 = C5
Setting double bond: C2 = N3
Success: G5
GN Leaf Nodes [19, 11]
GN: New Longest Valid Path Found: [19, 23, 24, 14, 13, 11]
GN path [19, 23, 24, 14, 13, 11]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: C2 = N3
Setting double bond: C4 = C5
Setting double bond: C8 = N7
Success: GN
Success: OHE
U Leaf Nodes [13, 15]
U: New Longest Valid Path Found: [13, 15]
U path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: U
U3 Leaf Nodes [13, 15]
U3: New Longest Valid Path Found: [13, 15]
U3 path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: U3
U5 Leaf Nodes [11, 13]
U5: New Longest Valid Path Found: [11, 13]
U5 path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: U5
UN Leaf Nodes [11, 13]
UN: New Longest Valid Path Found: [11, 13]
UN path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: UN
RNA.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/terminalphos.LJbb-RNA.lib
AMP Leaf Nodes [13]
AMP: New Longest Valid Path Found: [13, 15, 16, 17, 21, 22, 24, 25]
AMP path [13, 15, 16, 17, 21, 22, 24, 25]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: C8 = N7
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: AMP
CMP Leaf Nodes [13, 21]
CMP: New Longest Valid Path Found: [13, 15, 17, 21]
CMP path [13, 15, 17, 21]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: C4 = N3
Success: CMP
GMP Leaf Nodes [21, 13]
GMP: New Longest Valid Path Found: [21, 25, 26, 16, 15, 13]
GMP path [21, 25, 26, 16, 15, 13]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: N3 = C2
Setting double bond: C5 = C4
Setting double bond: C8 = N7
Success: GMP
UMP Leaf Nodes [13, 15]
UMP: New Longest Valid Path Found: [13, 15]
UMP path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: UMP
terminalphos.LJbb-RNA.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/DNA.OL15.lib
DA Leaf Nodes [13]
DA: New Longest Valid Path Found: [25, 24, 22, 21, 17, 16, 15, 13]
DA path [25, 24, 22, 21, 17, 16, 15, 13]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: DA
DA3 Leaf Nodes [13]
DA3: New Longest Valid Path Found: [25, 24, 22, 21, 17, 16, 15, 13]
DA3 path [25, 24, 22, 21, 17, 16, 15, 13]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: DA3
DA5 Leaf Nodes [11]
DA5: New Longest Valid Path Found: [15, 19, 20, 22, 23, 14, 13, 11]
DA5 path [15, 19, 20, 22, 23, 14, 13, 11]
Found path: C6-N1-C2-N3-C4-C5-N7-C8
Setting double bond: N1 = C6
Setting double bond: C2 = N3
Setting double bond: C5 = C4
Setting double bond: C8 = N7
Success: DA5
DAN Leaf Nodes [11]
DAN: New Longest Valid Path Found: [23, 22, 20, 19, 15, 14, 13, 11]
DAN path [23, 22, 20, 19, 15, 14, 13, 11]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: DAN
DC Leaf Nodes [21, 13]
DC: New Longest Valid Path Found: [21, 17, 15, 13]
DC path [21, 17, 15, 13]
Found path: N3-C4-C5-C6
Setting double bond: C4 = N3
Setting double bond: C6 = C5
Success: DC
DC3 Leaf Nodes [13, 21]
DC3: New Longest Valid Path Found: [13, 15, 17, 21]
DC3 path [13, 15, 17, 21]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: C4 = N3
Success: DC3
DC5 Leaf Nodes [19, 11]
DC5: New Longest Valid Path Found: [19, 15, 13, 11]
DC5 path [19, 15, 13, 11]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C6 = C5
Success: DC5
DCN Leaf Nodes [19, 11]
DCN: New Longest Valid Path Found: [19, 15, 13, 11]
DCN path [19, 15, 13, 11]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C6 = C5
Success: DCN
DG Leaf Nodes [13, 21]
DG: New Longest Valid Path Found: [13, 15, 16, 26, 25, 21]
DG path [13, 15, 16, 26, 25, 21]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: DG
DG3 Leaf Nodes [13, 21]
DG3: New Longest Valid Path Found: [13, 15, 16, 26, 25, 21]
DG3 path [13, 15, 16, 26, 25, 21]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: DG3
DG5 Leaf Nodes [11, 19]
DG5: New Longest Valid Path Found: [11, 13, 14, 24, 23, 19]
DG5 path [11, 13, 14, 24, 23, 19]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C4 = C5
Setting double bond: C2 = N3
Success: DG5
DGN Leaf Nodes [19, 11]
DGN: New Longest Valid Path Found: [19, 23, 24, 14, 13, 11]
DGN path [19, 23, 24, 14, 13, 11]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: C2 = N3
Setting double bond: C4 = C5
