Hello everyone,
I've been following this finish this tutorial, but applied to a new
chromophore ligand:
http://ambermd.org/tutorials/basic/tutorial5/
Although, when I try to apply the same steps to the new chromophore, I get
this error in xLeap:
************************************************************
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************************************************************
************************
Checking Unit.
WARNING: There is a bond of 25.389654 angstroms between:
------- .R<HIE 136>.A<C 16> and .R<ALA 137>.A<N 1>
WARNING: The unperturbed charge of the unit: -22.999999 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - NT
Building angle parameters.
Could not find angle parameter: O - C - NT
Could not find angle parameter: C - NT - CT
Could not find angle parameter: CX - C - NT
Building proper torsion parameters.
** No torsion terms for O-C-NT-CT
** No torsion terms for CX-C-NT-CT
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
old PREP-specified impropers:
<CH6 197>: CA1 N3 C1 N2
<CH6 197>: C2 CB2 CA2 N2
<CH6 197>: CG2 CA2 CB2 HB2
<CH6 197>: CD2 CD1 CG2 CB2
<CH6 197>: CG2 CE2 CD2 HD2
<CH6 197>: CD2 CZ CE2 HE2
<CH6 197>: CE2 CE1 CZ OH
<CH6 197>: CZ CD1 CE1 HE1
<CH6 197>: CG2 CE1 CD1 HD1
<CH6 197>: CA2 N3 C2 O2
<CH6 197>: C2 C1 N3 CA3
<CH6 197>: CA3 +M C3 O3
total 1240 improper torsions applied
12 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
************************************************************
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************************************************************
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>From my understanding, I am supposed to remove all lines in the frcmod1.cro
file that contain ATTN, since these angle parameters are not present and
then follow the specific steps for xLeap.
Maybe I didn't, but I'd greatly appreciate some help on this. I'm a bit
confused.
Here are my leap.log, frcmod1.cro [I called it ch6.cro], frcmod2.cro[I
called it ch62.cro] and ch6.prepin files.
Leap.log
************************************************************
***********************************
log started: Tue Nov 7 08:56:07 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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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
>
> set default PBRadii mbondi3
Using ArgH and AspGluO modified Bondi2 radii
> loadAmberPrep ch6.prepin
Loading Prep file: ./ch6.prepin
Loaded UNIT: CH6
> loadAmberparams ch62.cro
Loading parameters: ./ch62.cro
Reading title:
> loadAmaberparams ch63.cro
ERROR: syntax error
> loadAmberParams ch63.cro
Loading parameters: ./ch63.cro
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> source leaprc.water.tip3p
----- Source: /home/taylormi/Softwares/amber16/dat/leap/cmd/leaprc.
water.tip3p
----- Source of
/home/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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)
>>
>
> loadamberaparms frcmod.ionsjc_tip3p
ERROR: syntax error
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /home/taylormi/Softwares/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)
> pdb = loadpdb 4I2Y.pdb
Loading PDB file: ./4I2Y.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER.
(Residue 1: ARG, Nonterminal, was not found in name map.)
(Residue 2: ARG, Nonterminal, was not found in name map.)
(Residue 3: LYS, Nonterminal, was not found in name map.)
(Residue 4: TRP, Nonterminal, was not found in name map.)
(Residue 5: ASN, Nonterminal, was not found in name map.)
(Residue 6: LYS, Nonterminal, was not found in name map.)
(Residue 7: ALA, Nonterminal, was not found in name map.)
(Residue 8: GLY, Nonterminal, was not found in name map.)
(Residue 9: HIS, Nonterminal, was not found in name map.)
(Residue 10: ALA, Nonterminal, was not found in name map.)
(Residue 11: VAL, Nonterminal, was not found in name map.)
(Residue 12: ARG, Nonterminal, was not found in name map.)
(Residue 13: ALA, Nonterminal, was not found in name map.)
(Residue 14: ILE, Nonterminal, was not found in name map.)
(Residue 15: GLY, Nonterminal, was not found in name map.)
(Residue 16: ARG, Nonterminal, was not found in name map.)
(Residue 17: LEU, Nonterminal, was not found in name map.)
(Residue 18: SER, Nonterminal, was not found in name map.)
(Residue 19: SER, Nonterminal, was not found in name map.)
(Residue 20: ARG, Nonterminal, was not found in name map.)
(Residue 21: TRP, Nonterminal, was not found in name map.)
(Residue 22: VAL, Nonterminal, was not found in name map.)
(Residue 23: SER, Nonterminal, was not found in name map.)
(Residue 24: GLU, Nonterminal, was not found in name map.)
(Residue 25: TRP, Nonterminal, was not found in name map.)
(Residue 26: MET, Nonterminal, was not found in name map.)
(Residue 27: TYR, Nonterminal, was not found in name map.)
(Residue 28: PRO, Nonterminal, was not found in name map.)
(Residue 29: GLU, Nonterminal, was not found in name map.)
(Residue 30: ASP, Nonterminal, was not found in name map.)
(Residue 31: GLY, Nonterminal, was not found in name map.)
(Residue 32: ALA, Nonterminal, was not found in name map.)
(Residue 33: LEU, Nonterminal, was not found in name map.)
(Residue 34: LYS, Nonterminal, was not found in name map.)
(Residue 35: SER, Nonterminal, was not found in name map.)
(Residue 36: VAL, Nonterminal, was not found in name map.)
(Residue 37: ILE, Nonterminal, was not found in name map.)
(Residue 38: LYS, Nonterminal, was not found in name map.)
(Residue 39: GLU, Nonterminal, was not found in name map.)
(Residue 40: GLY, Nonterminal, was not found in name map.)
(Residue 41: LEU, Nonterminal, was not found in name map.)
(Residue 42: ARG, Nonterminal, was not found in name map.)
(Residue 43: LEU, Nonterminal, was not found in name map.)
(Residue 44: LYS, Nonterminal, was not found in name map.)
(Residue 45: ASP, Nonterminal, was not found in name map.)
(Residue 46: GLY, Nonterminal, was not found in name map.)
(Residue 47: GLY, Nonterminal, was not found in name map.)
(Residue 48: HIS, Nonterminal, was not found in name map.)
(Residue 49: TYR, Nonterminal, was not found in name map.)
(Residue 50: ALA, Nonterminal, was not found in name map.)
(Residue 51: ALA, Nonterminal, was not found in name map.)
(Residue 52: GLU, Nonterminal, was not found in name map.)
(Residue 53: VAL, Nonterminal, was not found in name map.)
(Residue 54: LYS, Nonterminal, was not found in name map.)
(Residue 55: THR, Nonterminal, was not found in name map.)
(Residue 56: THR, Nonterminal, was not found in name map.)
(Residue 57: TYR, Nonterminal, was not found in name map.)
(Residue 58: LYS, Nonterminal, was not found in name map.)
(Residue 59: ALA, Nonterminal, was not found in name map.)
(Residue 60: LYS, Nonterminal, was not found in name map.)
(Residue 61: LYS, Nonterminal, was not found in name map.)
(Residue 62: PRO, Nonterminal, was not found in name map.)
(Residue 63: VAL, Nonterminal, was not found in name map.)
(Residue 64: GLN, Nonterminal, was not found in name map.)
(Residue 65: LEU, Nonterminal, was not found in name map.)
(Residue 66: PRO, Nonterminal, was not found in name map.)
(Residue 67: GLY, Nonterminal, was not found in name map.)
(Residue 68: ALA, Nonterminal, was not found in name map.)
(Residue 69: TYR, Nonterminal, was not found in name map.)
(Residue 70: ILE, Nonterminal, was not found in name map.)
(Residue 71: VAL, Nonterminal, was not found in name map.)
(Residue 72: ASP, Nonterminal, was not found in name map.)
(Residue 73: ILE, Nonterminal, was not found in name map.)
(Residue 74: LYS, Nonterminal, was not found in name map.)
(Residue 75: LEU, Nonterminal, was not found in name map.)
(Residue 76: ASP, Nonterminal, was not found in name map.)
(Residue 77: ILE, Nonterminal, was not found in name map.)
(Residue 78: VAL, Nonterminal, was not found in name map.)
(Residue 79: SER, Nonterminal, was not found in name map.)
(Residue 80: HIS, Nonterminal, was not found in name map.)
(Residue 81: ASN, Nonterminal, was not found in name map.)
(Residue 82: GLU, Nonterminal, was not found in name map.)
(Residue 83: ASP, Nonterminal, was not found in name map.)
(Residue 84: TYR, Nonterminal, was not found in name map.)
(Residue 85: THR, Nonterminal, was not found in name map.)
(Residue 86: ILE, Nonterminal, was not found in name map.)
(Residue 87: VAL, Nonterminal, was not found in name map.)
(Residue 88: GLU, Nonterminal, was not found in name map.)
(Residue 89: GLN, Nonterminal, was not found in name map.)
(Residue 90: CYS, Nonterminal, was not found in name map.)
(Residue 91: GLU, Nonterminal, was not found in name map.)
(Residue 92: ARG, Nonterminal, was not found in name map.)
(Residue 93: ALA, Nonterminal, was not found in name map.)
(Residue 94: GLU, Nonterminal, was not found in name map.)
(Residue 95: GLY, Nonterminal, was not found in name map.)
(Residue 96: ARG, Nonterminal, was not found in name map.)
(Residue 97: HIS, Nonterminal, was not found in name map.)
(Residue 98: ALA, Nonterminal, was not found in name map.)
(Residue 99: ILE, Nonterminal, was not found in name map.)
(Residue 100: ILE, Nonterminal, was not found in name map.)
(Residue 101: LYS, Nonterminal, was not found in name map.)
(Residue 102: GLU, Nonterminal, was not found in name map.)
(Residue 103: PHE, Nonterminal, was not found in name map.)
(Residue 104: MET, Nonterminal, was not found in name map.)
(Residue 105: ARG, Nonterminal, was not found in name map.)
(Residue 106: PHE, Nonterminal, was not found in name map.)
(Residue 107: LYS, Nonterminal, was not found in name map.)
(Residue 108: VAL, Nonterminal, was not found in name map.)
(Residue 109: HIS, Nonterminal, was not found in name map.)
(Residue 110: MET, Nonterminal, was not found in name map.)
(Residue 111: GLU, Nonterminal, was not found in name map.)
(Residue 112: GLY, Nonterminal, was not found in name map.)
(Residue 113: SER, Nonterminal, was not found in name map.)
(Residue 114: VAL, Nonterminal, was not found in name map.)
(Residue 115: ASN, Nonterminal, was not found in name map.)
(Residue 116: GLY, Nonterminal, was not found in name map.)
(Residue 117: HIS, Nonterminal, was not found in name map.)
(Residue 118: GLU, Nonterminal, was not found in name map.)
(Residue 119: PHE, Nonterminal, was not found in name map.)
(Residue 120: GLU, Nonterminal, was not found in name map.)
(Residue 121: ILE, Nonterminal, was not found in name map.)
(Residue 122: GLU, Nonterminal, was not found in name map.)
(Residue 123: GLY, Nonterminal, was not found in name map.)
(Residue 124: GLU, Nonterminal, was not found in name map.)
(Residue 125: GLY, Nonterminal, was not found in name map.)
(Residue 126: GLU, Nonterminal, was not found in name map.)
(Residue 127: GLY, Nonterminal, was not found in name map.)
(Residue 128: ARG, Nonterminal, was not found in name map.)
(Residue 129: PRO, Nonterminal, was not found in name map.)
(Residue 130: TYR, Nonterminal, was not found in name map.)
(Residue 131: GLU, Nonterminal, was not found in name map.)
(Residue 132: ALA, Nonterminal, was not found in name map.)
(Residue 133: PHE, Nonterminal, was not found in name map.)
(Residue 134: GLN, Nonterminal, was not found in name map.)
(Residue 135: THR, Nonterminal, was not found in name map.)
(Residue 136: ALA, Nonterminal, was not found in name map.)
(Residue 137: LYS, Nonterminal, was not found in name map.)
(Residue 138: LEU, Nonterminal, was not found in name map.)
(Residue 139: LYS, Nonterminal, was not found in name map.)
(Residue 140: VAL, Nonterminal, was not found in name map.)
(Residue 141: THR, Nonterminal, was not found in name map.)
(Residue 142: LYS, Nonterminal, was not found in name map.)
(Residue 143: GLY, Nonterminal, was not found in name map.)
(Residue 144: GLY, Nonterminal, was not found in name map.)
(Residue 145: PRO, Nonterminal, was not found in name map.)
(Residue 146: LEU, Nonterminal, was not found in name map.)
(Residue 147: PRO, Nonterminal, was not found in name map.)
(Residue 148: PHE, Nonterminal, was not found in name map.)
(Residue 149: ALA, Nonterminal, was not found in name map.)
(Residue 150: TRP, Nonterminal, was not found in name map.)
(Residue 151: ASP, Nonterminal, was not found in name map.)
(Residue 152: ILE, Nonterminal, was not found in name map.)
(Residue 153: LEU, Nonterminal, was not found in name map.)
(Residue 154: SER, Nonterminal, was not found in name map.)
(Residue 155: LEU, Nonterminal, was not found in name map.)
(Residue 156: GLN, Nonterminal, was not found in name map.)
(Residue 157: PHE, Nonterminal, was not found in name map.)
(Residue 158: CH6, Nonterminal, was not found in name map.)
(Residue 159: SER, Nonterminal, was not found in name map.)
(Residue 160: LYS, Nonterminal, was not found in name map.)
(Residue 161: ALA, Nonterminal, was not found in name map.)
(Residue 162: TYR, Nonterminal, was not found in name map.)
(Residue 163: ILE, Nonterminal, was not found in name map.)
(Residue 164: LYS, Nonterminal, was not found in name map.)
(Residue 165: HIS, Nonterminal, was not found in name map.)
(Residue 166: PRO, Nonterminal, was not found in name map.)
(Residue 167: ALA, Nonterminal, was not found in name map.)
(Residue 168: ASP, Nonterminal, was not found in name map.)
(Residue 169: ILE, Nonterminal, was not found in name map.)
(Residue 170: PRO, Nonterminal, was not found in name map.)
(Residue 171: ASP, Nonterminal, was not found in name map.)
(Residue 172: TYR, Nonterminal, was not found in name map.)
(Residue 173: PHE, Nonterminal, was not found in name map.)
(Residue 174: LYS, Nonterminal, was not found in name map.)
(Residue 175: LEU, Nonterminal, was not found in name map.)
(Residue 176: SER, Nonterminal, was not found in name map.)
(Residue 177: PHE, Nonterminal, was not found in name map.)
(Residue 178: PRO, Nonterminal, was not found in name map.)
(Residue 179: GLU, Nonterminal, was not found in name map.)
(Residue 180: GLY, Nonterminal, was not found in name map.)
(Residue 181: PHE, Nonterminal, was not found in name map.)
(Residue 182: ARG, Nonterminal, was not found in name map.)
(Residue 183: TRP, Nonterminal, was not found in name map.)
(Residue 184: GLU, Nonterminal, was not found in name map.)
(Residue 185: ARG, Nonterminal, was not found in name map.)
(Residue 186: VAL, Nonterminal, was not found in name map.)
(Residue 187: MET, Nonterminal, was not found in name map.)
(Residue 188: ILE, Nonterminal, was not found in name map.)
(Residue 189: PHE, Nonterminal, was not found in name map.)
(Residue 190: GLU, Nonterminal, was not found in name map.)
(Residue 191: ASP, Nonterminal, was not found in name map.)
(Residue 192: GLY, Nonterminal, was not found in name map.)
(Residue 193: GLY, Nonterminal, was not found in name map.)
(Residue 194: ILE, Nonterminal, was not found in name map.)
(Residue 195: ILE, Nonterminal, was not found in name map.)
(Residue 196: HIS, Nonterminal, was not found in name map.)
(Residue 197: VAL, Nonterminal, was not found in name map.)
(Residue 198: ASN, Nonterminal, was not found in name map.)
(Residue 199: GLN, Nonterminal, was not found in name map.)
(Residue 200: ASP, Nonterminal, was not found in name map.)
(Residue 201: SER, Nonterminal, was not found in name map.)
(Residue 202: SER, Nonterminal, was not found in name map.)
(Residue 203: LEU, Nonterminal, was not found in name map.)
(Residue 204: GLN, Nonterminal, was not found in name map.)
(Residue 205: ASP, Nonterminal, was not found in name map.)
(Residue 206: GLY, Nonterminal, was not found in name map.)
(Residue 207: VAL, Nonterminal, was not found in name map.)
(Residue 208: PHE, Nonterminal, was not found in name map.)
(Residue 209: ILE, Nonterminal, was not found in name map.)
(Residue 210: TYR, Nonterminal, was not found in name map.)
(Residue 211: LYS, Nonterminal, was not found in name map.)
(Residue 212: VAL, Nonterminal, was not found in name map.)
(Residue 213: LYS, Nonterminal, was not found in name map.)
(Residue 214: LEU, Nonterminal, was not found in name map.)
(Residue 215: ARG, Nonterminal, was not found in name map.)
(Residue 216: GLY, Nonterminal, was not found in name map.)
(Residue 217: THR, Nonterminal, was not found in name map.)
(Residue 218: ASN, Nonterminal, was not found in name map.)
(Residue 219: PHE, Nonterminal, was not found in name map.)
(Residue 220: PRO, Nonterminal, was not found in name map.)
(Residue 221: PRO, Nonterminal, was not found in name map.)
(Residue 222: ASP, Nonterminal, was not found in name map.)
(Residue 223: GLY, Nonterminal, was not found in name map.)
(Residue 224: PRO, Nonterminal, was not found in name map.)
(Residue 225: VAL, Nonterminal, was not found in name map.)
(Residue 226: MET, Nonterminal, was not found in name map.)
(Residue 227: GLN, Nonterminal, was not found in name map.)
(Residue 228: LYS, Nonterminal, was not found in name map.)
(Residue 229: LYS, Nonterminal, was not found in name map.)
(Residue 230: THR, Nonterminal, was not found in name map.)
(Residue 231: MET, Nonterminal, was not found in name map.)
(Residue 232: GLY, Nonterminal, was not found in name map.)
(Residue 233: TRP, Nonterminal, was not found in name map.)
(Residue 234: GLU, Nonterminal, was not found in name map.)
(Residue 235: PRO, Nonterminal, was not found in name map.)
(Residue 236: THR, Nonterminal, was not found in name map.)
(Residue 237: ARG, Nonterminal, was not found in name map.)
(Residue 238: ASP, Nonterminal, was not found in name map.)
(Residue 239: GLN, Nonterminal, was not found in name map.)
(Residue 240: LEU, Nonterminal, was not found in name map.)
(Residue 241: THR, Nonterminal, was not found in name map.)
(Residue 242: GLU, Nonterminal, was not found in name map.)
(Residue 243: GLU, Nonterminal, was not found in name map.)
(Residue 244: GLN, Nonterminal, was not found in name map.)
(Residue 245: ILE, Nonterminal, was not found in name map.)
(Residue 246: ALA, Nonterminal, was not found in name map.)
(Residue 247: GLU, Nonterminal, was not found in name map.)
(Residue 248: PHE, Nonterminal, was not found in name map.)
(Residue 249: LYS, Nonterminal, was not found in name map.)
(Residue 250: GLU, Nonterminal, was not found in name map.)
(Residue 251: ALA, Nonterminal, was not found in name map.)
(Residue 252: PHE, Nonterminal, was not found in name map.)
(Residue 253: SER, Nonterminal, was not found in name map.)
(Residue 254: LEU, Nonterminal, was not found in name map.)
(Residue 255: PHE, Nonterminal, was not found in name map.)
(Residue 256: ASP, Nonterminal, was not found in name map.)
(Residue 257: LYS, Nonterminal, was not found in name map.)
(Residue 258: ASP, Nonterminal, was not found in name map.)
(Residue 259: GLY, Nonterminal, was not found in name map.)
(Residue 260: ASP, Nonterminal, was not found in name map.)
(Residue 261: GLY, Nonterminal, was not found in name map.)
(Residue 262: THR, Nonterminal, was not found in name map.)
(Residue 263: ILE, Nonterminal, was not found in name map.)
(Residue 264: THR, Nonterminal, was not found in name map.)
(Residue 265: THR, Nonterminal, was not found in name map.)
(Residue 266: LYS, Nonterminal, was not found in name map.)
(Residue 267: GLU, Nonterminal, was not found in name map.)
(Residue 268: LEU, Nonterminal, was not found in name map.)
