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leap.log
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log started: Thu Jun 25 15:38:48 2020
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: /miniconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /miniconda3/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: /miniconda3/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: /miniconda3/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: /miniconda3/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" "HYP" } { 1 "HYP" "CHYP" }
>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>> }
>>
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>
> source leaprc.water.tip3p
----- Source: /miniconda3/dat/leap/cmd/leaprc.water.tip3p
----- Source of /miniconda3/dat/leap/cmd/leaprc.water.tip3p done
>> #
>> # Load water and ions for TIP3P + Li/Merz monovalent ions
>> # + Joung-Chetham monovalent ions
>> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
>> #
>> # Note: the Li/Merz monovalent set is loaded only to get Tl+,
>> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second,
>> # the alkali halide parameters come from the Joung-Cheatham set
>> #
>> addAtomTypes {
>> { "HW" "H" "sp3" }
>> { "OW" "O" "sp3" }
>> { "F-" "F" "sp3" }
>> { "Cl-" "Cl" "sp3" }
>> { "Br-" "Br" "sp3" }
>> { "I-" "I" "sp3" }
>> { "Li+" "Li" "sp3" }
>> { "Na+" "Na" "sp3" }
>> { "K+" "K" "sp3" }
>> { "Rb+" "Rb" "sp3" }
>> { "Cs+" "Cs" "sp3" }
>> { "Mg+" "Mg" "sp3" }
>> { "Tl+" "Tl" "sp3" }
>> { "Cu+" "Cu" "sp3" }
>> { "Ag+" "Ag" "sp3" }
>> { "NH4+" "N" "sp3" }
>> { "H3O+" "O" "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: /miniconda3/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: /miniconda3/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OP3
Loading: OPC
Loading: OPC3BOX
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.tip3p
Loading parameters: /miniconda3/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
>> loadAmberParams frcmod.ions1lm_126_tip3p
Loading parameters: /miniconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /miniconda3/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: /miniconda3/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)
>>
>
>
> #Load Amber prepi files for the fluorinated proline residues
> loadamberprep ./tleap_prep/rf.prepin
Loading Prep file: ./tleap_prep/rf.prepin
(UNKNOWN ATOM TYPE: Hf)
Loaded UNIT: PRF
> loadamberprep ./tleap_prep/sf.prepin
Loading Prep file: ./tleap_prep/sf.prepin
(UNKNOWN ATOM TYPE: Hf)
Loaded UNIT: PSF
>
> # Load gaff2 for bond, angle and dihedrals containing fluorine
> # Load vdw parameters for F and Hf (H bonded to fluorinated carbon) - Robalo et al. Phys. Chem. Chem. Phys., 2019,21, 2029-2038
> loadamberparams ./tleap_prep/F.frcmod
Loading parameters: ./tleap_prep/F.frcmod
Reading force field modification type file (frcmod)
Reading title:
Force field parameters from rf2.prmtop
(UNKNOWN ATOM TYPE: Hf)
>
> #####################################################################
> # User can choose the peptide to simulate below
> #####################################################################
> #Example 1 (Simple 4R fluorinated Proline dipeptide) (RF in short)
> amber=sequence{ACE PRF NME}
Sequence: ACE
Sequence: PRF
Sequence: NME
>
> #Example 2 (Simple 4S fluorinated Proline dipeptide) (SF in short)
> #amber=sequence{ACE PSF NME}
>
> #Example 3 (Tetrapeptide)
> #amber=sequence{ACE PRF PRF PSF NME}
> #####################################################################
>
> #Add waters
> solvatebox amber TIP3PBOX 8
Solute vdw bounding box: 10.288 8.934 7.544
Total bounding box for atom centers: 26.288 24.934 23.544
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 2 y= 2 z= 2
Total vdw box size: 28.912 28.370 26.192 angstroms.
Volume: 21483.105 A^3
Total mass 7881.036 amu, Density 0.609 g/cc
Added 427 residues.