Setting double bond: C8 = N7
Success: DGN
DT Leaf Nodes [13, 15]
DT: New Longest Valid Path Found: [13, 15]
DT path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT
DT3 Leaf Nodes [13, 15]
DT3: New Longest Valid Path Found: [13, 15]
DT3 path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT3
DT5 Leaf Nodes [11, 13]
DT5: New Longest Valid Path Found: [11, 13]
DT5 path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT5
DTN Leaf Nodes [11, 13]
DTN: New Longest Valid Path Found: [11, 13]
DTN path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DTN
DNA.OL15.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/parmBSC1.lib
DA Leaf Nodes [13]
DA: New Longest Valid Path Found: [25, 24, 22, 21, 17, 16, 15, 13]
DA path [25, 24, 22, 21, 17, 16, 15, 13]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: C8 = N7
Success: DA
DA3 Leaf Nodes [13]
DA3: New Longest Valid Path Found: [13, 15, 16, 17, 21, 22, 24, 25]
DA3 path [13, 15, 16, 17, 21, 22, 24, 25]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: C8 = N7
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: DA3
DA5 Leaf Nodes [11]
DA5: New Longest Valid Path Found: [11, 13, 14, 15, 19, 20, 22, 23]
DA5 path [11, 13, 14, 15, 19, 20, 22, 23]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: C8 = N7
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: DA5
DAN Leaf Nodes [11]
DAN: New Longest Valid Path Found: [11, 13, 14, 15, 19, 20, 22, 23]
DAN path [11, 13, 14, 15, 19, 20, 22, 23]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: C8 = N7
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: DAN
DC Leaf Nodes [13, 21]
DC: New Longest Valid Path Found: [13, 15, 17, 21]
DC path [13, 15, 17, 21]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: C4 = N3
Success: DC
DC3 Leaf Nodes [21, 13]
DC3: New Longest Valid Path Found: [21, 17, 15, 13]
DC3 path [21, 17, 15, 13]
Found path: N3-C4-C5-C6
Setting double bond: C4 = N3
Setting double bond: C6 = C5
Success: DC3
DC5 Leaf Nodes [11, 19]
DC5: New Longest Valid Path Found: [11, 13, 15, 19]
DC5 path [11, 13, 15, 19]
Found path: C6-C5-C4-N3
Setting double bond: C6 = C5
Setting double bond: N3 = C4
Success: DC5
DCN Leaf Nodes [19, 11]
DCN: New Longest Valid Path Found: [19, 15, 13, 11]
DCN path [19, 15, 13, 11]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C6 = C5
Success: DCN
DG Leaf Nodes [13, 21]
DG: New Longest Valid Path Found: [13, 15, 16, 26, 25, 21]
DG path [13, 15, 16, 26, 25, 21]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: DG
DG3 Leaf Nodes [21, 13]
DG3: New Longest Valid Path Found: [21, 25, 26, 16, 15, 13]
DG3 path [21, 25, 26, 16, 15, 13]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: N3 = C2
Setting double bond: C5 = C4
Setting double bond: C8 = N7
Success: DG3
DG5 Leaf Nodes [19, 11]
DG5: New Longest Valid Path Found: [19, 23, 24, 14, 13, 11]
DG5 path [19, 23, 24, 14, 13, 11]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: C2 = N3
Setting double bond: C4 = C5
Setting double bond: C8 = N7
Success: DG5
DGN Leaf Nodes [19, 11]
DGN: New Longest Valid Path Found: [19, 23, 24, 14, 13, 11]
DGN path [19, 23, 24, 14, 13, 11]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: C2 = N3
Setting double bond: C4 = C5
Setting double bond: C8 = N7
Success: DGN
DT Leaf Nodes [13, 15]
DT: New Longest Valid Path Found: [13, 15]
DT path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT
DT3 Leaf Nodes [13, 15]
DT3: New Longest Valid Path Found: [13, 15]
DT3 path [13, 15]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT3
DT5 Leaf Nodes [11, 13]
DT5: New Longest Valid Path Found: [11, 13]
DT5 path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DT5
DTN Leaf Nodes [11, 13]
DTN: New Longest Valid Path Found: [11, 13]
DTN path [11, 13]
Found path: C6-C5
Setting double bond: C6 = C5
Success: DTN
parmBSC1.json <-- Json File for New Chemical Templates
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/all_modrna08.lib
13P Leaf Nodes [21, 14]
13P: New Longest Valid Path Found: [21, 14]
13P path [21, 14]
Found path: C6-C5
Setting double bond: C6 = C5
Success: 13P
1MA Leaf Nodes [15, 18, 23]
too many leaf nodes
{15: 2, 18: 1, 23: 3}
Setting C=[N+]: C6 - N6