(Residue 269: GLY, Nonterminal, was not found in name map.)
(Residue 270: THR, Nonterminal, was not found in name map.)
(Residue 271: VAL, Nonterminal, was not found in name map.)
(Residue 272: LEU, Nonterminal, was not found in name map.)
(Residue 273: ARG, Nonterminal, was not found in name map.)
(Residue 274: SER, Nonterminal, was not found in name map.)
(Residue 275: LEU, Nonterminal, was not found in name map.)
(Residue 276: GLY, Nonterminal, was not found in name map.)
(Residue 277: GLN, Nonterminal, was not found in name map.)
(Residue 278: ASN, Nonterminal, was not found in name map.)
(Residue 279: PRO, Nonterminal, was not found in name map.)
(Residue 280: THR, Nonterminal, was not found in name map.)
(Residue 281: GLU, Nonterminal, was not found in name map.)
(Residue 282: ALA, Nonterminal, was not found in name map.)
(Residue 283: GLU, Nonterminal, was not found in name map.)
(Residue 284: LEU, Nonterminal, was not found in name map.)
(Residue 285: GLN, Nonterminal, was not found in name map.)
(Residue 286: ASP, Nonterminal, was not found in name map.)
(Residue 287: MET, Nonterminal, was not found in name map.)
(Residue 288: ILE, Nonterminal, was not found in name map.)
(Residue 289: ASN, Nonterminal, was not found in name map.)
(Residue 290: GLU, Nonterminal, was not found in name map.)
(Residue 291: VAL, Nonterminal, was not found in name map.)
(Residue 292: ASP, Nonterminal, was not found in name map.)
(Residue 293: ALA, Nonterminal, was not found in name map.)
(Residue 294: ASP, Nonterminal, was not found in name map.)
(Residue 295: GLY, Nonterminal, was not found in name map.)
(Residue 296: ASP, Nonterminal, was not found in name map.)
(Residue 297: GLY, Nonterminal, was not found in name map.)
(Residue 298: THR, Nonterminal, was not found in name map.)
(Residue 299: PHE, Nonterminal, was not found in name map.)
(Residue 300: ASP, Nonterminal, was not found in name map.)
(Residue 301: PHE, Nonterminal, was not found in name map.)
(Residue 302: PRO, Nonterminal, was not found in name map.)
(Residue 303: GLU, Nonterminal, was not found in name map.)
(Residue 304: PHE, Nonterminal, was not found in name map.)
(Residue 305: LEU, Nonterminal, was not found in name map.)
(Residue 306: THR, Nonterminal, was not found in name map.)
(Residue 307: MET, Nonterminal, was not found in name map.)
(Residue 308: MET, Nonterminal, was not found in name map.)
(Residue 309: ALA, Nonterminal, was not found in name map.)
(Residue 310: ARG, Nonterminal, was not found in name map.)
(Residue 311: LYS, Nonterminal, was not found in name map.)
(Residue 312: MET, Nonterminal, was not found in name map.)
(Residue 313: ASN, Nonterminal, was not found in name map.)
(Residue 314: ASP, Nonterminal, was not found in name map.)
(Residue 315: SER, Nonterminal, was not found in name map.)
(Residue 316: ASP, Nonterminal, was not found in name map.)
(Residue 317: SER, Nonterminal, was not found in name map.)
(Residue 318: GLU, Nonterminal, was not found in name map.)
(Residue 319: GLU, Nonterminal, was not found in name map.)
(Residue 320: GLU, Nonterminal, was not found in name map.)
(Residue 321: ILE, Nonterminal, was not found in name map.)
(Residue 322: ARG, Nonterminal, was not found in name map.)
(Residue 323: GLU, Nonterminal, was not found in name map.)
(Residue 324: ALA, Nonterminal, was not found in name map.)
(Residue 325: PHE, Nonterminal, was not found in name map.)
(Residue 326: ARG, Nonterminal, was not found in name map.)
(Residue 327: VAL, Nonterminal, was not found in name map.)
(Residue 328: PHE, Nonterminal, was not found in name map.)
(Residue 329: ASP, Nonterminal, was not found in name map.)
(Residue 330: LYS, Nonterminal, was not found in name map.)
(Residue 331: ASP, Nonterminal, was not found in name map.)
(Residue 332: GLY, Nonterminal, was not found in name map.)
(Residue 333: ASN, Nonterminal, was not found in name map.)
(Residue 334: GLY, Nonterminal, was not found in name map.)
(Residue 335: TYR, Nonterminal, was not found in name map.)
(Residue 336: ILE, Nonterminal, was not found in name map.)
(Residue 337: GLY, Nonterminal, was not found in name map.)
(Residue 338: ALA, Nonterminal, was not found in name map.)
(Residue 339: ALA, Nonterminal, was not found in name map.)
(Residue 340: GLU, Nonterminal, was not found in name map.)
(Residue 341: LEU, Nonterminal, was not found in name map.)
(Residue 342: ARG, Nonterminal, was not found in name map.)
(Residue 343: HIS, Nonterminal, was not found in name map.)
(Residue 344: VAL, Nonterminal, was not found in name map.)
(Residue 345: MET, Nonterminal, was not found in name map.)
(Residue 346: THR, Nonterminal, was not found in name map.)
(Residue 347: ASP, Nonterminal, was not found in name map.)
(Residue 348: LEU, Nonterminal, was not found in name map.)
(Residue 349: GLY, Nonterminal, was not found in name map.)
(Residue 350: GLU, Nonterminal, was not found in name map.)
(Residue 351: LYS, Nonterminal, was not found in name map.)
(Residue 352: LEU, Nonterminal, was not found in name map.)
(Residue 353: THR, Nonterminal, was not found in name map.)
(Residue 354: ASP, Nonterminal, was not found in name map.)
(Residue 355: GLU, Nonterminal, was not found in name map.)
(Residue 356: GLU, Nonterminal, was not found in name map.)
(Residue 357: VAL, Nonterminal, was not found in name map.)
(Residue 358: ASP, Nonterminal, was not found in name map.)
(Residue 359: GLU, Nonterminal, was not found in name map.)
(Residue 360: MET, Nonterminal, was not found in name map.)
(Residue 361: ILE, Nonterminal, was not found in name map.)
(Residue 362: ARG, Nonterminal, was not found in name map.)
(Residue 363: VAL, Nonterminal, was not found in name map.)
(Residue 364: ALA, Nonterminal, was not found in name map.)
(Residue 365: ASP, Nonterminal, was not found in name map.)
(Residue 366: ILE, Nonterminal, was not found in name map.)
(Residue 367: ASP, Nonterminal, was not found in name map.)
(Residue 368: GLY, Nonterminal, was not found in name map.)
(Residue 369: ASP, Nonterminal, was not found in name map.)
(Residue 370: GLY, Nonterminal, was not found in name map.)
(Residue 371: GLN, Nonterminal, was not found in name map.)
(Residue 372: VAL, Nonterminal, was not found in name map.)
(Residue 373: ASN, Nonterminal, was not found in name map.)
(Residue 374: TYR, Nonterminal, was not found in name map.)
(Residue 375: GLU, Nonterminal, was not found in name map.)
(Residue 376: GLU, Nonterminal, was not found in name map.)
(Residue 377: PHE, Nonterminal, was not found in name map.)
(Residue 378: VAL, Nonterminal, was not found in name map.)
(Residue 379: GLN, Nonterminal, was not found in name map.)
(Residue 380: MET, Nonterminal, was not found in name map.)
Mapped residue MET, term: Terminal/last, seq. number: 381 to: CMET.
Joining NSER - ARG
Joining ARG - ARG
Joining ARG - LYS
Joining LYS - TRP
Joining TRP - ASN
Joining ASN - LYS
Joining LYS - ALA
Joining ALA - GLY
Joining GLY - HIE
Joining HIE - ALA
Joining ALA - VAL
Joining VAL - ARG
Joining ARG - ALA
Joining ALA - ILE
Joining ILE - GLY
Joining GLY - ARG
Joining ARG - LEU
Joining LEU - SER
Joining SER - SER
Joining SER - ARG
Joining ARG - TRP
Joining TRP - VAL
Joining VAL - SER
Joining SER - GLU
Joining GLU - TRP
Joining TRP - MET
Joining MET - TYR
Joining TYR - PRO
Joining PRO - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - ALA
Joining ALA - LEU
Joining LEU - LYS
Joining LYS - SER
Joining SER - VAL
Joining VAL - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - GLY
Joining GLY - LEU
Joining LEU - ARG
Joining ARG - LEU
Joining LEU - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - HIE
Joining HIE - TYR
Joining TYR - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - VAL
Joining VAL - LYS
Joining LYS - THR
Joining THR - THR
Joining THR - TYR
Joining TYR - LYS
Joining LYS - ALA
Joining ALA - LYS
Joining LYS - LYS
Joining LYS - PRO
Joining PRO - VAL
Joining VAL - GLN
Joining GLN - LEU
Joining LEU - PRO
Joining PRO - GLY
Joining GLY - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - VAL
Joining VAL - ASP
Joining ASP - ILE
Joining ILE - LYS
Joining LYS - LEU
Joining LEU - ASP
Joining ASP - ILE
Joining ILE - VAL
Joining VAL - SER
Joining SER - HIE
Joining HIE - ASN
Joining ASN - GLU
Joining GLU - ASP
Joining ASP - TYR
Joining TYR - THR
Joining THR - ILE
Joining ILE - VAL
Joining VAL - GLU
Joining GLU - GLN
Joining GLN - CYS
Joining CYS - GLU
Joining GLU - ARG
Joining ARG - ALA
Joining ALA - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - HIE
Joining HIE - ALA
Joining ALA - ILE
Joining ILE - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - PHE
Joining PHE - MET
Joining MET - ARG
Joining ARG - PHE
Joining PHE - LYS
Joining LYS - VAL
Joining VAL - HIE
Joining HIE - MET
Joining MET - GLU
Joining GLU - GLY
Joining GLY - SER
Joining SER - VAL
Joining VAL - ASN
Joining ASN - GLY
Joining GLY - HIE
Joining HIE - GLU
Joining GLU - PHE
Joining PHE - GLU
Joining GLU - ILE
Joining ILE - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - PRO
Joining PRO - TYR
Joining TYR - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - GLN
Joining GLN - THR
Joining THR - ALA
Joining ALA - LYS
Joining LYS - LEU
Joining LEU - LYS
Joining LYS - VAL
Joining VAL - THR
Joining THR - LYS
Joining LYS - GLY
Joining GLY - GLY
Joining GLY - PRO
Joining PRO - LEU
Joining LEU - PRO
Joining PRO - PHE
Joining PHE - ALA
Joining ALA - TRP
Joining TRP - ASP
Joining ASP - ILE
Joining ILE - LEU
Joining LEU - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - PHE
Joining PHE - CH6
Joining CH6 - SER
Joining SER - LYS
Joining LYS - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - LYS
Joining LYS - HIE
Joining HIE - PRO
Joining PRO - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - PRO
Joining PRO - ASP
Joining ASP - TYR
Joining TYR - PHE
Joining PHE - LYS
Joining LYS - LEU
Joining LEU - SER
Joining SER - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - GLY
Joining GLY - PHE
Joining PHE - ARG
Joining ARG - TRP
Joining TRP - GLU
Joining GLU - ARG
Joining ARG - VAL
Joining VAL - MET
Joining MET - ILE
Joining ILE - PHE
Joining PHE - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - ILE
Joining ILE - ILE
Joining ILE - HIE
Joining HIE - VAL
Joining VAL - ASN
Joining ASN - GLN
Joining GLN - ASP
Joining ASP - SER
Joining SER - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - GLY
Joining GLY - VAL
Joining VAL - PHE
Joining PHE - ILE
Joining ILE - TYR
Joining TYR - LYS
Joining LYS - VAL
Joining VAL - LYS
Joining LYS - LEU
Joining LEU - ARG
Joining ARG - GLY
Joining GLY - THR
Joining THR - ASN
Joining ASN - PHE
Joining PHE - PRO
Joining PRO - PRO
Joining PRO - ASP
Joining ASP - GLY
Joining GLY - PRO
Joining PRO - VAL
Joining VAL - MET
Joining MET - GLN
Joining GLN - LYS
Joining LYS - LYS
Joining LYS - THR
Joining THR - MET
Joining MET - GLY
Joining GLY - TRP
Joining TRP - GLU
Joining GLU - PRO
Joining PRO - THR
Joining THR - ARG
Joining ARG - ASP
Joining ASP - GLN
Joining GLN - LEU
Joining LEU - THR
Joining THR - GLU
Joining GLU - GLU
Joining GLU - GLN
Joining GLN - ILE
Joining ILE - ALA
Joining ALA - GLU
Joining GLU - PHE
Joining PHE - LYS
Joining LYS - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - SER
Joining SER - LEU
Joining LEU - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - ILE
Joining ILE - THR
Joining THR - THR
Joining THR - LYS
Joining LYS - GLU
Joining GLU - LEU
Joining LEU - GLY
Joining GLY - THR
Joining THR - VAL
Joining VAL - LEU
Joining LEU - ARG
Joining ARG - SER
Joining SER - LEU
Joining LEU - GLY
Joining GLY - GLN
Joining GLN - ASN
Joining ASN - PRO
Joining PRO - THR
Joining THR - GLU
Joining GLU - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - MET
Joining MET - ILE
Joining ILE - ASN
Joining ASN - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - ALA
Joining ALA - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - PHE
Joining PHE - ASP
Joining ASP - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - PHE
Joining PHE - LEU
Joining LEU - THR
Joining THR - MET
Joining MET - MET
Joining MET - ALA
Joining ALA - ARG
Joining ARG - LYS
Joining LYS - MET
Joining MET - ASN
Joining ASN - ASP
Joining ASP - SER
Joining SER - ASP
Joining ASP - SER
Joining SER - GLU
Joining GLU - GLU
Joining GLU - GLU
Joining GLU - ILE
Joining ILE - ARG
Joining ARG - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - ARG
Joining ARG - VAL
Joining VAL - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASN
Joining ASN - GLY
Joining GLY - TYR
Joining TYR - ILE
Joining ILE - GLY
Joining GLY - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - ARG
Joining ARG - HIE
Joining HIE - VAL
Joining VAL - MET
Joining MET - THR
Joining THR - ASP
Joining ASP - LEU
Joining LEU - GLY
Joining GLY - GLU
Joining GLU - LYS
Joining LYS - LEU
Joining LEU - THR
Joining THR - ASP
Joining ASP - GLU
Joining GLU - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - GLU
Joining GLU - MET
Joining MET - ILE
Joining ILE - ARG
Joining ARG - VAL
Joining VAL - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - GLN
Joining GLN - VAL
Joining VAL - ASN
Joining ASN - TYR
Joining TYR - GLU
Joining GLU - GLU
Joining GLU - PHE
Joining PHE - VAL
Joining VAL - GLN
Joining GLN - MET
Joining MET - CMET
Added missing heavy atom: .R<CMET 420>.A<OXT 18>
total atoms in file: 3074
Leap added 2968 missing atoms according to residue templates:
1 Heavy
2967 H / lone pairs
> solvatebox pdb tip3pbox 10.0
solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> solvatebox pdb TIP3PBOX 10.0
Solute vdw bounding box: 47.448 63.375 77.601
Total bounding box for atom centers: 67.448 83.375 97.601
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 4 y= 5 z= 6
Adding box at: x=0 y=0 z=0
Center of solvent box is: 28.161524, 37.548698, 46.935873
Adding box at: x=0 y=0 z=1
Center of solvent box is: 28.161524, 37.548698, 28.161524
Adding box at: x=0 y=0 z=2
Center of solvent box is: 28.161524, 37.548698, 9.387175
Adding box at: x=0 y=0 z=3
Center of solvent box is: 28.161524, 37.548698, -9.387175
Adding box at: x=0 y=0 z=4
Center of solvent box is: 28.161524, 37.548698, -28.161524
Adding box at: x=0 y=0 z=5
Center of solvent box is: 28.161524, 37.548698, -46.935873
Adding box at: x=0 y=1 z=0
Center of solvent box is: 28.161524, 18.774349, 46.935873
Adding box at: x=0 y=1 z=1
Center of solvent box is: 28.161524, 18.774349, 28.161524
Adding box at: x=0 y=1 z=2
Center of solvent box is: 28.161524, 18.774349, 9.387175
Adding box at: x=0 y=1 z=3
Center of solvent box is: 28.161524, 18.774349, -9.387175
Adding box at: x=0 y=1 z=4
Center of solvent box is: 28.161524, 18.774349, -28.161524
Adding box at: x=0 y=1 z=5
Center of solvent box is: 28.161524, 18.774349, -46.935873
Adding box at: x=0 y=2 z=0
Center of solvent box is: 28.161524, 0.000000, 46.935873
Adding box at: x=0 y=2 z=1
Center of solvent box is: 28.161524, 0.000000, 28.161524
Adding box at: x=0 y=2 z=2
Center of solvent box is: 28.161524, 0.000000, 9.387175
Adding box at: x=0 y=2 z=3
Center of solvent box is: 28.161524, 0.000000, -9.387175
Adding box at: x=0 y=2 z=4
Center of solvent box is: 28.161524, 0.000000, -28.161524
Adding box at: x=0 y=2 z=5
Center of solvent box is: 28.161524, 0.000000, -46.935873
Adding box at: x=0 y=3 z=0
Center of solvent box is: 28.161524, -18.774349, 46.935873
Adding box at: x=0 y=3 z=1
Center of solvent box is: 28.161524, -18.774349, 28.161524
Adding box at: x=0 y=3 z=2
Center of solvent box is: 28.161524, -18.774349, 9.387175
Adding box at: x=0 y=3 z=3
Center of solvent box is: 28.161524, -18.774349, -9.387175
Adding box at: x=0 y=3 z=4
Center of solvent box is: 28.161524, -18.774349, -28.161524
Adding box at: x=0 y=3 z=5
Center of solvent box is: 28.161524, -18.774349, -46.935873
Adding box at: x=0 y=4 z=0
Center of solvent box is: 28.161524, -37.548698, 46.935873
Adding box at: x=0 y=4 z=1
Center of solvent box is: 28.161524, -37.548698, 28.161524
Adding box at: x=0 y=4 z=2
Center of solvent box is: 28.161524, -37.548698, 9.387175
Adding box at: x=0 y=4 z=3
Center of solvent box is: 28.161524, -37.548698, -9.387175
Adding box at: x=0 y=4 z=4
Center of solvent box is: 28.161524, -37.548698, -28.161524
Adding box at: x=0 y=4 z=5
Center of solvent box is: 28.161524, -37.548698, -46.935873
Adding box at: x=1 y=0 z=0
Center of solvent box is: 9.387175, 37.548698, 46.935873
Adding box at: x=1 y=0 z=1
Center of solvent box is: 9.387175, 37.548698, 28.161524
Adding box at: x=1 y=0 z=2
Center of solvent box is: 9.387175, 37.548698, 9.387175
Adding box at: x=1 y=0 z=3
Center of solvent box is: 9.387175, 37.548698, -9.387175
Adding box at: x=1 y=0 z=4
Center of solvent box is: 9.387175, 37.548698, -28.161524
Adding box at: x=1 y=0 z=5
Center of solvent box is: 9.387175, 37.548698, -46.935873
Adding box at: x=1 y=1 z=0
Center of solvent box is: 9.387175, 18.774349, 46.935873
Adding box at: x=1 y=1 z=1
Center of solvent box is: 9.387175, 18.774349, 28.161524
Adding box at: x=1 y=1 z=2
Center of solvent box is: 9.387175, 18.774349, 9.387175
Adding box at: x=1 y=1 z=3
Center of solvent box is: 9.387175, 18.774349, -9.387175
Adding box at: x=1 y=1 z=4
Center of solvent box is: 9.387175, 18.774349, -28.161524
Adding box at: x=1 y=1 z=5
Center of solvent box is: 9.387175, 18.774349, -46.935873
Adding box at: x=1 y=2 z=0
Center of solvent box is: 9.387175, 0.000000, 46.935873
Adding box at: x=1 y=2 z=1
Center of solvent box is: 9.387175, 0.000000, 28.161524
Adding box at: x=1 y=2 z=2
Center of solvent box is: 9.387175, 0.000000, 9.387175
Adding box at: x=1 y=2 z=3
Center of solvent box is: 9.387175, 0.000000, -9.387175