>
> #save pdb and amber topologies
> savepdb amber amber_ff/amber.pdb
Writing pdb file: amber_ff/amber.pdb
printing CRYST1 record to PDB file with box info
> saveamberparm amber amber_ff/amber.prmtop amber_ff/amber.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<PRF 2>: -M CA N CD
<PRF 2>: CA +M C O
total 4 improper torsions applied
2 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 427
)
(no restraints)
>
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Thu Jun 25 16:17:06 2020
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: /miniconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /miniconda3/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: /miniconda3/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: /miniconda3/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: /miniconda3/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" "HYP" } { 1 "HYP" "CHYP" }
>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>> }
>>
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>
> source leaprc.water.tip3p
----- Source: /miniconda3/dat/leap/cmd/leaprc.water.tip3p
----- Source of /miniconda3/dat/leap/cmd/leaprc.water.tip3p done
>> #
>> # Load water and ions for TIP3P + Li/Merz monovalent ions
>> # + Joung-Chetham monovalent ions
>> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
>> #
>> # Note: the Li/Merz monovalent set is loaded only to get Tl+,
>> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second,
>> # the alkali halide parameters come from the Joung-Cheatham set
>> #
>> addAtomTypes {
>> { "HW" "H" "sp3" }
>> { "OW" "O" "sp3" }
>> { "F-" "F" "sp3" }
>> { "Cl-" "Cl" "sp3" }
>> { "Br-" "Br" "sp3" }
>> { "I-" "I" "sp3" }
>> { "Li+" "Li" "sp3" }
>> { "Na+" "Na" "sp3" }
>> { "K+" "K" "sp3" }
>> { "Rb+" "Rb" "sp3" }
>> { "Cs+" "Cs" "sp3" }
>> { "Mg+" "Mg" "sp3" }
>> { "Tl+" "Tl" "sp3" }
>> { "Cu+" "Cu" "sp3" }
>> { "Ag+" "Ag" "sp3" }
>> { "NH4+" "N" "sp3" }
>> { "H3O+" "O" "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: /miniconda3/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: /miniconda3/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OP3
Loading: OPC
Loading: OPC3BOX
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.tip3p
Loading parameters: /miniconda3/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
>> loadAmberParams frcmod.ions1lm_126_tip3p
Loading parameters: /miniconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters: /miniconda3/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: /miniconda3/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)
>>
>
>
> #Load Amber prepi files for the fluorinated proline residues
> loadamberprep ./tleap_prep/rf.prepin
Loading Prep file: ./tleap_prep/rf.prepin
(UNKNOWN ATOM TYPE: Hf)
Loaded UNIT: PRF
> loadamberprep ./tleap_prep/sf.prepin
Loading Prep file: ./tleap_prep/sf.prepin
(UNKNOWN ATOM TYPE: Hf)
Loaded UNIT: PSF
>
> # Load gaff2 for bond, angle and dihedrals containing fluorine
> # Load vdw parameters for F and Hf (H bonded to fluorinated carbon) - Robalo et al. Phys. Chem. Chem. Phys., 2019,21, 2029-2038
> loadamberparams ./tleap_prep/F.frcmod
Loading parameters: ./tleap_prep/F.frcmod
Reading force field modification type file (frcmod)
Reading title:
Force field parameters from rf2.prmtop
(UNKNOWN ATOM TYPE: Hf)
>
> #####################################################################
> # User can choose the peptide to simulate below
> #####################################################################
> #Example 1 (Simple 4R fluorinated Proline dipeptide) (RF in short)
> amber=sequence{ACE PRF NME}
Sequence: ACE
Sequence: PRF
Sequence: NME
>
> #Example 2 (Simple 4S fluorinated Proline dipeptide) (SF in short)
> #amber=sequence{ACE PSF NME}
>
> #Example 3 (Tetrapeptide)
> #amber=sequence{ACE PRF PRF PSF NME}
> #####################################################################
>
> #Add waters
> solvatebox amber TIP3PBOX 8
Solute vdw bounding box: 10.288 8.934 7.544
Total bounding box for atom centers: 26.288 24.934 23.544
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 2 y= 2 z= 2
Total vdw box size: 28.912 28.370 26.192 angstroms.
Volume: 21483.105 A^3
Total mass 7881.036 amu, Density 0.609 g/cc
Added 427 residues.
>
> #save pdb and amber topologies
> savepdb amber amber_ff/amber.pdb
Writing pdb file: amber_ff/amber.pdb
printing CRYST1 record to PDB file with box info
> saveamberparm amber amber_ff/amber.prmtop amber_ff/amber.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<PRF 2>: -M CA N CD
<PRF 2>: CA +M C O
total 4 improper torsions applied
2 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 427
)