1MA: New Longest Valid Path Found: [15, 16, 17, 25, 24, 23]
1MA path [15, 16, 17, 25, 24, 23]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: N7 = C8
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: 1MA
1MG Leaf Nodes [15, 21]
1MG: New Longest Valid Path Found: [15, 16, 17, 26, 25, 21]
1MG path [15, 16, 17, 26, 25, 21]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: N7 = C8
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Success: 1MG
1MI Leaf Nodes [21, 15]
1MI: New Longest Valid Path Found: [21, 22, 23, 17, 16, 15]
1MI path [21, 22, 23, 17, 16, 15]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: C2 = N3
Setting double bond: C5 = C4
Setting double bond: N7 = C8
Success: 1MI
1MP Leaf Nodes [21, 14]
1MP: New Longest Valid Path Found: [21, 14]
1MP path [21, 14]
Found path: C6-C5
Setting double bond: C6 = C5
Success: 1MP
26A Leaf Nodes [15]
26A: New Longest Valid Path Found: [44, 43, 42, 41, 18, 17, 16, 15]
26A path [44, 43, 42, 41, 18, 17, 16, 15]
Found path: C4-N3-C2-N1-C6-C5-N7-C8
Setting double bond: N3 = C4
Setting double bond: N1 = C2
Setting double bond: C5 = C6
Setting double bond: N7 = C8
Success: 26A
27G Leaf Nodes [17, 21]
27G: New Longest Valid Path Found: [17, 29, 28, 21]
27G path [17, 29, 28, 21]
Found path: C5-C4-N3-C2
Setting double bond: C5 = C4
Setting double bond: N3 = C2
Setting C=[N+]: C8 - N9
Success: 27G
2MA Leaf Nodes [15]
2MA: New Longest Valid Path Found: [15, 16, 17, 18, 22, 23, 24, 25]
2MA path [15, 16, 17, 18, 22, 23, 24, 25]
Found path: C8-N7-C5-C6-N1-C2-N3-C4
Setting double bond: N7 = C8
Setting double bond: C5 = C6
Setting double bond: N1 = C2
Setting double bond: N3 = C4
Success: 2MA
2MG Leaf Nodes [21, 15]
2MG: New Longest Valid Path Found: [21, 28, 29, 17, 16, 15]
2MG path [21, 28, 29, 17, 16, 15]
Found path: C2-N3-C4-C5-N7-C8
Setting double bond: N3 = C2
Setting double bond: C5 = C4
Setting double bond: N7 = C8
Success: 2MG
2RG Leaf Nodes [36, 42]
2RG: New Longest Valid Path Found: [36, 37, 38, 47, 46, 42]
2RG path [36, 37, 38, 47, 46, 42]
Found path: C8-N7-C5-C4-N3-C2
Setting double bond: C8 = N7
Setting double bond: C5 = C4
Setting double bond: C2 = N3
Success: 2RG
2SC Leaf Nodes [23, 15]
2SC: New Longest Valid Path Found: [23, 22, 18, 17, 15]
2SC path [23, 22, 18, 17, 15]
Found path: C6-C5-C4-N3-C2
Setting double bond: C5 = C6
Setting double bond: N3 = C4
Setting C=[N+]: C2 - N1
We have a problem... 2SC
Corrupt atomic number for S2 in 2SC
2SU Leaf Nodes [20, 21]
2SU: New Longest Valid Path Found: [20, 21]
2SU path [20, 21]
Found path: C5-C6
Setting double bond: C5 = C6
Setting C=[N+]: C2 - N1
We have a problem... 2SU
Corrupt atomic number for S2 in 2SU
3AU Leaf Nodes [20, 21]
3AU: New Longest Valid Path Found: [20, 21]
3AU path [20, 21]
Found path: C5-C6
Setting double bond: C5 = C6
Success: 3AU
3MC Leaf Nodes [19, 22]
3MC: New Longest Valid Path Found: [19, 18, 21, 22]
3MC path [19, 18, 21, 22]
Found path: N4-C4-C5-C6
Setting double bond: C4 = N4
Setting double bond: C5 = C6
Success: 3MC
3MP Leaf Nodes [21, 14]
3MP: New Longest Valid Path Found: [21, 14]
3MP path [21, 14]
Found path: C6-C5
Setting double bond: C6 = C5
Success: 3MP
3MU Leaf Nodes [20, 21]
3MU: New Longest Valid Path Found: [20, 21]
3MU path [20, 21]
Found path: C5-C6
Setting double bond: C5 = C6
Success: 3MU
4AC Leaf Nodes [17, 28]
4AC: New Longest Valid Path Found: [17, 18, 27, 28]
4AC path [17, 18, 27, 28]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C5 = C6
Success: 4AC
4MC Leaf Nodes [17, 26]
4MC: New Longest Valid Path Found: [17, 18, 25, 26]
4MC path [17, 18, 25, 26]
Found path: N3-C4-C5-C6
Setting double bond: N3 = C4
Setting double bond: C5 = C6
Success: 4MC
4SU Leaf Nodes [18, 21]
4SU: New Longest Valid Path Found: [18, 20, 21]
4SU path [18, 20, 21]
Found path: C4-C5-C6
Setting double bond: C4 = C5
Setting C=[N+]: C6 - N1
We have a problem... 4SU
Corrupt atomic number for S4 in 4SU
52U Leaf Nodes [20, 21]
52U: New Longest Valid Path Found: [20, 21]
52U path [20, 21]
Found path: C5-C6
Setting double bond: C5 = C6
Setting C=[N+]: C2 - N1
We have a problem... 52U
Corrupt atomic number for S2 in 52U
5AU Leaf Nodes [20, 21]
5AU: New Longest Valid Path Found: [20, 21]