Adding box at: x=1 y=2 z=4
Center of solvent box is: 9.387175, 0.000000, -28.161524
Adding box at: x=1 y=2 z=5
Center of solvent box is: 9.387175, 0.000000, -46.935873
Adding box at: x=1 y=3 z=0
Center of solvent box is: 9.387175, -18.774349, 46.935873
Adding box at: x=1 y=3 z=1
Center of solvent box is: 9.387175, -18.774349, 28.161524
Adding box at: x=1 y=3 z=2
Center of solvent box is: 9.387175, -18.774349, 9.387175
Adding box at: x=1 y=3 z=3
Center of solvent box is: 9.387175, -18.774349, -9.387175
Adding box at: x=1 y=3 z=4
Center of solvent box is: 9.387175, -18.774349, -28.161524
Adding box at: x=1 y=3 z=5
Center of solvent box is: 9.387175, -18.774349, -46.935873
Adding box at: x=1 y=4 z=0
Center of solvent box is: 9.387175, -37.548698, 46.935873
Adding box at: x=1 y=4 z=1
Center of solvent box is: 9.387175, -37.548698, 28.161524
Adding box at: x=1 y=4 z=2
Center of solvent box is: 9.387175, -37.548698, 9.387175
Adding box at: x=1 y=4 z=3
Center of solvent box is: 9.387175, -37.548698, -9.387175
Adding box at: x=1 y=4 z=4
Center of solvent box is: 9.387175, -37.548698, -28.161524
Adding box at: x=1 y=4 z=5
Center of solvent box is: 9.387175, -37.548698, -46.935873
Adding box at: x=2 y=0 z=0
Center of solvent box is: -9.387175, 37.548698, 46.935873
Adding box at: x=2 y=0 z=1
Center of solvent box is: -9.387175, 37.548698, 28.161524
Adding box at: x=2 y=0 z=2
Center of solvent box is: -9.387175, 37.548698, 9.387175
Adding box at: x=2 y=0 z=3
Center of solvent box is: -9.387175, 37.548698, -9.387175
Adding box at: x=2 y=0 z=4
Center of solvent box is: -9.387175, 37.548698, -28.161524
Adding box at: x=2 y=0 z=5
Center of solvent box is: -9.387175, 37.548698, -46.935873
Adding box at: x=2 y=1 z=0
Center of solvent box is: -9.387175, 18.774349, 46.935873
Adding box at: x=2 y=1 z=1
Center of solvent box is: -9.387175, 18.774349, 28.161524
Adding box at: x=2 y=1 z=2
Center of solvent box is: -9.387175, 18.774349, 9.387175
Adding box at: x=2 y=1 z=3
Center of solvent box is: -9.387175, 18.774349, -9.387175
Adding box at: x=2 y=1 z=4
Center of solvent box is: -9.387175, 18.774349, -28.161524
Adding box at: x=2 y=1 z=5
Center of solvent box is: -9.387175, 18.774349, -46.935873
Adding box at: x=2 y=2 z=0
Center of solvent box is: -9.387175, 0.000000, 46.935873
Adding box at: x=2 y=2 z=1
Center of solvent box is: -9.387175, 0.000000, 28.161524
Adding box at: x=2 y=2 z=2
Center of solvent box is: -9.387175, 0.000000, 9.387175
Adding box at: x=2 y=2 z=3
Center of solvent box is: -9.387175, 0.000000, -9.387175
Adding box at: x=2 y=2 z=4
Center of solvent box is: -9.387175, 0.000000, -28.161524
Adding box at: x=2 y=2 z=5
Center of solvent box is: -9.387175, 0.000000, -46.935873
Adding box at: x=2 y=3 z=0
Center of solvent box is: -9.387175, -18.774349, 46.935873
Adding box at: x=2 y=3 z=1
Center of solvent box is: -9.387175, -18.774349, 28.161524
Adding box at: x=2 y=3 z=2
Center of solvent box is: -9.387175, -18.774349, 9.387175
Adding box at: x=2 y=3 z=3
Center of solvent box is: -9.387175, -18.774349, -9.387175
Adding box at: x=2 y=3 z=4
Center of solvent box is: -9.387175, -18.774349, -28.161524
Adding box at: x=2 y=3 z=5
Center of solvent box is: -9.387175, -18.774349, -46.935873
Adding box at: x=2 y=4 z=0
Center of solvent box is: -9.387175, -37.548698, 46.935873
Adding box at: x=2 y=4 z=1
Center of solvent box is: -9.387175, -37.548698, 28.161524
Adding box at: x=2 y=4 z=2
Center of solvent box is: -9.387175, -37.548698, 9.387175
Adding box at: x=2 y=4 z=3
Center of solvent box is: -9.387175, -37.548698, -9.387175
Adding box at: x=2 y=4 z=4
Center of solvent box is: -9.387175, -37.548698, -28.161524
Adding box at: x=2 y=4 z=5
Center of solvent box is: -9.387175, -37.548698, -46.935873
Adding box at: x=3 y=0 z=0
Center of solvent box is: -28.161524, 37.548698, 46.935873
Adding box at: x=3 y=0 z=1
Center of solvent box is: -28.161524, 37.548698, 28.161524
Adding box at: x=3 y=0 z=2
Center of solvent box is: -28.161524, 37.548698, 9.387175
Adding box at: x=3 y=0 z=3
Center of solvent box is: -28.161524, 37.548698, -9.387175
Adding box at: x=3 y=0 z=4
Center of solvent box is: -28.161524, 37.548698, -28.161524
Adding box at: x=3 y=0 z=5
Center of solvent box is: -28.161524, 37.548698, -46.935873
Adding box at: x=3 y=1 z=0
Center of solvent box is: -28.161524, 18.774349, 46.935873
Adding box at: x=3 y=1 z=1
Center of solvent box is: -28.161524, 18.774349, 28.161524
Adding box at: x=3 y=1 z=2
Center of solvent box is: -28.161524, 18.774349, 9.387175
Adding box at: x=3 y=1 z=3
Center of solvent box is: -28.161524, 18.774349, -9.387175
Adding box at: x=3 y=1 z=4
Center of solvent box is: -28.161524, 18.774349, -28.161524
Adding box at: x=3 y=1 z=5
Center of solvent box is: -28.161524, 18.774349, -46.935873
Adding box at: x=3 y=2 z=0
Center of solvent box is: -28.161524, 0.000000, 46.935873
Adding box at: x=3 y=2 z=1
Center of solvent box is: -28.161524, 0.000000, 28.161524
Adding box at: x=3 y=2 z=2
Center of solvent box is: -28.161524, 0.000000, 9.387175
Adding box at: x=3 y=2 z=3
Center of solvent box is: -28.161524, 0.000000, -9.387175
Adding box at: x=3 y=2 z=4
Center of solvent box is: -28.161524, 0.000000, -28.161524
Adding box at: x=3 y=2 z=5
Center of solvent box is: -28.161524, 0.000000, -46.935873
Adding box at: x=3 y=3 z=0
Center of solvent box is: -28.161524, -18.774349, 46.935873
Adding box at: x=3 y=3 z=1
Center of solvent box is: -28.161524, -18.774349, 28.161524
Adding box at: x=3 y=3 z=2
Center of solvent box is: -28.161524, -18.774349, 9.387175
Adding box at: x=3 y=3 z=3
Center of solvent box is: -28.161524, -18.774349, -9.387175
Adding box at: x=3 y=3 z=4
Center of solvent box is: -28.161524, -18.774349, -28.161524
Adding box at: x=3 y=3 z=5
Center of solvent box is: -28.161524, -18.774349, -46.935873
Adding box at: x=3 y=4 z=0
Center of solvent box is: -28.161524, -37.548698, 46.935873
Adding box at: x=3 y=4 z=1
Center of solvent box is: -28.161524, -37.548698, 28.161524
Adding box at: x=3 y=4 z=2
Center of solvent box is: -28.161524, -37.548698, 9.387175
Adding box at: x=3 y=4 z=3
Center of solvent box is: -28.161524, -37.548698, -9.387175
Adding box at: x=3 y=4 z=4
Center of solvent box is: -28.161524, -37.548698, -28.161524
Adding box at: x=3 y=4 z=5
Center of solvent box is: -28.161524, -37.548698, -46.935873
Total vdw box size: 70.504 86.834 100.642 angstroms.
Volume: 616144.445 A^3
Total mass 307210.400 amu, Density 0.828 g/cc
Added 14629 residues.
> addions pdb Na+ 0
23 Na+ ions required to neutralize.
Adding 23 counter ions to "pdb" using 1A grid
Total solute charge: -23.00 Max atom radius: 2.00
Grid extends from solute vdw + 3.95 to 9.95
Box:
enclosing: -32.19 -39.97 -47.29 32.31 40.15 47.33
sized: 95.81 88.03 80.71
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 0 sec
Volume = 3.88% of box, grid points 81348
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 19 sec
(Replacing solvent molecule)
Placed Na+ in pdb at (15.00, -14.69, 5.74).
(Replacing solvent molecule)
Placed Na+ in pdb at (-15.65, -10.78, -38.02).
(Replacing solvent molecule)
Placed Na+ in pdb at (-13.59, -13.95, -12.59).
(Replacing solvent molecule)
Placed Na+ in pdb at (12.65, -8.99, 12.65).
(Replacing solvent molecule)
Placed Na+ in pdb at (0.85, -18.29, -39.07).
(Replacing solvent molecule)
Placed Na+ in pdb at (25.11, -12.30, -1.30).
(Replacing solvent molecule)
Placed Na+ in pdb at (-3.77, 4.08, -13.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (-18.08, -7.06, -22.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (10.07, -17.79, 9.73).
(Replacing solvent molecule)
Placed Na+ in pdb at (0.55, 3.34, -23.82).
(Replacing solvent molecule)
Placed Na+ in pdb at (-14.23, -18.24, 15.27).
(Replacing solvent molecule)
Placed Na+ in pdb at (19.40, -0.55, 1.45).
(Replacing solvent molecule)
Placed Na+ in pdb at (-10.13, -28.92, -31.35).
(Replacing solvent molecule)
Placed Na+ in pdb at (7.06, -31.23, -24.62).
(Replacing solvent molecule)
Placed Na+ in pdb at (-7.22, -10.62, -41.82).
(Replacing solvent molecule)
Placed Na+ in pdb at (-6.87, 11.22, 35.09).
(Replacing solvent molecule)
Placed Na+ in pdb at (20.47, -24.51, -6.71).
(Replacing solvent molecule)
Placed Na+ in pdb at (-12.15, 3.92, -8.73).
(Replacing solvent molecule)
Placed Na+ in pdb at (14.61, 15.34, -3.28).
(Replacing solvent molecule)
Placed Na+ in pdb at (-20.07, -10.13, -13.40).
(Replacing solvent molecule)
Placed Na+ in pdb at (-3.56, -32.92, 1.25).
(Replacing solvent molecule)
Placed Na+ in pdb at (2.31, -26.59, -37.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (11.55, -10.62, 33.28).
Done adding ions.
> saveamberparm pdb prmtop inpcrd
Checking Unit.
WARNING: There is a bond of 25.389654 angstroms between:
------- .R<HIE 136>.A<C 16> and .R<ALA 137>.A<N 1>
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - NT
Building angle parameters.
Could not find angle parameter: O - C - NT
Could not find angle parameter: C - NT - CT
Could not find angle parameter: CX - C - NT
Building proper torsion parameters.
** No torsion terms for O-C-NT-CT
** No torsion terms for CX-C-NT-CT
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
old PREP-specified impropers:
<CH6 197>: CA1 N3 C1 N2
<CH6 197>: C2 CB2 CA2 N2
<CH6 197>: CG2 CA2 CB2 HB2
<CH6 197>: CD2 CD1 CG2 CB2
<CH6 197>: CG2 CE2 CD2 HD2
<CH6 197>: CD2 CZ CE2 HE2
<CH6 197>: CE2 CE1 CZ OH
<CH6 197>: CZ CD1 CE1 HE1
<CH6 197>: CG2 CE1 CD1 HD1
<CH6 197>: CA2 N3 C2 O2
<CH6 197>: C2 C1 N3 CA3
<CH6 197>: CA3 +M C3 O3
total 1240 improper torsions applied
12 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
log started: Tue Nov 7 09:10:48 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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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
>
> set default PBRadii mbondi3
Using ArgH and AspGluO modified Bondi2 radii
> loadAmberPrep ch6.prepin
Loading Prep file: ./ch6.prepin
Loaded UNIT: CH6
> loadAmberParams ch63.cro
Loading parameters: ./ch63.cro
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadAmberParams ch6.cro
Loading parameters: ./ch6.cro
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> source leaprc.water.tip3p
----- Source: /home/taylormi/Softwares/amber16/dat/leap/cmd/leaprc.
water.tip3p
----- Source of
/home/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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)
>>
>
> loadamberparms frcmod.ionsjc_tip3p
ERROR: syntax error
> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /home/taylormi/Softwares/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)
> pdb = 4I2Y.pdb
> solvatebox pdb TIP3PBOX 10.0
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> solvatebox pdb TIP3PBOX 10.0
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> solvatebox pdb tip3pbox 10.0
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> pdb = loadPDB 4I2Y.pdb
Loading PDB file: ./4I2Y.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER.
(Residue 1: ARG, Nonterminal, was not found in name map.)
(Residue 2: ARG, Nonterminal, was not found in name map.)
(Residue 3: LYS, Nonterminal, was not found in name map.)
(Residue 4: TRP, Nonterminal, was not found in name map.)
(Residue 5: ASN, Nonterminal, was not found in name map.)
(Residue 6: LYS, Nonterminal, was not found in name map.)
(Residue 7: ALA, Nonterminal, was not found in name map.)
(Residue 8: GLY, Nonterminal, was not found in name map.)
(Residue 9: HIS, Nonterminal, was not found in name map.)
(Residue 10: ALA, Nonterminal, was not found in name map.)
(Residue 11: VAL, Nonterminal, was not found in name map.)
(Residue 12: ARG, Nonterminal, was not found in name map.)
(Residue 13: ALA, Nonterminal, was not found in name map.)
(Residue 14: ILE, Nonterminal, was not found in name map.)
(Residue 15: GLY, Nonterminal, was not found in name map.)
(Residue 16: ARG, Nonterminal, was not found in name map.)
(Residue 17: LEU, Nonterminal, was not found in name map.)
(Residue 18: SER, Nonterminal, was not found in name map.)
(Residue 19: SER, Nonterminal, was not found in name map.)
(Residue 20: ARG, Nonterminal, was not found in name map.)
(Residue 21: TRP, Nonterminal, was not found in name map.)
(Residue 22: VAL, Nonterminal, was not found in name map.)
(Residue 23: SER, Nonterminal, was not found in name map.)
(Residue 24: GLU, Nonterminal, was not found in name map.)
(Residue 25: TRP, Nonterminal, was not found in name map.)
(Residue 26: MET, Nonterminal, was not found in name map.)
(Residue 27: TYR, Nonterminal, was not found in name map.)
(Residue 28: PRO, Nonterminal, was not found in name map.)
(Residue 29: GLU, Nonterminal, was not found in name map.)
(Residue 30: ASP, Nonterminal, was not found in name map.)
(Residue 31: GLY, Nonterminal, was not found in name map.)
(Residue 32: ALA, Nonterminal, was not found in name map.)
(Residue 33: LEU, Nonterminal, was not found in name map.)
(Residue 34: LYS, Nonterminal, was not found in name map.)
(Residue 35: SER, Nonterminal, was not found in name map.)
(Residue 36: VAL, Nonterminal, was not found in name map.)
(Residue 37: ILE, Nonterminal, was not found in name map.)
(Residue 38: LYS, Nonterminal, was not found in name map.)
(Residue 39: GLU, Nonterminal, was not found in name map.)
(Residue 40: GLY, Nonterminal, was not found in name map.)
(Residue 41: LEU, Nonterminal, was not found in name map.)
(Residue 42: ARG, Nonterminal, was not found in name map.)
(Residue 43: LEU, Nonterminal, was not found in name map.)
(Residue 44: LYS, Nonterminal, was not found in name map.)
(Residue 45: ASP, Nonterminal, was not found in name map.)
(Residue 46: GLY, Nonterminal, was not found in name map.)
(Residue 47: GLY, Nonterminal, was not found in name map.)
(Residue 48: HIS, Nonterminal, was not found in name map.)
(Residue 49: TYR, Nonterminal, was not found in name map.)
(Residue 50: ALA, Nonterminal, was not found in name map.)
(Residue 51: ALA, Nonterminal, was not found in name map.)
(Residue 52: GLU, Nonterminal, was not found in name map.)
(Residue 53: VAL, Nonterminal, was not found in name map.)
(Residue 54: LYS, Nonterminal, was not found in name map.)
(Residue 55: THR, Nonterminal, was not found in name map.)
(Residue 56: THR, Nonterminal, was not found in name map.)
(Residue 57: TYR, Nonterminal, was not found in name map.)
(Residue 58: LYS, Nonterminal, was not found in name map.)
(Residue 59: ALA, Nonterminal, was not found in name map.)
(Residue 60: LYS, Nonterminal, was not found in name map.)
(Residue 61: LYS, Nonterminal, was not found in name map.)
(Residue 62: PRO, Nonterminal, was not found in name map.)
(Residue 63: VAL, Nonterminal, was not found in name map.)
(Residue 64: GLN, Nonterminal, was not found in name map.)
(Residue 65: LEU, Nonterminal, was not found in name map.)
(Residue 66: PRO, Nonterminal, was not found in name map.)
(Residue 67: GLY, Nonterminal, was not found in name map.)
(Residue 68: ALA, Nonterminal, was not found in name map.)
(Residue 69: TYR, Nonterminal, was not found in name map.)
(Residue 70: ILE, Nonterminal, was not found in name map.)
(Residue 71: VAL, Nonterminal, was not found in name map.)
(Residue 72: ASP, Nonterminal, was not found in name map.)
(Residue 73: ILE, Nonterminal, was not found in name map.)
(Residue 74: LYS, Nonterminal, was not found in name map.)
(Residue 75: LEU, Nonterminal, was not found in name map.)
(Residue 76: ASP, Nonterminal, was not found in name map.)
(Residue 77: ILE, Nonterminal, was not found in name map.)
(Residue 78: VAL, Nonterminal, was not found in name map.)
(Residue 79: SER, Nonterminal, was not found in name map.)
(Residue 80: HIS, Nonterminal, was not found in name map.)
(Residue 81: ASN, Nonterminal, was not found in name map.)
(Residue 82: GLU, Nonterminal, was not found in name map.)
(Residue 83: ASP, Nonterminal, was not found in name map.)
(Residue 84: TYR, Nonterminal, was not found in name map.)
(Residue 85: THR, Nonterminal, was not found in name map.)
(Residue 86: ILE, Nonterminal, was not found in name map.)
(Residue 87: VAL, Nonterminal, was not found in name map.)
(Residue 88: GLU, Nonterminal, was not found in name map.)
(Residue 89: GLN, Nonterminal, was not found in name map.)
(Residue 90: CYS, Nonterminal, was not found in name map.)
(Residue 91: GLU, Nonterminal, was not found in name map.)
(Residue 92: ARG, Nonterminal, was not found in name map.)
(Residue 93: ALA, Nonterminal, was not found in name map.)
(Residue 94: GLU, Nonterminal, was not found in name map.)
(Residue 95: GLY, Nonterminal, was not found in name map.)
(Residue 96: ARG, Nonterminal, was not found in name map.)
(Residue 97: HIS, Nonterminal, was not found in name map.)
(Residue 98: ALA, Nonterminal, was not found in name map.)
(Residue 99: ILE, Nonterminal, was not found in name map.)
(Residue 100: ILE, Nonterminal, was not found in name map.)
(Residue 101: LYS, Nonterminal, was not found in name map.)
(Residue 102: GLU, Nonterminal, was not found in name map.)
(Residue 103: PHE, Nonterminal, was not found in name map.)
(Residue 104: MET, Nonterminal, was not found in name map.)
(Residue 105: ARG, Nonterminal, was not found in name map.)
(Residue 106: PHE, Nonterminal, was not found in name map.)
(Residue 107: LYS, Nonterminal, was not found in name map.)
(Residue 108: VAL, Nonterminal, was not found in name map.)
(Residue 109: HIS, Nonterminal, was not found in name map.)
(Residue 110: MET, Nonterminal, was not found in name map.)
(Residue 111: GLU, Nonterminal, was not found in name map.)
(Residue 112: GLY, Nonterminal, was not found in name map.)
(Residue 113: SER, Nonterminal, was not found in name map.)
(Residue 114: VAL, Nonterminal, was not found in name map.)
(Residue 115: ASN, Nonterminal, was not found in name map.)
(Residue 116: GLY, Nonterminal, was not found in name map.)
(Residue 117: HIS, Nonterminal, was not found in name map.)
(Residue 118: GLU, Nonterminal, was not found in name map.)
(Residue 119: PHE, Nonterminal, was not found in name map.)
(Residue 120: GLU, Nonterminal, was not found in name map.)
(Residue 121: ILE, Nonterminal, was not found in name map.)
(Residue 122: GLU, Nonterminal, was not found in name map.)
(Residue 123: GLY, Nonterminal, was not found in name map.)
(Residue 124: GLU, Nonterminal, was not found in name map.)
(Residue 125: GLY, Nonterminal, was not found in name map.)
(Residue 126: GLU, Nonterminal, was not found in name map.)
(Residue 127: GLY, Nonterminal, was not found in name map.)
(Residue 128: ARG, Nonterminal, was not found in name map.)
(Residue 129: PRO, Nonterminal, was not found in name map.)
(Residue 130: TYR, Nonterminal, was not found in name map.)
(Residue 131: GLU, Nonterminal, was not found in name map.)
(Residue 132: ALA, Nonterminal, was not found in name map.)
(Residue 133: PHE, Nonterminal, was not found in name map.)
(Residue 134: GLN, Nonterminal, was not found in name map.)
(Residue 135: THR, Nonterminal, was not found in name map.)
(Residue 136: ALA, Nonterminal, was not found in name map.)
(Residue 137: LYS, Nonterminal, was not found in name map.)
(Residue 138: LEU, Nonterminal, was not found in name map.)
(Residue 139: LYS, Nonterminal, was not found in name map.)
(Residue 140: VAL, Nonterminal, was not found in name map.)
(Residue 141: THR, Nonterminal, was not found in name map.)
(Residue 142: LYS, Nonterminal, was not found in name map.)
(Residue 143: GLY, Nonterminal, was not found in name map.)
(Residue 144: GLY, Nonterminal, was not found in name map.)
(Residue 145: PRO, Nonterminal, was not found in name map.)
(Residue 146: LEU, Nonterminal, was not found in name map.)
(Residue 147: PRO, Nonterminal, was not found in name map.)
(Residue 148: PHE, Nonterminal, was not found in name map.)
(Residue 149: ALA, Nonterminal, was not found in name map.)
(Residue 150: TRP, Nonterminal, was not found in name map.)
(Residue 151: ASP, Nonterminal, was not found in name map.)
(Residue 152: ILE, Nonterminal, was not found in name map.)
(Residue 153: LEU, Nonterminal, was not found in name map.)
(Residue 154: SER, Nonterminal, was not found in name map.)
(Residue 155: LEU, Nonterminal, was not found in name map.)
(Residue 156: GLN, Nonterminal, was not found in name map.)
(Residue 157: PHE, Nonterminal, was not found in name map.)
(Residue 158: CH6, Nonterminal, was not found in name map.)
(Residue 159: SER, Nonterminal, was not found in name map.)
(Residue 160: LYS, Nonterminal, was not found in name map.)
(Residue 161: ALA, Nonterminal, was not found in name map.)
(Residue 162: TYR, Nonterminal, was not found in name map.)
(Residue 163: ILE, Nonterminal, was not found in name map.)
(Residue 164: LYS, Nonterminal, was not found in name map.)
(Residue 165: HIS, Nonterminal, was not found in name map.)
(Residue 166: PRO, Nonterminal, was not found in name map.)
(Residue 167: ALA, Nonterminal, was not found in name map.)
(Residue 168: ASP, Nonterminal, was not found in name map.)
(Residue 169: ILE, Nonterminal, was not found in name map.)
(Residue 170: PRO, Nonterminal, was not found in name map.)
(Residue 171: ASP, Nonterminal, was not found in name map.)
(Residue 172: TYR, Nonterminal, was not found in name map.)
(Residue 173: PHE, Nonterminal, was not found in name map.)
(Residue 174: LYS, Nonterminal, was not found in name map.)
(Residue 175: LEU, Nonterminal, was not found in name map.)
(Residue 176: SER, Nonterminal, was not found in name map.)
(Residue 177: PHE, Nonterminal, was not found in name map.)
(Residue 178: PRO, Nonterminal, was not found in name map.)
(Residue 179: GLU, Nonterminal, was not found in name map.)
(Residue 180: GLY, Nonterminal, was not found in name map.)
(Residue 181: PHE, Nonterminal, was not found in name map.)
(Residue 182: ARG, Nonterminal, was not found in name map.)
(Residue 183: TRP, Nonterminal, was not found in name map.)
(Residue 184: GLU, Nonterminal, was not found in name map.)
(Residue 185: ARG, Nonterminal, was not found in name map.)
(Residue 186: VAL, Nonterminal, was not found in name map.)
(Residue 187: MET, Nonterminal, was not found in name map.)
(Residue 188: ILE, Nonterminal, was not found in name map.)
(Residue 189: PHE, Nonterminal, was not found in name map.)
(Residue 190: GLU, Nonterminal, was not found in name map.)
(Residue 191: ASP, Nonterminal, was not found in name map.)
(Residue 192: GLY, Nonterminal, was not found in name map.)
(Residue 193: GLY, Nonterminal, was not found in name map.)
(Residue 194: ILE, Nonterminal, was not found in name map.)
(Residue 195: ILE, Nonterminal, was not found in name map.)
(Residue 196: HIS, Nonterminal, was not found in name map.)
(Residue 197: VAL, Nonterminal, was not found in name map.)
(Residue 198: ASN, Nonterminal, was not found in name map.)
(Residue 199: GLN, Nonterminal, was not found in name map.)
(Residue 200: ASP, Nonterminal, was not found in name map.)
(Residue 201: SER, Nonterminal, was not found in name map.)
(Residue 202: SER, Nonterminal, was not found in name map.)
(Residue 203: LEU, Nonterminal, was not found in name map.)
(Residue 204: GLN, Nonterminal, was not found in name map.)
(Residue 205: ASP, Nonterminal, was not found in name map.)
(Residue 206: GLY, Nonterminal, was not found in name map.)
(Residue 207: VAL, Nonterminal, was not found in name map.)
(Residue 208: PHE, Nonterminal, was not found in name map.)
(Residue 209: ILE, Nonterminal, was not found in name map.)
(Residue 210: TYR, Nonterminal, was not found in name map.)
(Residue 211: LYS, Nonterminal, was not found in name map.)
(Residue 212: VAL, Nonterminal, was not found in name map.)
(Residue 213: LYS, Nonterminal, was not found in name map.)
(Residue 214: LEU, Nonterminal, was not found in name map.)
(Residue 215: ARG, Nonterminal, was not found in name map.)
(Residue 216: GLY, Nonterminal, was not found in name map.)
(Residue 217: THR, Nonterminal, was not found in name map.)
(Residue 218: ASN, Nonterminal, was not found in name map.)
(Residue 219: PHE, Nonterminal, was not found in name map.)
(Residue 220: PRO, Nonterminal, was not found in name map.)
(Residue 221: PRO, Nonterminal, was not found in name map.)
(Residue 222: ASP, Nonterminal, was not found in name map.)
(Residue 223: GLY, Nonterminal, was not found in name map.)
(Residue 224: PRO, Nonterminal, was not found in name map.)
(Residue 225: VAL, Nonterminal, was not found in name map.)
(Residue 226: MET, Nonterminal, was not found in name map.)
(Residue 227: GLN, Nonterminal, was not found in name map.)
(Residue 228: LYS, Nonterminal, was not found in name map.)
(Residue 229: LYS, Nonterminal, was not found in name map.)
(Residue 230: THR, Nonterminal, was not found in name map.)
(Residue 231: MET, Nonterminal, was not found in name map.)
(Residue 232: GLY, Nonterminal, was not found in name map.)
(Residue 233: TRP, Nonterminal, was not found in name map.)
(Residue 234: GLU, Nonterminal, was not found in name map.)
(Residue 235: PRO, Nonterminal, was not found in name map.)
(Residue 236: THR, Nonterminal, was not found in name map.)
(Residue 237: ARG, Nonterminal, was not found in name map.)
(Residue 238: ASP, Nonterminal, was not found in name map.)
(Residue 239: GLN, Nonterminal, was not found in name map.)
(Residue 240: LEU, Nonterminal, was not found in name map.)
(Residue 241: THR, Nonterminal, was not found in name map.)
(Residue 242: GLU, Nonterminal, was not found in name map.)
(Residue 243: GLU, Nonterminal, was not found in name map.)
(Residue 244: GLN, Nonterminal, was not found in name map.)
(Residue 245: ILE, Nonterminal, was not found in name map.)
(Residue 246: ALA, Nonterminal, was not found in name map.)
(Residue 247: GLU, Nonterminal, was not found in name map.)
(Residue 248: PHE, Nonterminal, was not found in name map.)
(Residue 249: LYS, Nonterminal, was not found in name map.)
(Residue 250: GLU, Nonterminal, was not found in name map.)
(Residue 251: ALA, Nonterminal, was not found in name map.)
(Residue 252: PHE, Nonterminal, was not found in name map.)
(Residue 253: SER, Nonterminal, was not found in name map.)
(Residue 254: LEU, Nonterminal, was not found in name map.)
(Residue 255: PHE, Nonterminal, was not found in name map.)
(Residue 256: ASP, Nonterminal, was not found in name map.)
(Residue 257: LYS, Nonterminal, was not found in name map.)
(Residue 258: ASP, Nonterminal, was not found in name map.)
(Residue 259: GLY, Nonterminal, was not found in name map.)
(Residue 260: ASP, Nonterminal, was not found in name map.)
(Residue 261: GLY, Nonterminal, was not found in name map.)
(Residue 262: THR, Nonterminal, was not found in name map.)
(Residue 263: ILE, Nonterminal, was not found in name map.)
(Residue 264: THR, Nonterminal, was not found in name map.)
(Residue 265: THR, Nonterminal, was not found in name map.)
(Residue 266: LYS, Nonterminal, was not found in name map.)
(Residue 267: GLU, Nonterminal, was not found in name map.)
(Residue 268: LEU, Nonterminal, was not found in name map.)
(Residue 269: GLY, Nonterminal, was not found in name map.)
(Residue 270: THR, Nonterminal, was not found in name map.)
(Residue 271: VAL, Nonterminal, was not found in name map.)
(Residue 272: LEU, Nonterminal, was not found in name map.)
(Residue 273: ARG, Nonterminal, was not found in name map.)
(Residue 274: SER, Nonterminal, was not found in name map.)
(Residue 275: LEU, Nonterminal, was not found in name map.)
(Residue 276: GLY, Nonterminal, was not found in name map.)
(Residue 277: GLN, Nonterminal, was not found in name map.)
(Residue 278: ASN, Nonterminal, was not found in name map.)
(Residue 279: PRO, Nonterminal, was not found in name map.)
(Residue 280: THR, Nonterminal, was not found in name map.)
(Residue 281: GLU, Nonterminal, was not found in name map.)
(Residue 282: ALA, Nonterminal, was not found in name map.)
(Residue 283: GLU, Nonterminal, was not found in name map.)
(Residue 284: LEU, Nonterminal, was not found in name map.)
(Residue 285: GLN, Nonterminal, was not found in name map.)
(Residue 286: ASP, Nonterminal, was not found in name map.)
(Residue 287: MET, Nonterminal, was not found in name map.)
(Residue 288: ILE, Nonterminal, was not found in name map.)
(Residue 289: ASN, Nonterminal, was not found in name map.)
(Residue 290: GLU, Nonterminal, was not found in name map.)
(Residue 291: VAL, Nonterminal, was not found in name map.)
(Residue 292: ASP, Nonterminal, was not found in name map.)
(Residue 293: ALA, Nonterminal, was not found in name map.)
(Residue 294: ASP, Nonterminal, was not found in name map.)
(Residue 295: GLY, Nonterminal, was not found in name map.)
(Residue 296: ASP, Nonterminal, was not found in name map.)
(Residue 297: GLY, Nonterminal, was not found in name map.)
(Residue 298: THR, Nonterminal, was not found in name map.)
(Residue 299: PHE, Nonterminal, was not found in name map.)
(Residue 300: ASP, Nonterminal, was not found in name map.)
(Residue 301: PHE, Nonterminal, was not found in name map.)
(Residue 302: PRO, Nonterminal, was not found in name map.)
(Residue 303: GLU, Nonterminal, was not found in name map.)
(Residue 304: PHE, Nonterminal, was not found in name map.)
(Residue 305: LEU, Nonterminal, was not found in name map.)
(Residue 306: THR, Nonterminal, was not found in name map.)
(Residue 307: MET, Nonterminal, was not found in name map.)
(Residue 308: MET, Nonterminal, was not found in name map.)
(Residue 309: ALA, Nonterminal, was not found in name map.)
(Residue 310: ARG, Nonterminal, was not found in name map.)
(Residue 311: LYS, Nonterminal, was not found in name map.)
(Residue 312: MET, Nonterminal, was not found in name map.)
(Residue 313: ASN, Nonterminal, was not found in name map.)
(Residue 314: ASP, Nonterminal, was not found in name map.)
(Residue 315: SER, Nonterminal, was not found in name map.)
(Residue 316: ASP, Nonterminal, was not found in name map.)
(Residue 317: SER, Nonterminal, was not found in name map.)
(Residue 318: GLU, Nonterminal, was not found in name map.)
(Residue 319: GLU, Nonterminal, was not found in name map.)
(Residue 320: GLU, Nonterminal, was not found in name map.)
(Residue 321: ILE, Nonterminal, was not found in name map.)
(Residue 322: ARG, Nonterminal, was not found in name map.)
(Residue 323: GLU, Nonterminal, was not found in name map.)
(Residue 324: ALA, Nonterminal, was not found in name map.)
(Residue 325: PHE, Nonterminal, was not found in name map.)
(Residue 326: ARG, Nonterminal, was not found in name map.)
(Residue 327: VAL, Nonterminal, was not found in name map.)
(Residue 328: PHE, Nonterminal, was not found in name map.)
(Residue 329: ASP, Nonterminal, was not found in name map.)
(Residue 330: LYS, Nonterminal, was not found in name map.)
(Residue 331: ASP, Nonterminal, was not found in name map.)
(Residue 332: GLY, Nonterminal, was not found in name map.)
(Residue 333: ASN, Nonterminal, was not found in name map.)
(Residue 334: GLY, Nonterminal, was not found in name map.)
(Residue 335: TYR, Nonterminal, was not found in name map.)
(Residue 336: ILE, Nonterminal, was not found in name map.)
(Residue 337: GLY, Nonterminal, was not found in name map.)
(Residue 338: ALA, Nonterminal, was not found in name map.)
(Residue 339: ALA, Nonterminal, was not found in name map.)
(Residue 340: GLU, Nonterminal, was not found in name map.)
(Residue 341: LEU, Nonterminal, was not found in name map.)
(Residue 342: ARG, Nonterminal, was not found in name map.)
(Residue 343: HIS, Nonterminal, was not found in name map.)
(Residue 344: VAL, Nonterminal, was not found in name map.)
(Residue 345: MET, Nonterminal, was not found in name map.)
(Residue 346: THR, Nonterminal, was not found in name map.)
(Residue 347: ASP, Nonterminal, was not found in name map.)
(Residue 348: LEU, Nonterminal, was not found in name map.)
(Residue 349: GLY, Nonterminal, was not found in name map.)
(Residue 350: GLU, Nonterminal, was not found in name map.)
(Residue 351: LYS, Nonterminal, was not found in name map.)
(Residue 352: LEU, Nonterminal, was not found in name map.)
(Residue 353: THR, Nonterminal, was not found in name map.)
(Residue 354: ASP, Nonterminal, was not found in name map.)
(Residue 355: GLU, Nonterminal, was not found in name map.)
(Residue 356: GLU, Nonterminal, was not found in name map.)
(Residue 357: VAL, Nonterminal, was not found in name map.)
(Residue 358: ASP, Nonterminal, was not found in name map.)
(Residue 359: GLU, Nonterminal, was not found in name map.)
(Residue 360: MET, Nonterminal, was not found in name map.)
(Residue 361: ILE, Nonterminal, was not found in name map.)
(Residue 362: ARG, Nonterminal, was not found in name map.)
(Residue 363: VAL, Nonterminal, was not found in name map.)
(Residue 364: ALA, Nonterminal, was not found in name map.)
(Residue 365: ASP, Nonterminal, was not found in name map.)
(Residue 366: ILE, Nonterminal, was not found in name map.)
(Residue 367: ASP, Nonterminal, was not found in name map.)
(Residue 368: GLY, Nonterminal, was not found in name map.)
(Residue 369: ASP, Nonterminal, was not found in name map.)
(Residue 370: GLY, Nonterminal, was not found in name map.)
(Residue 371: GLN, Nonterminal, was not found in name map.)
(Residue 372: VAL, Nonterminal, was not found in name map.)
(Residue 373: ASN, Nonterminal, was not found in name map.)
(Residue 374: TYR, Nonterminal, was not found in name map.)
(Residue 375: GLU, Nonterminal, was not found in name map.)
(Residue 376: GLU, Nonterminal, was not found in name map.)
(Residue 377: PHE, Nonterminal, was not found in name map.)
(Residue 378: VAL, Nonterminal, was not found in name map.)
(Residue 379: GLN, Nonterminal, was not found in name map.)
(Residue 380: MET, Nonterminal, was not found in name map.)
Mapped residue MET, term: Terminal/last, seq. number: 381 to: CMET.
Joining NSER - ARG
Joining ARG - ARG
Joining ARG - LYS
Joining LYS - TRP
Joining TRP - ASN
Joining ASN - LYS
Joining LYS - ALA
Joining ALA - GLY
Joining GLY - HIE
Joining HIE - ALA
Joining ALA - VAL
Joining VAL - ARG
Joining ARG - ALA
Joining ALA - ILE
Joining ILE - GLY
Joining GLY - ARG
Joining ARG - LEU
Joining LEU - SER
Joining SER - SER
Joining SER - ARG
Joining ARG - TRP
Joining TRP - VAL
Joining VAL - SER
Joining SER - GLU
Joining GLU - TRP
Joining TRP - MET
Joining MET - TYR
Joining TYR - PRO
Joining PRO - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - ALA
Joining ALA - LEU
Joining LEU - LYS
Joining LYS - SER
Joining SER - VAL
Joining VAL - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - GLY
Joining GLY - LEU
Joining LEU - ARG
Joining ARG - LEU
Joining LEU - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - HIE
Joining HIE - TYR
Joining TYR - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - VAL
Joining VAL - LYS
Joining LYS - THR
Joining THR - THR
Joining THR - TYR
Joining TYR - LYS
Joining LYS - ALA
Joining ALA - LYS
Joining LYS - LYS
Joining LYS - PRO
Joining PRO - VAL
Joining VAL - GLN
Joining GLN - LEU
Joining LEU - PRO
Joining PRO - GLY
Joining GLY - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - VAL
Joining VAL - ASP
Joining ASP - ILE
Joining ILE - LYS
Joining LYS - LEU
Joining LEU - ASP
Joining ASP - ILE
Joining ILE - VAL
Joining VAL - SER
Joining SER - HIE
Joining HIE - ASN
Joining ASN - GLU
Joining GLU - ASP
Joining ASP - TYR
Joining TYR - THR
Joining THR - ILE
Joining ILE - VAL
Joining VAL - GLU
Joining GLU - GLN
Joining GLN - CYS
Joining CYS - GLU
Joining GLU - ARG
Joining ARG - ALA
Joining ALA - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - HIE
Joining HIE - ALA
Joining ALA - ILE
Joining ILE - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - PHE
Joining PHE - MET
Joining MET - ARG
Joining ARG - PHE
Joining PHE - LYS
Joining LYS - VAL
Joining VAL - HIE
Joining HIE - MET
Joining MET - GLU
Joining GLU - GLY
Joining GLY - SER
Joining SER - VAL
Joining VAL - ASN
Joining ASN - GLY
Joining GLY - HIE
Joining HIE - GLU
Joining GLU - PHE
Joining PHE - GLU
Joining GLU - ILE
Joining ILE - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - PRO
Joining PRO - TYR
Joining TYR - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - GLN
Joining GLN - THR
Joining THR - ALA
Joining ALA - LYS
Joining LYS - LEU
Joining LEU - LYS
Joining LYS - VAL
Joining VAL - THR
Joining THR - LYS
Joining LYS - GLY
Joining GLY - GLY
Joining GLY - PRO
Joining PRO - LEU
Joining LEU - PRO
Joining PRO - PHE
Joining PHE - ALA
Joining ALA - TRP
Joining TRP - ASP
Joining ASP - ILE
Joining ILE - LEU
Joining LEU - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - PHE
Joining PHE - CH6
Joining CH6 - SER
Joining SER - LYS
Joining LYS - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - LYS
Joining LYS - HIE
Joining HIE - PRO
Joining PRO - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - PRO
Joining PRO - ASP
Joining ASP - TYR
Joining TYR - PHE
Joining PHE - LYS
Joining LYS - LEU
Joining LEU - SER
Joining SER - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - GLY
Joining GLY - PHE
Joining PHE - ARG
Joining ARG - TRP
Joining TRP - GLU
Joining GLU - ARG
Joining ARG - VAL
Joining VAL - MET
Joining MET - ILE
Joining ILE - PHE
Joining PHE - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - ILE
Joining ILE - ILE
Joining ILE - HIE
Joining HIE - VAL
Joining VAL - ASN
Joining ASN - GLN
Joining GLN - ASP
Joining ASP - SER
Joining SER - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - GLY
Joining GLY - VAL
Joining VAL - PHE
Joining PHE - ILE
Joining ILE - TYR
Joining TYR - LYS
Joining LYS - VAL
Joining VAL - LYS
Joining LYS - LEU
Joining LEU - ARG
Joining ARG - GLY
Joining GLY - THR
Joining THR - ASN
Joining ASN - PHE
Joining PHE - PRO
Joining PRO - PRO
Joining PRO - ASP
Joining ASP - GLY
Joining GLY - PRO
Joining PRO - VAL
Joining VAL - MET
Joining MET - GLN
Joining GLN - LYS
Joining LYS - LYS
Joining LYS - THR
Joining THR - MET
Joining MET - GLY
Joining GLY - TRP
Joining TRP - GLU
Joining GLU - PRO
Joining PRO - THR
Joining THR - ARG
Joining ARG - ASP
Joining ASP - GLN
Joining GLN - LEU
Joining LEU - THR
Joining THR - GLU
Joining GLU - GLU
Joining GLU - GLN
Joining GLN - ILE
Joining ILE - ALA
Joining ALA - GLU
Joining GLU - PHE
Joining PHE - LYS
Joining LYS - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - SER
Joining SER - LEU
Joining LEU - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - ILE
Joining ILE - THR
Joining THR - THR
Joining THR - LYS
Joining LYS - GLU
Joining GLU - LEU
Joining LEU - GLY
Joining GLY - THR
Joining THR - VAL
Joining VAL - LEU
Joining LEU - ARG
Joining ARG - SER
Joining SER - LEU
Joining LEU - GLY
Joining GLY - GLN
Joining GLN - ASN
Joining ASN - PRO
Joining PRO - THR
Joining THR - GLU
Joining GLU - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - MET
Joining MET - ILE
Joining ILE - ASN
Joining ASN - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - ALA
Joining ALA - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - PHE
Joining PHE - ASP
Joining ASP - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - PHE
Joining PHE - LEU
Joining LEU - THR
Joining THR - MET
Joining MET - MET
Joining MET - ALA
Joining ALA - ARG
Joining ARG - LYS
Joining LYS - MET
Joining MET - ASN
Joining ASN - ASP
Joining ASP - SER
Joining SER - ASP
Joining ASP - SER
Joining SER - GLU
Joining GLU - GLU
Joining GLU - GLU
Joining GLU - ILE
Joining ILE - ARG
Joining ARG - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - ARG
Joining ARG - VAL
Joining VAL - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASN
Joining ASN - GLY
Joining GLY - TYR
Joining TYR - ILE
Joining ILE - GLY
Joining GLY - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - ARG
Joining ARG - HIE
Joining HIE - VAL
Joining VAL - MET
Joining MET - THR
Joining THR - ASP
Joining ASP - LEU
Joining LEU - GLY
Joining GLY - GLU
Joining GLU - LYS
Joining LYS - LEU
Joining LEU - THR
Joining THR - ASP
Joining ASP - GLU
Joining GLU - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - GLU
Joining GLU - MET
Joining MET - ILE
Joining ILE - ARG
Joining ARG - VAL
Joining VAL - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - GLN
Joining GLN - VAL
Joining VAL - ASN
Joining ASN - TYR
Joining TYR - GLU
Joining GLU - GLU
Joining GLU - PHE
Joining PHE - VAL
Joining VAL - GLN
Joining GLN - MET
Joining MET - CMET
Added missing heavy atom: .R<CMET 420>.A<OXT 18>
total atoms in file: 3074
Leap added 2968 missing atoms according to residue templates:
1 Heavy
2967 H / lone pairs
> solvatebox pdb TIP3PBOX 10.0
Solute vdw bounding box: 47.448 63.375 77.601
Total bounding box for atom centers: 67.448 83.375 97.601
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 4 y= 5 z= 6
Adding box at: x=0 y=0 z=0
Center of solvent box is: 28.161524, 37.548698, 46.935873
Adding box at: x=0 y=0 z=1
Center of solvent box is: 28.161524, 37.548698, 28.161524
Adding box at: x=0 y=0 z=2
Center of solvent box is: 28.161524, 37.548698, 9.387175
Adding box at: x=0 y=0 z=3
Center of solvent box is: 28.161524, 37.548698, -9.387175
Adding box at: x=0 y=0 z=4
Center of solvent box is: 28.161524, 37.548698, -28.161524
Adding box at: x=0 y=0 z=5
Center of solvent box is: 28.161524, 37.548698, -46.935873
Adding box at: x=0 y=1 z=0
Center of solvent box is: 28.161524, 18.774349, 46.935873
Adding box at: x=0 y=1 z=1
Center of solvent box is: 28.161524, 18.774349, 28.161524
Adding box at: x=0 y=1 z=2
Center of solvent box is: 28.161524, 18.774349, 9.387175
Adding box at: x=0 y=1 z=3
Center of solvent box is: 28.161524, 18.774349, -9.387175
Adding box at: x=0 y=1 z=4
Center of solvent box is: 28.161524, 18.774349, -28.161524
Adding box at: x=0 y=1 z=5
Center of solvent box is: 28.161524, 18.774349, -46.935873
Adding box at: x=0 y=2 z=0
Center of solvent box is: 28.161524, 0.000000, 46.935873
Adding box at: x=0 y=2 z=1
Center of solvent box is: 28.161524, 0.000000, 28.161524
Adding box at: x=0 y=2 z=2
Center of solvent box is: 28.161524, 0.000000, 9.387175
Adding box at: x=0 y=2 z=3
Center of solvent box is: 28.161524, 0.000000, -9.387175
Adding box at: x=0 y=2 z=4
Center of solvent box is: 28.161524, 0.000000, -28.161524
Adding box at: x=0 y=2 z=5
Center of solvent box is: 28.161524, 0.000000, -46.935873
Adding box at: x=0 y=3 z=0
Center of solvent box is: 28.161524, -18.774349, 46.935873
Adding box at: x=0 y=3 z=1
Center of solvent box is: 28.161524, -18.774349, 28.161524
Adding box at: x=0 y=3 z=2
Center of solvent box is: 28.161524, -18.774349, 9.387175
Adding box at: x=0 y=3 z=3
Center of solvent box is: 28.161524, -18.774349, -9.387175
Adding box at: x=0 y=3 z=4
Center of solvent box is: 28.161524, -18.774349, -28.161524
Adding box at: x=0 y=3 z=5
Center of solvent box is: 28.161524, -18.774349, -46.935873
Adding box at: x=0 y=4 z=0
Center of solvent box is: 28.161524, -37.548698, 46.935873
Adding box at: x=0 y=4 z=1
Center of solvent box is: 28.161524, -37.548698, 28.161524
Adding box at: x=0 y=4 z=2
Center of solvent box is: 28.161524, -37.548698, 9.387175
Adding box at: x=0 y=4 z=3
Center of solvent box is: 28.161524, -37.548698, -9.387175
Adding box at: x=0 y=4 z=4
Center of solvent box is: 28.161524, -37.548698, -28.161524
Adding box at: x=0 y=4 z=5
Center of solvent box is: 28.161524, -37.548698, -46.935873
Adding box at: x=1 y=0 z=0
Center of solvent box is: 9.387175, 37.548698, 46.935873
Adding box at: x=1 y=0 z=1
Center of solvent box is: 9.387175, 37.548698, 28.161524
Adding box at: x=1 y=0 z=2
Center of solvent box is: 9.387175, 37.548698, 9.387175
Adding box at: x=1 y=0 z=3
Center of solvent box is: 9.387175, 37.548698, -9.387175
Adding box at: x=1 y=0 z=4
Center of solvent box is: 9.387175, 37.548698, -28.161524
Adding box at: x=1 y=0 z=5
Center of solvent box is: 9.387175, 37.548698, -46.935873
Adding box at: x=1 y=1 z=0
Center of solvent box is: 9.387175, 18.774349, 46.935873
Adding box at: x=1 y=1 z=1
Center of solvent box is: 9.387175, 18.774349, 28.161524
Adding box at: x=1 y=1 z=2
Center of solvent box is: 9.387175, 18.774349, 9.387175
Adding box at: x=1 y=1 z=3
Center of solvent box is: 9.387175, 18.774349, -9.387175
Adding box at: x=1 y=1 z=4
Center of solvent box is: 9.387175, 18.774349, -28.161524
Adding box at: x=1 y=1 z=5
Center of solvent box is: 9.387175, 18.774349, -46.935873
Adding box at: x=1 y=2 z=0
Center of solvent box is: 9.387175, 0.000000, 46.935873
Adding box at: x=1 y=2 z=1
Center of solvent box is: 9.387175, 0.000000, 28.161524
Adding box at: x=1 y=2 z=2
Center of solvent box is: 9.387175, 0.000000, 9.387175
Adding box at: x=1 y=2 z=3
Center of solvent box is: 9.387175, 0.000000, -9.387175
Adding box at: x=1 y=2 z=4
Center of solvent box is: 9.387175, 0.000000, -28.161524
Adding box at: x=1 y=2 z=5
Center of solvent box is: 9.387175, 0.000000, -46.935873
Adding box at: x=1 y=3 z=0
Center of solvent box is: 9.387175, -18.774349, 46.935873
Adding box at: x=1 y=3 z=1
Center of solvent box is: 9.387175, -18.774349, 28.161524
Adding box at: x=1 y=3 z=2
Center of solvent box is: 9.387175, -18.774349, 9.387175
Adding box at: x=1 y=3 z=3
Center of solvent box is: 9.387175, -18.774349, -9.387175
Adding box at: x=1 y=3 z=4
Center of solvent box is: 9.387175, -18.774349, -28.161524
Adding box at: x=1 y=3 z=5
Center of solvent box is: 9.387175, -18.774349, -46.935873
Adding box at: x=1 y=4 z=0
Center of solvent box is: 9.387175, -37.548698, 46.935873
Adding box at: x=1 y=4 z=1
Center of solvent box is: 9.387175, -37.548698, 28.161524
Adding box at: x=1 y=4 z=2
Center of solvent box is: 9.387175, -37.548698, 9.387175
Adding box at: x=1 y=4 z=3
Center of solvent box is: 9.387175, -37.548698, -9.387175
Adding box at: x=1 y=4 z=4
Center of solvent box is: 9.387175, -37.548698, -28.161524
Adding box at: x=1 y=4 z=5
Center of solvent box is: 9.387175, -37.548698, -46.935873
Adding box at: x=2 y=0 z=0
Center of solvent box is: -9.387175, 37.548698, 46.935873
Adding box at: x=2 y=0 z=1
Center of solvent box is: -9.387175, 37.548698, 28.161524
Adding box at: x=2 y=0 z=2
Center of solvent box is: -9.387175, 37.548698, 9.387175
Adding box at: x=2 y=0 z=3
Center of solvent box is: -9.387175, 37.548698, -9.387175
Adding box at: x=2 y=0 z=4
Center of solvent box is: -9.387175, 37.548698, -28.161524
Adding box at: x=2 y=0 z=5
Center of solvent box is: -9.387175, 37.548698, -46.935873
Adding box at: x=2 y=1 z=0
Center of solvent box is: -9.387175, 18.774349, 46.935873
Adding box at: x=2 y=1 z=1
Center of solvent box is: -9.387175, 18.774349, 28.161524
Adding box at: x=2 y=1 z=2
Center of solvent box is: -9.387175, 18.774349, 9.387175
Adding box at: x=2 y=1 z=3
Center of solvent box is: -9.387175, 18.774349, -9.387175
Adding box at: x=2 y=1 z=4
Center of solvent box is: -9.387175, 18.774349, -28.161524
Adding box at: x=2 y=1 z=5
Center of solvent box is: -9.387175, 18.774349, -46.935873
Adding box at: x=2 y=2 z=0
Center of solvent box is: -9.387175, 0.000000, 46.935873
Adding box at: x=2 y=2 z=1
Center of solvent box is: -9.387175, 0.000000, 28.161524
Adding box at: x=2 y=2 z=2
Center of solvent box is: -9.387175, 0.000000, 9.387175
Adding box at: x=2 y=2 z=3
Center of solvent box is: -9.387175, 0.000000, -9.387175
Adding box at: x=2 y=2 z=4
Center of solvent box is: -9.387175, 0.000000, -28.161524
Adding box at: x=2 y=2 z=5
Center of solvent box is: -9.387175, 0.000000, -46.935873
Adding box at: x=2 y=3 z=0
Center of solvent box is: -9.387175, -18.774349, 46.935873
Adding box at: x=2 y=3 z=1
Center of solvent box is: -9.387175, -18.774349, 28.161524
Adding box at: x=2 y=3 z=2
Center of solvent box is: -9.387175, -18.774349, 9.387175
Adding box at: x=2 y=3 z=3
Center of solvent box is: -9.387175, -18.774349, -9.387175
Adding box at: x=2 y=3 z=4
Center of solvent box is: -9.387175, -18.774349, -28.161524
Adding box at: x=2 y=3 z=5
Center of solvent box is: -9.387175, -18.774349, -46.935873
Adding box at: x=2 y=4 z=0
Center of solvent box is: -9.387175, -37.548698, 46.935873
Adding box at: x=2 y=4 z=1
Center of solvent box is: -9.387175, -37.548698, 28.161524
Adding box at: x=2 y=4 z=2
Center of solvent box is: -9.387175, -37.548698, 9.387175
Adding box at: x=2 y=4 z=3
Center of solvent box is: -9.387175, -37.548698, -9.387175
Adding box at: x=2 y=4 z=4
Center of solvent box is: -9.387175, -37.548698, -28.161524
Adding box at: x=2 y=4 z=5
Center of solvent box is: -9.387175, -37.548698, -46.935873
Adding box at: x=3 y=0 z=0
Center of solvent box is: -28.161524, 37.548698, 46.935873
Adding box at: x=3 y=0 z=1
Center of solvent box is: -28.161524, 37.548698, 28.161524
Adding box at: x=3 y=0 z=2
Center of solvent box is: -28.161524, 37.548698, 9.387175
Adding box at: x=3 y=0 z=3
Center of solvent box is: -28.161524, 37.548698, -9.387175
Adding box at: x=3 y=0 z=4
Center of solvent box is: -28.161524, 37.548698, -28.161524
Adding box at: x=3 y=0 z=5
Center of solvent box is: -28.161524, 37.548698, -46.935873
Adding box at: x=3 y=1 z=0
Center of solvent box is: -28.161524, 18.774349, 46.935873
Adding box at: x=3 y=1 z=1
Center of solvent box is: -28.161524, 18.774349, 28.161524
Adding box at: x=3 y=1 z=2
Center of solvent box is: -28.161524, 18.774349, 9.387175
Adding box at: x=3 y=1 z=3
Center of solvent box is: -28.161524, 18.774349, -9.387175
Adding box at: x=3 y=1 z=4
Center of solvent box is: -28.161524, 18.774349, -28.161524
Adding box at: x=3 y=1 z=5
Center of solvent box is: -28.161524, 18.774349, -46.935873
Adding box at: x=3 y=2 z=0
Center of solvent box is: -28.161524, 0.000000, 46.935873
Adding box at: x=3 y=2 z=1
Center of solvent box is: -28.161524, 0.000000, 28.161524
Adding box at: x=3 y=2 z=2
Center of solvent box is: -28.161524, 0.000000, 9.387175
Adding box at: x=3 y=2 z=3
Center of solvent box is: -28.161524, 0.000000, -9.387175
Adding box at: x=3 y=2 z=4
Center of solvent box is: -28.161524, 0.000000, -28.161524
Adding box at: x=3 y=2 z=5
Center of solvent box is: -28.161524, 0.000000, -46.935873
Adding box at: x=3 y=3 z=0
Center of solvent box is: -28.161524, -18.774349, 46.935873
Adding box at: x=3 y=3 z=1
Center of solvent box is: -28.161524, -18.774349, 28.161524
Adding box at: x=3 y=3 z=2
Center of solvent box is: -28.161524, -18.774349, 9.387175
Adding box at: x=3 y=3 z=3
Center of solvent box is: -28.161524, -18.774349, -9.387175
Adding box at: x=3 y=3 z=4
Center of solvent box is: -28.161524, -18.774349, -28.161524
Adding box at: x=3 y=3 z=5
Center of solvent box is: -28.161524, -18.774349, -46.935873
Adding box at: x=3 y=4 z=0
Center of solvent box is: -28.161524, -37.548698, 46.935873
Adding box at: x=3 y=4 z=1
Center of solvent box is: -28.161524, -37.548698, 28.161524
Adding box at: x=3 y=4 z=2
Center of solvent box is: -28.161524, -37.548698, 9.387175
Adding box at: x=3 y=4 z=3
Center of solvent box is: -28.161524, -37.548698, -9.387175
Adding box at: x=3 y=4 z=4
Center of solvent box is: -28.161524, -37.548698, -28.161524
Adding box at: x=3 y=4 z=5
Center of solvent box is: -28.161524, -37.548698, -46.935873
Total vdw box size: 70.504 86.834 100.642 angstroms.
Volume: 616144.445 A^3
Total mass 307210.400 amu, Density 0.828 g/cc
Added 14629 residues.
> addions pdb Na+ 0
23 Na+ ions required to neutralize.
Adding 23 counter ions to "pdb" using 1A grid
Total solute charge: -23.00 Max atom radius: 2.00
Grid extends from solute vdw + 3.95 to 9.95
Box:
enclosing: -32.19 -39.97 -47.29 32.31 40.15 47.33
sized: 95.81 88.03 80.71
edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7
grid build: 0 sec
Volume = 3.88% of box, grid points 81348
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 11 sec
(Replacing solvent molecule)
Placed Na+ in pdb at (15.00, -14.69, 5.74).
(Replacing solvent molecule)
Placed Na+ in pdb at (-15.65, -10.78, -38.02).
(Replacing solvent molecule)
Placed Na+ in pdb at (-13.59, -13.95, -12.59).
(Replacing solvent molecule)
Placed Na+ in pdb at (12.65, -8.99, 12.65).
(Replacing solvent molecule)
Placed Na+ in pdb at (0.85, -18.29, -39.07).
(Replacing solvent molecule)
Placed Na+ in pdb at (25.11, -12.30, -1.30).
(Replacing solvent molecule)
Placed Na+ in pdb at (-3.77, 4.08, -13.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (-18.08, -7.06, -22.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (10.07, -17.79, 9.73).
(Replacing solvent molecule)
Placed Na+ in pdb at (0.55, 3.34, -23.82).
(Replacing solvent molecule)
Placed Na+ in pdb at (-14.23, -18.24, 15.27).
(Replacing solvent molecule)
Placed Na+ in pdb at (19.40, -0.55, 1.45).
(Replacing solvent molecule)
Placed Na+ in pdb at (-10.13, -28.92, -31.35).
(Replacing solvent molecule)
Placed Na+ in pdb at (7.06, -31.23, -24.62).
(Replacing solvent molecule)
Placed Na+ in pdb at (-7.22, -10.62, -41.82).
(Replacing solvent molecule)
Placed Na+ in pdb at (-6.87, 11.22, 35.09).
(Replacing solvent molecule)
Placed Na+ in pdb at (20.47, -24.51, -6.71).
(Replacing solvent molecule)
Placed Na+ in pdb at (-12.15, 3.92, -8.73).
(Replacing solvent molecule)
Placed Na+ in pdb at (14.61, 15.34, -3.28).
(Replacing solvent molecule)
Placed Na+ in pdb at (-20.07, -10.13, -13.40).
(Replacing solvent molecule)
Placed Na+ in pdb at (-3.56, -32.92, 1.25).
(Replacing solvent molecule)
Placed Na+ in pdb at (2.31, -26.59, -37.04).
(Replacing solvent molecule)
Placed Na+ in pdb at (11.55, -10.62, 33.28).
Done adding ions.
> saveamberparm pdb prmtop inpcrd
Checking Unit.
WARNING: There is a bond of 25.389654 angstroms between:
------- .R<HIE 136>.A<C 16> and .R<ALA 137>.A<N 1>
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - NT
Building angle parameters.
Could not find angle parameter: O - C - NT
Could not find angle parameter: C - NT - CT
Could not find angle parameter: CX - C - NT
Building proper torsion parameters.
** No torsion terms for O-C-NT-CT
** No torsion terms for CX-C-NT-CT
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
old PREP-specified impropers:
<CH6 197>: CA1 N3 C1 N2
<CH6 197>: C2 CB2 CA2 N2
<CH6 197>: CG2 CA2 CB2 HB2
<CH6 197>: CD2 CD1 CG2 CB2
<CH6 197>: CG2 CE2 CD2 HD2
<CH6 197>: CD2 CZ CE2 HE2
<CH6 197>: CE2 CE1 CZ OH
<CH6 197>: CZ CD1 CE1 HE1
<CH6 197>: CG2 CE1 CD1 HD1
<CH6 197>: CA2 N3 C2 O2
<CH6 197>: C2 C1 N3 CA3
<CH6 197>: CA3 +M C3 O3
total 1240 improper torsions applied
12 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
>
log started: Tue Nov 7 10:06:30 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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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/taylormi/Softwares/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
>
> set default PBRadii mbondi3
Using ArgH and AspGluO modified Bondi2 radii
> loadAmberPrep ch6.prepin
Loading Prep file: ./ch6.prepin
Loaded UNIT: CH6
> loadAmberParams ch63.cro
Loading parameters: ./ch63.cro
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadAmberParams ch6.cro
Loading parameters: ./ch6.cro
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> pdb = loadPDB 4I2Y.pdb
Loading PDB file: ./4I2Y.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER.
(Residue 1: ARG, Nonterminal, was not found in name map.)
(Residue 2: ARG, Nonterminal, was not found in name map.)
(Residue 3: LYS, Nonterminal, was not found in name map.)
(Residue 4: TRP, Nonterminal, was not found in name map.)
(Residue 5: ASN, Nonterminal, was not found in name map.)
(Residue 6: LYS, Nonterminal, was not found in name map.)
(Residue 7: ALA, Nonterminal, was not found in name map.)
(Residue 8: GLY, Nonterminal, was not found in name map.)
(Residue 9: HIS, Nonterminal, was not found in name map.)
(Residue 10: ALA, Nonterminal, was not found in name map.)
(Residue 11: VAL, Nonterminal, was not found in name map.)
(Residue 12: ARG, Nonterminal, was not found in name map.)
(Residue 13: ALA, Nonterminal, was not found in name map.)
(Residue 14: ILE, Nonterminal, was not found in name map.)
(Residue 15: GLY, Nonterminal, was not found in name map.)
(Residue 16: ARG, Nonterminal, was not found in name map.)
(Residue 17: LEU, Nonterminal, was not found in name map.)
(Residue 18: SER, Nonterminal, was not found in name map.)
(Residue 19: SER, Nonterminal, was not found in name map.)
(Residue 20: ARG, Nonterminal, was not found in name map.)
(Residue 21: TRP, Nonterminal, was not found in name map.)
(Residue 22: VAL, Nonterminal, was not found in name map.)
(Residue 23: SER, Nonterminal, was not found in name map.)
(Residue 24: GLU, Nonterminal, was not found in name map.)
(Residue 25: TRP, Nonterminal, was not found in name map.)
(Residue 26: MET, Nonterminal, was not found in name map.)
(Residue 27: TYR, Nonterminal, was not found in name map.)
(Residue 28: PRO, Nonterminal, was not found in name map.)
(Residue 29: GLU, Nonterminal, was not found in name map.)
(Residue 30: ASP, Nonterminal, was not found in name map.)
(Residue 31: GLY, Nonterminal, was not found in name map.)
(Residue 32: ALA, Nonterminal, was not found in name map.)
(Residue 33: LEU, Nonterminal, was not found in name map.)
(Residue 34: LYS, Nonterminal, was not found in name map.)
(Residue 35: SER, Nonterminal, was not found in name map.)
(Residue 36: VAL, Nonterminal, was not found in name map.)
(Residue 37: ILE, Nonterminal, was not found in name map.)
(Residue 38: LYS, Nonterminal, was not found in name map.)
(Residue 39: GLU, Nonterminal, was not found in name map.)
(Residue 40: GLY, Nonterminal, was not found in name map.)
(Residue 41: LEU, Nonterminal, was not found in name map.)
(Residue 42: ARG, Nonterminal, was not found in name map.)
(Residue 43: LEU, Nonterminal, was not found in name map.)
(Residue 44: LYS, Nonterminal, was not found in name map.)
(Residue 45: ASP, Nonterminal, was not found in name map.)
(Residue 46: GLY, Nonterminal, was not found in name map.)
(Residue 47: GLY, Nonterminal, was not found in name map.)
(Residue 48: HIS, Nonterminal, was not found in name map.)
(Residue 49: TYR, Nonterminal, was not found in name map.)
(Residue 50: ALA, Nonterminal, was not found in name map.)
(Residue 51: ALA, Nonterminal, was not found in name map.)
(Residue 52: GLU, Nonterminal, was not found in name map.)
(Residue 53: VAL, Nonterminal, was not found in name map.)
(Residue 54: LYS, Nonterminal, was not found in name map.)
(Residue 55: THR, Nonterminal, was not found in name map.)
(Residue 56: THR, Nonterminal, was not found in name map.)
(Residue 57: TYR, Nonterminal, was not found in name map.)
(Residue 58: LYS, Nonterminal, was not found in name map.)
(Residue 59: ALA, Nonterminal, was not found in name map.)
(Residue 60: LYS, Nonterminal, was not found in name map.)
(Residue 61: LYS, Nonterminal, was not found in name map.)
(Residue 62: PRO, Nonterminal, was not found in name map.)
(Residue 63: VAL, Nonterminal, was not found in name map.)
(Residue 64: GLN, Nonterminal, was not found in name map.)
(Residue 65: LEU, Nonterminal, was not found in name map.)
(Residue 66: PRO, Nonterminal, was not found in name map.)
(Residue 67: GLY, Nonterminal, was not found in name map.)
(Residue 68: ALA, Nonterminal, was not found in name map.)
(Residue 69: TYR, Nonterminal, was not found in name map.)
(Residue 70: ILE, Nonterminal, was not found in name map.)
(Residue 71: VAL, Nonterminal, was not found in name map.)
(Residue 72: ASP, Nonterminal, was not found in name map.)
(Residue 73: ILE, Nonterminal, was not found in name map.)
(Residue 74: LYS, Nonterminal, was not found in name map.)
(Residue 75: LEU, Nonterminal, was not found in name map.)
(Residue 76: ASP, Nonterminal, was not found in name map.)
(Residue 77: ILE, Nonterminal, was not found in name map.)
(Residue 78: VAL, Nonterminal, was not found in name map.)
(Residue 79: SER, Nonterminal, was not found in name map.)
(Residue 80: HIS, Nonterminal, was not found in name map.)
(Residue 81: ASN, Nonterminal, was not found in name map.)
(Residue 82: GLU, Nonterminal, was not found in name map.)
(Residue 83: ASP, Nonterminal, was not found in name map.)
(Residue 84: TYR, Nonterminal, was not found in name map.)
(Residue 85: THR, Nonterminal, was not found in name map.)
(Residue 86: ILE, Nonterminal, was not found in name map.)
(Residue 87: VAL, Nonterminal, was not found in name map.)
(Residue 88: GLU, Nonterminal, was not found in name map.)
(Residue 89: GLN, Nonterminal, was not found in name map.)
(Residue 90: CYS, Nonterminal, was not found in name map.)
(Residue 91: GLU, Nonterminal, was not found in name map.)
(Residue 92: ARG, Nonterminal, was not found in name map.)
(Residue 93: ALA, Nonterminal, was not found in name map.)
(Residue 94: GLU, Nonterminal, was not found in name map.)
(Residue 95: GLY, Nonterminal, was not found in name map.)
(Residue 96: ARG, Nonterminal, was not found in name map.)
(Residue 97: HIS, Nonterminal, was not found in name map.)
(Residue 98: ALA, Nonterminal, was not found in name map.)
(Residue 99: ILE, Nonterminal, was not found in name map.)
(Residue 100: ILE, Nonterminal, was not found in name map.)
(Residue 101: LYS, Nonterminal, was not found in name map.)
(Residue 102: GLU, Nonterminal, was not found in name map.)
(Residue 103: PHE, Nonterminal, was not found in name map.)
(Residue 104: MET, Nonterminal, was not found in name map.)
(Residue 105: ARG, Nonterminal, was not found in name map.)
(Residue 106: PHE, Nonterminal, was not found in name map.)
(Residue 107: LYS, Nonterminal, was not found in name map.)
(Residue 108: VAL, Nonterminal, was not found in name map.)
(Residue 109: HIS, Nonterminal, was not found in name map.)
(Residue 110: MET, Nonterminal, was not found in name map.)
(Residue 111: GLU, Nonterminal, was not found in name map.)
(Residue 112: GLY, Nonterminal, was not found in name map.)
(Residue 113: SER, Nonterminal, was not found in name map.)
(Residue 114: VAL, Nonterminal, was not found in name map.)
(Residue 115: ASN, Nonterminal, was not found in name map.)
(Residue 116: GLY, Nonterminal, was not found in name map.)
(Residue 117: HIS, Nonterminal, was not found in name map.)
(Residue 118: GLU, Nonterminal, was not found in name map.)
(Residue 119: PHE, Nonterminal, was not found in name map.)
(Residue 120: GLU, Nonterminal, was not found in name map.)
(Residue 121: ILE, Nonterminal, was not found in name map.)
(Residue 122: GLU, Nonterminal, was not found in name map.)
(Residue 123: GLY, Nonterminal, was not found in name map.)
(Residue 124: GLU, Nonterminal, was not found in name map.)
(Residue 125: GLY, Nonterminal, was not found in name map.)
(Residue 126: GLU, Nonterminal, was not found in name map.)
(Residue 127: GLY, Nonterminal, was not found in name map.)
(Residue 128: ARG, Nonterminal, was not found in name map.)
(Residue 129: PRO, Nonterminal, was not found in name map.)
(Residue 130: TYR, Nonterminal, was not found in name map.)
(Residue 131: GLU, Nonterminal, was not found in name map.)
(Residue 132: ALA, Nonterminal, was not found in name map.)
(Residue 133: PHE, Nonterminal, was not found in name map.)
(Residue 134: GLN, Nonterminal, was not found in name map.)
(Residue 135: THR, Nonterminal, was not found in name map.)
(Residue 136: ALA, Nonterminal, was not found in name map.)
(Residue 137: LYS, Nonterminal, was not found in name map.)
(Residue 138: LEU, Nonterminal, was not found in name map.)
(Residue 139: LYS, Nonterminal, was not found in name map.)
(Residue 140: VAL, Nonterminal, was not found in name map.)
(Residue 141: THR, Nonterminal, was not found in name map.)
(Residue 142: LYS, Nonterminal, was not found in name map.)
(Residue 143: GLY, Nonterminal, was not found in name map.)
(Residue 144: GLY, Nonterminal, was not found in name map.)
(Residue 145: PRO, Nonterminal, was not found in name map.)
(Residue 146: LEU, Nonterminal, was not found in name map.)
(Residue 147: PRO, Nonterminal, was not found in name map.)
(Residue 148: PHE, Nonterminal, was not found in name map.)
(Residue 149: ALA, Nonterminal, was not found in name map.)
(Residue 150: TRP, Nonterminal, was not found in name map.)
(Residue 151: ASP, Nonterminal, was not found in name map.)
(Residue 152: ILE, Nonterminal, was not found in name map.)
(Residue 153: LEU, Nonterminal, was not found in name map.)
(Residue 154: SER, Nonterminal, was not found in name map.)
(Residue 155: LEU, Nonterminal, was not found in name map.)
(Residue 156: GLN, Nonterminal, was not found in name map.)
(Residue 157: PHE, Nonterminal, was not found in name map.)
(Residue 158: CH6, Nonterminal, was not found in name map.)
(Residue 159: SER, Nonterminal, was not found in name map.)
(Residue 160: LYS, Nonterminal, was not found in name map.)
(Residue 161: ALA, Nonterminal, was not found in name map.)
(Residue 162: TYR, Nonterminal, was not found in name map.)
(Residue 163: ILE, Nonterminal, was not found in name map.)
(Residue 164: LYS, Nonterminal, was not found in name map.)
(Residue 165: HIS, Nonterminal, was not found in name map.)
(Residue 166: PRO, Nonterminal, was not found in name map.)
(Residue 167: ALA, Nonterminal, was not found in name map.)
(Residue 168: ASP, Nonterminal, was not found in name map.)
(Residue 169: ILE, Nonterminal, was not found in name map.)
(Residue 170: PRO, Nonterminal, was not found in name map.)
(Residue 171: ASP, Nonterminal, was not found in name map.)
(Residue 172: TYR, Nonterminal, was not found in name map.)
(Residue 173: PHE, Nonterminal, was not found in name map.)
(Residue 174: LYS, Nonterminal, was not found in name map.)
(Residue 175: LEU, Nonterminal, was not found in name map.)
(Residue 176: SER, Nonterminal, was not found in name map.)
(Residue 177: PHE, Nonterminal, was not found in name map.)
(Residue 178: PRO, Nonterminal, was not found in name map.)
(Residue 179: GLU, Nonterminal, was not found in name map.)
(Residue 180: GLY, Nonterminal, was not found in name map.)
(Residue 181: PHE, Nonterminal, was not found in name map.)
(Residue 182: ARG, Nonterminal, was not found in name map.)
(Residue 183: TRP, Nonterminal, was not found in name map.)
(Residue 184: GLU, Nonterminal, was not found in name map.)
(Residue 185: ARG, Nonterminal, was not found in name map.)
(Residue 186: VAL, Nonterminal, was not found in name map.)
(Residue 187: MET, Nonterminal, was not found in name map.)
(Residue 188: ILE, Nonterminal, was not found in name map.)
(Residue 189: PHE, Nonterminal, was not found in name map.)
(Residue 190: GLU, Nonterminal, was not found in name map.)
(Residue 191: ASP, Nonterminal, was not found in name map.)
(Residue 192: GLY, Nonterminal, was not found in name map.)
(Residue 193: GLY, Nonterminal, was not found in name map.)
(Residue 194: ILE, Nonterminal, was not found in name map.)
(Residue 195: ILE, Nonterminal, was not found in name map.)
(Residue 196: HIS, Nonterminal, was not found in name map.)
(Residue 197: VAL, Nonterminal, was not found in name map.)
(Residue 198: ASN, Nonterminal, was not found in name map.)
(Residue 199: GLN, Nonterminal, was not found in name map.)
(Residue 200: ASP, Nonterminal, was not found in name map.)
(Residue 201: SER, Nonterminal, was not found in name map.)
(Residue 202: SER, Nonterminal, was not found in name map.)
(Residue 203: LEU, Nonterminal, was not found in name map.)
(Residue 204: GLN, Nonterminal, was not found in name map.)
(Residue 205: ASP, Nonterminal, was not found in name map.)
(Residue 206: GLY, Nonterminal, was not found in name map.)
(Residue 207: VAL, Nonterminal, was not found in name map.)
(Residue 208: PHE, Nonterminal, was not found in name map.)
(Residue 209: ILE, Nonterminal, was not found in name map.)
(Residue 210: TYR, Nonterminal, was not found in name map.)
(Residue 211: LYS, Nonterminal, was not found in name map.)
(Residue 212: VAL, Nonterminal, was not found in name map.)
(Residue 213: LYS, Nonterminal, was not found in name map.)
(Residue 214: LEU, Nonterminal, was not found in name map.)
(Residue 215: ARG, Nonterminal, was not found in name map.)
(Residue 216: GLY, Nonterminal, was not found in name map.)
(Residue 217: THR, Nonterminal, was not found in name map.)
(Residue 218: ASN, Nonterminal, was not found in name map.)
(Residue 219: PHE, Nonterminal, was not found in name map.)
(Residue 220: PRO, Nonterminal, was not found in name map.)
(Residue 221: PRO, Nonterminal, was not found in name map.)
(Residue 222: ASP, Nonterminal, was not found in name map.)
(Residue 223: GLY, Nonterminal, was not found in name map.)
(Residue 224: PRO, Nonterminal, was not found in name map.)
(Residue 225: VAL, Nonterminal, was not found in name map.)
(Residue 226: MET, Nonterminal, was not found in name map.)
(Residue 227: GLN, Nonterminal, was not found in name map.)
(Residue 228: LYS, Nonterminal, was not found in name map.)
(Residue 229: LYS, Nonterminal, was not found in name map.)
(Residue 230: THR, Nonterminal, was not found in name map.)
(Residue 231: MET, Nonterminal, was not found in name map.)
(Residue 232: GLY, Nonterminal, was not found in name map.)
(Residue 233: TRP, Nonterminal, was not found in name map.)
(Residue 234: GLU, Nonterminal, was not found in name map.)
(Residue 235: PRO, Nonterminal, was not found in name map.)
(Residue 236: THR, Nonterminal, was not found in name map.)
(Residue 237: ARG, Nonterminal, was not found in name map.)
(Residue 238: ASP, Nonterminal, was not found in name map.)
(Residue 239: GLN, Nonterminal, was not found in name map.)
(Residue 240: LEU, Nonterminal, was not found in name map.)
(Residue 241: THR, Nonterminal, was not found in name map.)
(Residue 242: GLU, Nonterminal, was not found in name map.)
(Residue 243: GLU, Nonterminal, was not found in name map.)
(Residue 244: GLN, Nonterminal, was not found in name map.)
(Residue 245: ILE, Nonterminal, was not found in name map.)
(Residue 246: ALA, Nonterminal, was not found in name map.)
(Residue 247: GLU, Nonterminal, was not found in name map.)
(Residue 248: PHE, Nonterminal, was not found in name map.)
(Residue 249: LYS, Nonterminal, was not found in name map.)
(Residue 250: GLU, Nonterminal, was not found in name map.)
(Residue 251: ALA, Nonterminal, was not found in name map.)
(Residue 252: PHE, Nonterminal, was not found in name map.)
(Residue 253: SER, Nonterminal, was not found in name map.)
(Residue 254: LEU, Nonterminal, was not found in name map.)
(Residue 255: PHE, Nonterminal, was not found in name map.)
(Residue 256: ASP, Nonterminal, was not found in name map.)
(Residue 257: LYS, Nonterminal, was not found in name map.)
(Residue 258: ASP, Nonterminal, was not found in name map.)
(Residue 259: GLY, Nonterminal, was not found in name map.)
(Residue 260: ASP, Nonterminal, was not found in name map.)
(Residue 261: GLY, Nonterminal, was not found in name map.)
(Residue 262: THR, Nonterminal, was not found in name map.)
(Residue 263: ILE, Nonterminal, was not found in name map.)
(Residue 264: THR, Nonterminal, was not found in name map.)
(Residue 265: THR, Nonterminal, was not found in name map.)
(Residue 266: LYS, Nonterminal, was not found in name map.)
(Residue 267: GLU, Nonterminal, was not found in name map.)
(Residue 268: LEU, Nonterminal, was not found in name map.)
(Residue 269: GLY, Nonterminal, was not found in name map.)
(Residue 270: THR, Nonterminal, was not found in name map.)
(Residue 271: VAL, Nonterminal, was not found in name map.)
(Residue 272: LEU, Nonterminal, was not found in name map.)
(Residue 273: ARG, Nonterminal, was not found in name map.)
(Residue 274: SER, Nonterminal, was not found in name map.)
(Residue 275: LEU, Nonterminal, was not found in name map.)
(Residue 276: GLY, Nonterminal, was not found in name map.)
(Residue 277: GLN, Nonterminal, was not found in name map.)
(Residue 278: ASN, Nonterminal, was not found in name map.)
(Residue 279: PRO, Nonterminal, was not found in name map.)
(Residue 280: THR, Nonterminal, was not found in name map.)
(Residue 281: GLU, Nonterminal, was not found in name map.)
(Residue 282: ALA, Nonterminal, was not found in name map.)
(Residue 283: GLU, Nonterminal, was not found in name map.)
(Residue 284: LEU, Nonterminal, was not found in name map.)
(Residue 285: GLN, Nonterminal, was not found in name map.)
(Residue 286: ASP, Nonterminal, was not found in name map.)
(Residue 287: MET, Nonterminal, was not found in name map.)
(Residue 288: ILE, Nonterminal, was not found in name map.)
(Residue 289: ASN, Nonterminal, was not found in name map.)
(Residue 290: GLU, Nonterminal, was not found in name map.)
(Residue 291: VAL, Nonterminal, was not found in name map.)
(Residue 292: ASP, Nonterminal, was not found in name map.)
(Residue 293: ALA, Nonterminal, was not found in name map.)
(Residue 294: ASP, Nonterminal, was not found in name map.)
(Residue 295: GLY, Nonterminal, was not found in name map.)
(Residue 296: ASP, Nonterminal, was not found in name map.)
(Residue 297: GLY, Nonterminal, was not found in name map.)
(Residue 298: THR, Nonterminal, was not found in name map.)
(Residue 299: PHE, Nonterminal, was not found in name map.)
(Residue 300: ASP, Nonterminal, was not found in name map.)
(Residue 301: PHE, Nonterminal, was not found in name map.)
(Residue 302: PRO, Nonterminal, was not found in name map.)
(Residue 303: GLU, Nonterminal, was not found in name map.)
(Residue 304: PHE, Nonterminal, was not found in name map.)
(Residue 305: LEU, Nonterminal, was not found in name map.)
(Residue 306: THR, Nonterminal, was not found in name map.)
(Residue 307: MET, Nonterminal, was not found in name map.)
(Residue 308: MET, Nonterminal, was not found in name map.)
(Residue 309: ALA, Nonterminal, was not found in name map.)
(Residue 310: ARG, Nonterminal, was not found in name map.)
(Residue 311: LYS, Nonterminal, was not found in name map.)
(Residue 312: MET, Nonterminal, was not found in name map.)
(Residue 313: ASN, Nonterminal, was not found in name map.)
(Residue 314: ASP, Nonterminal, was not found in name map.)
(Residue 315: SER, Nonterminal, was not found in name map.)
(Residue 316: ASP, Nonterminal, was not found in name map.)
(Residue 317: SER, Nonterminal, was not found in name map.)
(Residue 318: GLU, Nonterminal, was not found in name map.)
(Residue 319: GLU, Nonterminal, was not found in name map.)
(Residue 320: GLU, Nonterminal, was not found in name map.)
(Residue 321: ILE, Nonterminal, was not found in name map.)
(Residue 322: ARG, Nonterminal, was not found in name map.)
(Residue 323: GLU, Nonterminal, was not found in name map.)
(Residue 324: ALA, Nonterminal, was not found in name map.)
(Residue 325: PHE, Nonterminal, was not found in name map.)
(Residue 326: ARG, Nonterminal, was not found in name map.)
(Residue 327: VAL, Nonterminal, was not found in name map.)
(Residue 328: PHE, Nonterminal, was not found in name map.)
(Residue 329: ASP, Nonterminal, was not found in name map.)
(Residue 330: LYS, Nonterminal, was not found in name map.)
(Residue 331: ASP, Nonterminal, was not found in name map.)
(Residue 332: GLY, Nonterminal, was not found in name map.)
(Residue 333: ASN, Nonterminal, was not found in name map.)
(Residue 334: GLY, Nonterminal, was not found in name map.)
(Residue 335: TYR, Nonterminal, was not found in name map.)
(Residue 336: ILE, Nonterminal, was not found in name map.)
(Residue 337: GLY, Nonterminal, was not found in name map.)
(Residue 338: ALA, Nonterminal, was not found in name map.)
(Residue 339: ALA, Nonterminal, was not found in name map.)
(Residue 340: GLU, Nonterminal, was not found in name map.)
(Residue 341: LEU, Nonterminal, was not found in name map.)
(Residue 342: ARG, Nonterminal, was not found in name map.)
(Residue 343: HIS, Nonterminal, was not found in name map.)
(Residue 344: VAL, Nonterminal, was not found in name map.)
(Residue 345: MET, Nonterminal, was not found in name map.)
(Residue 346: THR, Nonterminal, was not found in name map.)
(Residue 347: ASP, Nonterminal, was not found in name map.)
(Residue 348: LEU, Nonterminal, was not found in name map.)
(Residue 349: GLY, Nonterminal, was not found in name map.)
(Residue 350: GLU, Nonterminal, was not found in name map.)
(Residue 351: LYS, Nonterminal, was not found in name map.)
(Residue 352: LEU, Nonterminal, was not found in name map.)
(Residue 353: THR, Nonterminal, was not found in name map.)
(Residue 354: ASP, Nonterminal, was not found in name map.)
(Residue 355: GLU, Nonterminal, was not found in name map.)
(Residue 356: GLU, Nonterminal, was not found in name map.)
(Residue 357: VAL, Nonterminal, was not found in name map.)
(Residue 358: ASP, Nonterminal, was not found in name map.)
(Residue 359: GLU, Nonterminal, was not found in name map.)
(Residue 360: MET, Nonterminal, was not found in name map.)
(Residue 361: ILE, Nonterminal, was not found in name map.)
(Residue 362: ARG, Nonterminal, was not found in name map.)
(Residue 363: VAL, Nonterminal, was not found in name map.)
(Residue 364: ALA, Nonterminal, was not found in name map.)
(Residue 365: ASP, Nonterminal, was not found in name map.)
(Residue 366: ILE, Nonterminal, was not found in name map.)
(Residue 367: ASP, Nonterminal, was not found in name map.)
(Residue 368: GLY, Nonterminal, was not found in name map.)
(Residue 369: ASP, Nonterminal, was not found in name map.)
(Residue 370: GLY, Nonterminal, was not found in name map.)
(Residue 371: GLN, Nonterminal, was not found in name map.)
(Residue 372: VAL, Nonterminal, was not found in name map.)
(Residue 373: ASN, Nonterminal, was not found in name map.)
(Residue 374: TYR, Nonterminal, was not found in name map.)
(Residue 375: GLU, Nonterminal, was not found in name map.)
(Residue 376: GLU, Nonterminal, was not found in name map.)
(Residue 377: PHE, Nonterminal, was not found in name map.)
(Residue 378: VAL, Nonterminal, was not found in name map.)
(Residue 379: GLN, Nonterminal, was not found in name map.)
(Residue 380: MET, Nonterminal, was not found in name map.)
Mapped residue MET, term: Terminal/last, seq. number: 381 to: CMET.
Joining NSER - ARG
Joining ARG - ARG
Joining ARG - LYS
Joining LYS - TRP
Joining TRP - ASN
Joining ASN - LYS
Joining LYS - ALA
Joining ALA - GLY
Joining GLY - HIE
Joining HIE - ALA
Joining ALA - VAL
Joining VAL - ARG
Joining ARG - ALA
Joining ALA - ILE
Joining ILE - GLY
Joining GLY - ARG
Joining ARG - LEU
Joining LEU - SER
Joining SER - SER
Joining SER - ARG
Joining ARG - TRP
Joining TRP - VAL
Joining VAL - SER
Joining SER - GLU
Joining GLU - TRP
Joining TRP - MET
Joining MET - TYR
Joining TYR - PRO
Joining PRO - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - ALA
Joining ALA - LEU
Joining LEU - LYS
Joining LYS - SER
Joining SER - VAL
Joining VAL - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - GLY
Joining GLY - LEU
Joining LEU - ARG
Joining ARG - LEU
Joining LEU - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - HIE
Joining HIE - TYR
Joining TYR - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - VAL
Joining VAL - LYS
Joining LYS - THR
Joining THR - THR
Joining THR - TYR
Joining TYR - LYS
Joining LYS - ALA
Joining ALA - LYS
Joining LYS - LYS
Joining LYS - PRO
Joining PRO - VAL
Joining VAL - GLN
Joining GLN - LEU
Joining LEU - PRO
Joining PRO - GLY
Joining GLY - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - VAL
Joining VAL - ASP
Joining ASP - ILE
Joining ILE - LYS
Joining LYS - LEU
Joining LEU - ASP
Joining ASP - ILE
Joining ILE - VAL
Joining VAL - SER
Joining SER - HIE
Joining HIE - ASN
Joining ASN - GLU
Joining GLU - ASP
Joining ASP - TYR
Joining TYR - THR
Joining THR - ILE
Joining ILE - VAL
Joining VAL - GLU
Joining GLU - GLN
Joining GLN - CYS
Joining CYS - GLU
Joining GLU - ARG
Joining ARG - ALA
Joining ALA - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - HIE
Joining HIE - ALA
Joining ALA - ILE
Joining ILE - ILE
Joining ILE - LYS
Joining LYS - GLU
Joining GLU - PHE
Joining PHE - MET
Joining MET - ARG
Joining ARG - PHE
Joining PHE - LYS
Joining LYS - VAL
Joining VAL - HIE
Joining HIE - MET
Joining MET - GLU
Joining GLU - GLY
Joining GLY - SER
Joining SER - VAL
Joining VAL - ASN
Joining ASN - GLY
Joining GLY - HIE
Joining HIE - GLU
Joining GLU - PHE
Joining PHE - GLU
Joining GLU - ILE
Joining ILE - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - PRO
Joining PRO - TYR
Joining TYR - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - GLN
Joining GLN - THR
Joining THR - ALA
Joining ALA - LYS
Joining LYS - LEU
Joining LEU - LYS
Joining LYS - VAL
Joining VAL - THR
Joining THR - LYS
Joining LYS - GLY
Joining GLY - GLY
Joining GLY - PRO
Joining PRO - LEU
Joining LEU - PRO
Joining PRO - PHE
Joining PHE - ALA
Joining ALA - TRP
Joining TRP - ASP
Joining ASP - ILE
Joining ILE - LEU
Joining LEU - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - PHE
Joining PHE - CH6
Joining CH6 - SER
Joining SER - LYS
Joining LYS - ALA
Joining ALA - TYR
Joining TYR - ILE
Joining ILE - LYS
Joining LYS - HIE
Joining HIE - PRO
Joining PRO - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - PRO
Joining PRO - ASP
Joining ASP - TYR
Joining TYR - PHE
Joining PHE - LYS
Joining LYS - LEU
Joining LEU - SER
Joining SER - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - GLY
Joining GLY - PHE
Joining PHE - ARG
Joining ARG - TRP
Joining TRP - GLU
Joining GLU - ARG
Joining ARG - VAL
Joining VAL - MET
Joining MET - ILE
Joining ILE - PHE
Joining PHE - GLU
Joining GLU - ASP
Joining ASP - GLY
Joining GLY - GLY
Joining GLY - ILE
Joining ILE - ILE
Joining ILE - HIE
Joining HIE - VAL
Joining VAL - ASN
Joining ASN - GLN
Joining GLN - ASP
Joining ASP - SER
Joining SER - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - GLY
Joining GLY - VAL
Joining VAL - PHE
Joining PHE - ILE
Joining ILE - TYR
Joining TYR - LYS
Joining LYS - VAL
Joining VAL - LYS
Joining LYS - LEU
Joining LEU - ARG
Joining ARG - GLY
Joining GLY - THR
Joining THR - ASN
Joining ASN - PHE
Joining PHE - PRO
Joining PRO - PRO
Joining PRO - ASP
Joining ASP - GLY
Joining GLY - PRO
Joining PRO - VAL
Joining VAL - MET
Joining MET - GLN
Joining GLN - LYS
Joining LYS - LYS
Joining LYS - THR
Joining THR - MET
Joining MET - GLY
Joining GLY - TRP
Joining TRP - GLU
Joining GLU - PRO
Joining PRO - THR
Joining THR - ARG
Joining ARG - ASP
Joining ASP - GLN
Joining GLN - LEU
Joining LEU - THR
Joining THR - GLU
Joining GLU - GLU
Joining GLU - GLN
Joining GLN - ILE
Joining ILE - ALA
Joining ALA - GLU
Joining GLU - PHE
Joining PHE - LYS
Joining LYS - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - SER
Joining SER - LEU
Joining LEU - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - ILE
Joining ILE - THR
Joining THR - THR
Joining THR - LYS
Joining LYS - GLU
Joining GLU - LEU
Joining LEU - GLY
Joining GLY - THR
Joining THR - VAL
Joining VAL - LEU
Joining LEU - ARG
Joining ARG - SER
Joining SER - LEU
Joining LEU - GLY
Joining GLY - GLN
Joining GLN - ASN
Joining ASN - PRO
Joining PRO - THR
Joining THR - GLU
Joining GLU - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - GLN
Joining GLN - ASP
Joining ASP - MET
Joining MET - ILE
Joining ILE - ASN
Joining ASN - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - ALA
Joining ALA - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - THR
Joining THR - PHE
Joining PHE - ASP
Joining ASP - PHE
Joining PHE - PRO
Joining PRO - GLU
Joining GLU - PHE
Joining PHE - LEU
Joining LEU - THR
Joining THR - MET
Joining MET - MET
Joining MET - ALA
Joining ALA - ARG
Joining ARG - LYS
Joining LYS - MET
Joining MET - ASN
Joining ASN - ASP
Joining ASP - SER
Joining SER - ASP
Joining ASP - SER
Joining SER - GLU
Joining GLU - GLU
Joining GLU - GLU
Joining GLU - ILE
Joining ILE - ARG
Joining ARG - GLU
Joining GLU - ALA
Joining ALA - PHE
Joining PHE - ARG
Joining ARG - VAL
Joining VAL - PHE
Joining PHE - ASP
Joining ASP - LYS
Joining LYS - ASP
Joining ASP - GLY
Joining GLY - ASN
Joining ASN - GLY
Joining GLY - TYR
Joining TYR - ILE
Joining ILE - GLY
Joining GLY - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - LEU
Joining LEU - ARG
Joining ARG - HIE
Joining HIE - VAL
Joining VAL - MET
Joining MET - THR
Joining THR - ASP
Joining ASP - LEU
Joining LEU - GLY
Joining GLY - GLU
Joining GLU - LYS
Joining LYS - LEU
Joining LEU - THR
Joining THR - ASP
Joining ASP - GLU
Joining GLU - GLU
Joining GLU - VAL
Joining VAL - ASP
Joining ASP - GLU
Joining GLU - MET
Joining MET - ILE
Joining ILE - ARG
Joining ARG - VAL
Joining VAL - ALA
Joining ALA - ASP
Joining ASP - ILE
Joining ILE - ASP
Joining ASP - GLY
Joining GLY - ASP
Joining ASP - GLY
Joining GLY - GLN
Joining GLN - VAL
Joining VAL - ASN
Joining ASN - TYR
Joining TYR - GLU
Joining GLU - GLU
Joining GLU - PHE
Joining PHE - VAL
Joining VAL - GLN
Joining GLN - MET
Joining MET - CMET
Added missing heavy atom: .R<CMET 420>.A<OXT 18>
total atoms in file: 3074
Leap added 2968 missing atoms according to residue templates:
1 Heavy
2967 H / lone pairs
> saveAmberParm pdb prmtop inpcrd
Checking Unit.
WARNING: There is a bond of 25.389654 angstroms between:
------- .R<HIE 136>.A<C 16> and .R<ALA 137>.A<N 1>
WARNING: The unperturbed charge of the unit: -22.999999 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - NT
Building angle parameters.
Could not find angle parameter: O - C - NT
Could not find angle parameter: C - NT - CT
Could not find angle parameter: CX - C - NT
Building proper torsion parameters.
** No torsion terms for O-C-NT-CT
** No torsion terms for CX-C-NT-CT
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
old PREP-specified impropers:
<CH6 197>: CA1 N3 C1 N2
<CH6 197>: C2 CB2 CA2 N2
<CH6 197>: CG2 CA2 CB2 HB2
<CH6 197>: CD2 CD1 CG2 CB2
<CH6 197>: CG2 CE2 CD2 HD2
<CH6 197>: CD2 CZ CE2 HE2
<CH6 197>: CE2 CE1 CZ OH
<CH6 197>: CZ CD1 CE1 HE1
<CH6 197>: CG2 CE1 CD1 HD1
<CH6 197>: CA2 N3 C2 O2
<CH6 197>: C2 C1 N3 CA3
<CH6 197>: CA3 +M C3 O3
total 1240 improper torsions applied
12 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
> quit
Quit
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frcmod1.cro [ch6.cro]
************************************************************
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Remark line goes here
MASS
NT 14.010 0.530
CT 12.010 0.878
S 32.060 2.900
H1 1.008 0.135
HC 1.008 0.135
CK 12.010 0.360
NB 14.010 0.530
CC 12.010 0.360
CD 12.010 0.360
CA 12.010 0.360
OH 16.000 0.465
HO 1.008 0.135
HA 1.008 0.167
C 12.010 0.616
O 16.000 0.434
N* 14.010 0.530
BOND
CT-NT 367.00 1.471
CT-CT 310.00 1.526
CT-H1 340.00 1.090
CK-CT 317.00 1.510 same as CM-CT, penalty score= 0.6
CT-HC 340.00 1.090
CT-S 227.00 1.810
CK-NB 529.00 1.304
CK-N* 440.00 1.371
CC-NB 410.00 1.394
CC-CD 469.00 1.400 same as CD-CD, penalty score= 0.2
C -CC 410.00 1.444 same as C-CM, penalty score= 0.2
CA-CD 469.00 1.400 same as CC-CD, penalty score= 0.4
CD-HA 367.00 1.080
CA-CA 469.00 1.400
CA-HA 367.00 1.080
CA-OH 450.00 1.364
HO-OH 553.00 0.960
C -O 570.00 1.229
C -N* 424.00 1.383
CT-N* 337.00 1.475
C -CT 317.00 1.522
ANGLE
CT-CT-NT 80.000 111.200
H1-CT-NT 50.000 109.500
CT-CT-CT 40.000 109.500
CT-CT-HC 50.000 109.500
CT-CT-H1 50.000 109.500
CK-CT-CT 63.000 111.000 same as CM-CT-CT, penalty score= 0.5
CT-CT-S 50.000 114.700
CT-S -CT 62.000 98.900
H1-CT-S 50.000 109.500
H1-CT-H1 35.000 109.500
HC-CT-HC 35.000 109.500
CK-CT-H1 50.000 109.500 same as H1-CT-CM, penalty score= 0.5
CC-NB-CK 70.000 103.800 same as CB-NB-CK, penalty score= 0.6
C -N*-CK 70.000 121.600 same as C -N*-CM, penalty score= 0.5
CK-N*-CT 70.000 128.800
N*-CK-NB 70.000 113.900
CD-CC-NB 70.000 121.500 same as CM-CA-NC, penalty score= 10.2
C -CC-NB 70.000 130.000 same as C -CB-NB, penalty score= 6.0
CA-CD-CC 63.000 120.000 same as CD-CD-CM, penalty score= 5.2
CC-CD-HA 50.000 120.000 same as HA-CD-CD, penalty score= 0.2
CC-C -O 80.000 125.300 same as CM-C -O , penalty score= 0.2
CC-C -N* 0.000 0.000 ATTN, need revision
C -CC-CD 63.000 120.700 same as C -CM-CM, penalty score= 4.9
CA-CA-CD 63.000 120.000 same as CA-CA-CA, penalty score= 5.2
CA-CD-HA 50.000 120.000 same as CC-CD-HA, penalty score= 0.5
CA-CA-CA 63.000 120.000
CA-CA-HA 50.000 120.000
CA-CA-OH 70.000 120.000
CA-OH-HO 50.000 113.000
C -N*-CT 70.000 117.600
N*-C -O 80.000 120.900
H1-CT-N* 50.000 109.500
CT-C -O 80.000 120.400
C -CT-H1 50.000 109.500
DIHE
CT-CT-CT-NT 9 1.400 0.000 3.000
HC-CT-CT-NT 9 1.400 0.000 3.000
NB-CK-CT-NT 6 0.000 0.000 3.000 same as X
-CM-CT-X , penalty score= 1.0
N*-CK-CT-NT 6 0.000 0.000 3.000 same as
NB-CK-CT-NT, penalty score= 54.0
CT-CT-CT-S 9 1.400 0.000 3.000
CT-CT-CT-H1 9 1.400 0.000 3.000
CT-CK-NB-CC 2 20.000 180.000 2.000
CT-CK-N*-C 4 6.800 180.000 2.000
CT-CK-N*-CT 4 6.800 180.000 2.000
NB-CK-CT-CT 6 0.000 0.000 3.000 same as X
-CM-CT-X , penalty score= 1.0
N*-CK-CT-CT 6 0.000 0.000 3.000 same as
NB-CK-CT-CT, penalty score= 54.0
CT-CT-S -CT 3 1.000 0.000 3.000
CK-CT-CT-CT 9 1.400 0.000 3.000
H1-CT-S -CT 3 1.000 0.000 3.000
HC-CT-CT-S 9 1.400 0.000 3.000
H1-CT-CT-HC 9 1.400 0.000 3.000
CK-CT-CT-HC 9 1.400 0.000 3.000
NB-CK-CT-H1 6 0.000 0.000 3.000 same as X
-CM-CT-X , penalty score= 1.0
N*-CK-CT-H1 6 0.000 0.000 3.000 same as
NB-CK-CT-H1, penalty score= 54.0
CD-CC-NB-CK 2 4.800 180.000 2.000
C -CC-NB-CK 2 4.800 180.000 2.000
CC-C -N*-CK 4 5.800 180.000 2.000
O -C -N*-CK 4 5.800 180.000 2.000
H1-CT-N*-CK 6 0.000 0.000 2.000
C -CT-N*-CK 6 0.000 0.000 2.000
NB-CK-N*-C 4 6.800 180.000 2.000
NB-CK-N*-CT 4 6.800 180.000 2.000
NB-CC-CD-CA 4 20.600 180.000 2.000 same as X
-CC-CV-X , penalty score=540.0
NB-CC-CD-HA 4 20.600 180.000 2.000 same as X
-CC-CV-X , penalty score=540.0
O -C -CC-NB 4 14.500 180.000 2.000 same as X -C
-CA-X , penalty score=540.0
N*-C -CC-NB 4 14.500 180.000 2.000 same as X -C
-CA-X , penalty score=540.0
N*-CK-NB-CC 2 20.000 180.000 2.000
CA-CA-CD-CC 4 4.000 180.000 2.000 same as X
-CD-CD-X , penalty score=540.0
CC-C -N*-CT 4 5.800 180.000 2.000
O -C -CC-CD 1 2.175 180.000 -2.000 same as CM-CM-C
-O
O -C -CC-CD 1 0.300 0.000 3.000 same as CM-CM-C
-O , penalty score=594.0
N*-C -CC-CD 4 14.500 180.000 2.000 same as X -C
-CA-X , penalty score=540.0
CA-CA-CA-CD 4 14.500 180.000 2.000
CD-CA-CA-HA 4 14.500 180.000 2.000
C -CC-CD-CA 4 4.000 180.000 2.000 same as X
-CD-CD-X , penalty score=540.0
CA-CA-CA-CA 4 14.500 180.000 2.000
CA-CA-CA-HA 4 14.500 180.000 2.000
CA-CA-CD-HA 4 14.500 180.000 2.000 same as X
-CA-CA-X , penalty score=540.0
CA-CA-CA-OH 4 14.500 180.000 2.000
CA-CA-OH-HO 2 1.800 180.000 2.000
HA-CA-CA-OH 4 14.500 180.000 2.000
HA-CA-CA-HA 4 14.500 180.000 2.000
C -CC-CD-HA 4 4.000 180.000 2.000 same as X
-CD-CD-X , penalty score=540.0
H1-CT-N*-C 6 0.000 0.000 2.000
C -CT-N*-C 6 0.000 0.000 2.000
O -C -N*-CT 4 5.800 180.000 2.000
O -C -CT-N* 6 0.000 0.000 2.000
O -C -CT-H1 1 0.800 0.000 -1.000
O -C -CT-H1 1 0.000 0.000 -2.000
O -C -CT-H1 1 0.080 180.000 3.000
IMPROPER
CT-N*-CK-NB 1.1 180.0 2.0 Using the
default value
C -CD-CC-NB 1.1 180.0 2.0 Using the
default value
CA-CC-CD-HA 1.1 180.0 2.0 Same as X -X
-CM-HA, penalty score= 39.9 (use general term))
CA-CA-CA-CD 1.1 180.0 2.0 Using the
default value
CA-CA-CA-HA 1.1 180.0 2.0 Using general
improper torsional angle X- X-CA-HA, penalty score= 20.0)
CA-CA-CA-OH 1.1 180.0 2.0
CC-N*-C -O 10.5 180.0 2.0 Using general
improper torsional angle X- X- C- O, penalty score= 20.0)
C -CK-N*-CT 1.1 180.0 2.0 Using the
default value
NONBON
NT 1.8240 0.1700
CT 1.9080 0.1094
S 2.0000 0.2500
H1 1.3870 0.0157
HC 1.4870 0.0157
CK 1.9080 0.0860
NB 1.8240 0.1700
CC 1.9080 0.0860
CD 1.9080 0.0860
CA 1.9080 0.0860
OH 1.7210 0.2104
HO 0.0000 0.0000
HA 1.4590 0.0150
C 1.9080 0.0860
O 1.6612 0.2100
N* 1.8240 0.1700
************************************************************
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frcmod2.cro [ch63.cro]
************************************************************
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Remark line goes here
MASS
NT 14.010 0.530 same as n3
CT 12.010 0.878 same as c3
S 32.060 2.900 same as ss
H1 1.008 0.135 same as h1
HC 1.008 0.135 same as hc
CK 12.010 0.360 same as cc
NB 14.010 0.530 same as nc
CC 12.010 0.360 same as cc
CD 12.010 0.360 same as cc
CA 12.010 0.360 same as ca
OH 16.000 0.465 same as oh
HO 1.008 0.135 same as ho
HA 1.008 0.135 same as ha
C 12.010 0.616 same as c
O 16.000 0.434 same as o
N* 14.010 0.530 same as nc
BOND
CT-NT 320.60 1.470 same as c3-n3, penalty score= 0.0
CT-CT 303.10 1.535 same as c3-c3, penalty score= 0.0
CT-H1 335.90 1.093 same as c3-h1, penalty score= 0.0
CK-CT 337.30 1.499 same as c3-cc, penalty score= 0.0
CT-HC 337.30 1.092 same as c3-hc, penalty score= 0.0
CT-S 225.80 1.821 same as c3-ss, penalty score= 0.0
CK-NB 431.60 1.376 same as cc-nc, penalty score= 0.0
CK-N* 431.60 1.376 same as cc-nc, penalty score= 0.0
CC-NB 431.60 1.376 same as cc-nc, penalty score= 0.0
CC-CD 418.30 1.429 same as cc-cc, penalty score= 0.0
C -CC 377.40 1.462 same as c-cc, penalty score= 0.0
CA-CD 411.70 1.434 same as ca-cc, penalty score= 0.0
CD-HA 347.20 1.085 same as cc-ha, penalty score= 0.0
CA-CA 478.40 1.387 same as ca-ca, penalty score= 0.0
CA-HA 344.30 1.087 same as ca-ha, penalty score= 0.0
CA-OH 386.10 1.362 same as ca-oh, penalty score= 0.0
HO-OH 369.60 0.974 same as ho-oh, penalty score= 0.0
C -O 648.00 1.214 same as c- o, penalty score= 0.0
C -N* 428.30 1.378 same as c-nc, penalty score= 0.0
CT-N* 334.70 1.456 same as c3-nc, penalty score= 0.0
C -CT 328.30 1.508 same as c-c3, penalty score= 0.0
ANGLE
CT-CT-NT 66.180 110.380 same as c3-c3-n3, penalty score= 0.0
H1-CT-NT 49.390 109.920 same as h1-c3-n3, penalty score= 0.0
CK-CT-NT 66.670 111.570 same as cc-c3-n3, penalty score= 0.0
CT-CT-CT 63.210 110.630 same as c3-c3-c3, penalty score= 0.0
CT-CT-HC 46.370 110.050 same as c3-c3-hc, penalty score= 0.0
CT-CK-NB 65.880 121.000 same as c3-cc-nc, penalty score= 0.0
CT-CK-N* 65.880 121.000 same as c3-cc-nc, penalty score= 0.0
CT-CT-H1 46.360 110.070 same as c3-c3-h1, penalty score= 0.0
CK-CT-CT 63.570 111.920 same as c3-c3-cc, penalty score= 0.0
CT-CT-S 77.330 112.690 same as c3-c3-ss, penalty score= 0.0
CT-S -CT 37.940 99.920 same as c3-ss-c3, penalty score= 0.0
H1-CT-S 53.660 109.340 same as h1-c3-ss, penalty score= 0.0
H1-CT-H1 39.180 109.550 same as h1-c3-h1, penalty score= 0.0
HC-CT-HC 39.430 108.350 same as hc-c3-hc, penalty score= 0.0
CK-CT-H1 47.030 111.620 same as cc-c3-h1, penalty score= 0.0
CC-NB-CK 68.600 110.190 same as cc-nc-cc, penalty score= 0.0
C -N*-CK 66.550 120.320 same as c -nc-cd, penalty score= 0.0
CK-N*-CT 67.600 109.510 same as c3-nc-cd, penalty score= 0.0
N*-CK-NB 72.510 118.690 same as nc-cc-nd, penalty score= 0.0
CD-CC-NB 69.950 113.420 same as cc-cc-nc, penalty score= 0.0
C -CC-NB 66.280 123.150 same as c -cc-nc, penalty score= 0.0
CA-CD-CC 67.660 111.040 same as ca-cc-cc, penalty score= 0.0
CC-CD-HA 47.460 119.260 same as cc-cc-ha, penalty score= 0.0
CC-C -O 68.910 125.710 same as cc-c -o , penalty score= 0.0
CC-C -N* 67.520 116.400 same as cc-c -nd, penalty score= 0.0
C -CC-CD 63.720 122.690 same as c -cc-cc, penalty score= 0.0
CA-CA-CD 65.990 120.100 same as ca-ca-cc, penalty score= 0.0
CA-CD-HA 46.400 124.040 same as ca-cc-ha, penalty score= 0.0
CA-CA-CA 67.180 119.970 same as ca-ca-ca, penalty score= 0.0
CA-CA-HA 48.460 120.010 same as ca-ca-ha, penalty score= 0.0
CA-CA-OH 69.850 119.940 same as ca-ca-oh, penalty score= 0.0
CA-OH-HO 48.850 109.470 same as ca-oh-ho, penalty score= 0.0
C -N*-CT 67.600 109.510 same as c3-nd-cc, penalty score= 5.0
N*-C -O 74.050 123.980 same as nc-c -o , penalty score= 0.0
H1-CT-N* 50.110 108.570 same as h1-c3-nc, penalty score= 0.0
C -CT-N* 68.370 107.040 same as cc-c3-nc, penalty score= 5.0
CT-C -O 68.030 123.110 same as c3-c -o , penalty score= 0.0
C -CT-H1 47.630 107.660 same as c -c3-h1, penalty score= 0.0
DIHE
CT-CT-CT-NT 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
HC-CT-CT-NT 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
NB-CK-CT-NT 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
N*-CK-CT-NT 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
CT-CT-CT-S 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
CT-CT-CT-H1 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
CT-CK-NB-CC 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
CT-CK-N*-C 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
CT-CK-N*-CT 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
NB-CK-CT-CT 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
N*-CK-CT-CT 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
CT-CT-S -CT 3 1.000 0.000 3.000 same as X
-c3-ss-X , penalty score= 0.0
CK-CT-CT-CT 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
H1-CT-S -CT 3 1.000 0.000 3.000 same as X
-c3-ss-X , penalty score= 0.0
HC-CT-CT-S 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
H1-CT-CT-HC 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
CK-CT-CT-HC 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
NB-CK-CT-H1 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
N*-CK-CT-H1 6 0.000 0.000 3.000 same as X
-c3-cd-X , penalty score= 0.0
CD-CC-NB-CK 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
C -CC-NB-CK 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
CC-C -N*-CK 2 8.000 180.000 2.000 same as X -c
-nd-X , penalty score= 0.0
O -C -N*-CK 2 8.000 180.000 2.000 same as X -c
-nd-X , penalty score= 0.0
H1-CT-N*-CK 6 0.000 0.000 3.000 same as X
-c3-n2-X , penalty score=540.0
C -CT-N*-CK 6 0.000 0.000 3.000 same as X
-c3-n2-X , penalty score=540.0
NB-CK-N*-C 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
NB-CK-N*-CT 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
NB-CC-CD-CA 4 16.000 180.000 2.000 same as X
-cd-cd-X , penalty score= 0.0
NB-CC-CD-HA 4 16.000 180.000 2.000 same as X
-cd-cd-X , penalty score= 0.0
O -C -CC-NB 4 11.500 180.000 2.000 same as X -c
-cd-X , penalty score= 0.0
N*-C -CC-NB 4 11.500 180.000 2.000 same as X -c
-cd-X , penalty score= 0.0
N*-CK-NB-CC 2 9.500 180.000 2.000 same as X
-cd-nd-X , penalty score= 0.0
CA-CA-CD-CC 4 16.000 180.000 2.000 same as X
-cc-cc-X , penalty score=540.0
CC-C -N*-CT 2 8.000 180.000 2.000 same as X -c
-nd-X , penalty score= 0.0
O -C -CC-CD 4 11.500 180.000 2.000 same as X -c
-cd-X , penalty score= 0.0
N*-C -CC-CD 4 11.500 180.000 2.000 same as X -c
-cd-X , penalty score= 0.0
CA-CA-CA-CD 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CD-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
C -CC-CD-CA 4 16.000 180.000 2.000 same as X
-cd-cd-X , penalty score= 0.0
CA-CA-CA-CA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CD-HA 4 14.500 180.000 2.000 same as
CA-CA-CA-HA, penalty score=540.0
CA-CA-CA-OH 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-OH-HO 2 1.800 180.000 2.000 same as X
-ca-oh-X , penalty score= 0.0
HA-CA-CA-OH 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
HA-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
C -CC-CD-HA 4 16.000 180.000 2.000 same as X
-cd-cd-X , penalty score= 0.0
H1-CT-N*-C 6 0.000 0.000 3.000 same as X
-c3-n2-X , penalty score=540.0
C -CT-N*-C 6 0.000 0.000 3.000 same as X
-c3-n2-X , penalty score=540.0
O -C -N*-CT 2 8.000 180.000 2.000 same as X -c
-nd-X , penalty score= 0.0
O -C -CT-N* 6 0.000 180.000 2.000 same as X -c
-c3-X , penalty score= 0.0
O -C -CT-H1 1 0.800 0.000 -1.000 same as h1-c3-c
-o
O -C -CT-H1 1 0.080 180.000 3.000 same as h1-c3-c
-o , penalty score= 0.0
IMPROPER
CT-N*-CK-NB 10.5 180.0 2.0 Same as X
-n2-ca-n2, penalty score= 72.5 (use general term))
C -CD-CC-NB 1.1 180.0 2.0 Using the
default value
CA-CC-CD-HA 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 47.7 (use general term))
CA-CA-CA-CD 1.1 180.0 2.0 Using the
default value
CA-CA-CA-HA 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 20.0 (use general term))
CA-CA-CA-OH 1.1 180.0 2.0 Using the
default value
CC-N*-C -O 10.5 180.0 2.0 Same as X -X -c
-o , penalty score= 20.0 (use general term))
C -CK-N*-CT 1.1 180.0 2.0 Using the
default value
NONBON
NT 1.8240 0.1700 same as n3
CT 1.9080 0.1094 same as c3
S 2.0000 0.2500 same as ss
H1 1.3870 0.0157 same as h1
HC 1.4870 0.0157 same as hc
CK 1.9080 0.0860 same as cc
NB 1.8240 0.1700 same as nc
CC 1.9080 0.0860 same as cc
CD 1.9080 0.0860 same as cc
CA 1.9080 0.0860 same as ca
OH 1.7210 0.2104 same as oh
HO 0.0000 0.0000 same as ho
HA 1.4590 0.0150 same as ha
C 1.9080 0.0860 same as c
O 1.6612 0.2100 same as o
N* 1.8240 0.1700 same as nc
************************************************************
*****************************************
ch6.prepin
************************************************************
****************************************
0 0 2
This is a remark line
molecule.res
CH6 INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
4 N1 NT M 3 2 1 1.540 111.208 -180.000 -0.838284
5 CA1 CT M 4 3 2 1.470 61.689 38.757 0.174188
6 CB1 CT 3 5 4 3 1.530 109.459 71.438 -0.069391
7 CG1 CT 3 6 5 4 1.530 109.459 -65.012 -0.008674
8 SD S S 7 6 5 1.813 109.468 -179.988 -0.271594
9 CE CT 3 8 7 6 1.815 103.023 179.983 -0.040105
10 HE1A H1 E 9 8 7 1.090 109.499 -179.999 0.066922
11 HE2A H1 E 9 8 7 1.090 109.459 -59.980 0.066922
12 HE3 H1 E 9 8 7 1.090 109.444 59.999 0.066922
13 HG11 H1 E 7 6 5 1.090 109.454 60.009 0.069590
14 HG12 H1 E 7 6 5 1.090 109.442 -59.973 0.069590
15 HB11 HC E 6 5 4 1.090 109.479 175.012 0.081864
16 HB12 HC E 6 5 4 1.090 109.515 54.971 0.081864
17 HA1 H1 E 5 4 3 1.089 109.428 -48.603 0.073326
18 C1 CK M 5 4 3 1.507 109.468 -168.583 0.432162
19 N2 NB S 18 5 4 1.297 124.318 -34.645 -0.551488
20 CA2 CC B 19 18 5 1.367 109.284 -179.998 -0.017348
21 CB2 CD B 20 19 18 1.378 127.134 179.948 0.033941
22 CG2 CA S 21 20 19 1.465 119.965 5.072 -0.114532
23 CD2 CA B 22 21 20 1.403 120.159 -6.573 -0.051297
24 CE2 CA B 23 22 21 1.371 119.855 179.986 -0.184202
25 CZ CA B 24 23 22 1.391 120.133 0.309 0.155937
26 OH OH S 25 24 23 1.357 119.798 179.972 -0.459900
27 HOH HO E 26 25 24 0.967 114.002 90.050 0.451480
28 CE1 CA B 25 24 23 1.391 120.271 -0.102 -0.184202
29 CD1 CA S 28 25 24 1.371 120.145 0.083 -0.051297
30 HD1 HA E 29 28 25 1.080 120.065 179.890 0.158498
31 HE1 HA E 28 25 24 1.080 119.914 179.993 0.156364
32 HE2 HA E 24 23 22 1.080 119.879 -179.770 0.156364
33 HD2 HA E 23 22 21 1.080 120.032 0.291 0.158498
34 HB2 HA E 21 20 19 1.080 120.002 -174.963 0.160099
35 C2 C S 20 19 18 1.474 105.768 -0.047 0.727598
36 O2 O E 35 20 19 1.218 127.350 -179.967 -0.539550
37 N3 N* M 18 5 4 1.366 124.356 144.976 -0.399463
38 CA3 CT M 37 18 5 1.465 125.803 0.021 0.072578
39 HA31 H1 E 38 37 18 1.089 109.486 -150.015 0.109615
40 HA32 H1 E 38 37 18 1.091 109.490 -30.004 0.109615
41 C3 C M 38 37 18 1.508 109.466 89.958 0.642639
42 O3 O E 41 38 37 1.208 120.003 0.026 -0.495248
LOOP
CD1 CG2
N3 C2
IMPROPER
CA1 N3 C1 N2
C2 CB2 CA2 N2
CG2 CA2 CB2 HB2
CD2 CD1 CG2 CB2
CG2 CE2 CD2 HD2
CD2 CZ CE2 HE2
CE2 CE1 CZ OH
CZ CD1 CE1 HE1
CG2 CE1 CD1 HD1
CA2 N3 C2 O2
C2 C1 N3 CA3
CA3 +M C3 O3
DONE
STOP
************************************************************
****************************************
I can't thank you enough.
--
Sincerely,
Miles Taylor
Graduate Student
Physical Chemistry
Department of Chemistry
Oregon State University
Corvallis, OR 97331
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Received on Tue Nov 07 2017 - 14:00:02 PST
