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par_martini_in_charmm_davide.prm
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!
! MARTINI FORCE FIELD FOR CG SIMULATIONS
! IN CHARMM FORM FOR LAMMPS
!
! PARAMETERS FILE
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! !
! Francesca Collu e Enrico Spiga !
! ultima modifica 19-01-2009 !
! !
! Davide Alemani !
! last modified 30-06-2009 !
! Added LJ parameters for W1 !
! !
! !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
! backbone - backbone
!
P5p P5p 0.9556 3.5 ! any BNO-BN0 in coil
P5p Qdb 0.9556 3.5 ! any BN0 interacting with one nter
P5p Qab 0.9556 3.5 ! any BN0 interacting with one cter
P5p P4A 0.9556 3.5 ! any BN0 interacting with one ALA
P5p P5G 0.9556 3.5 ! any BN0 interacting with one GLY
P5p NaP 0.9556 3.5 ! any BN0 interacting with one PRO
Qdb P4A 0.9556 3.5 ! nter interacting with ALA
Qdb P5G 0.9556 3.5 ! nter interacting with GLY
Qdb NaP 0.9556 3.5 ! nter interacting with PRO
Qab P4A 0.9556 3.5 ! cter interacting with ALA
Qab P5G 0.9556 3.5 ! cter interacting with GLY
Qab NaP 0.9556 3.5 ! cter interacting with PRO
P4A P4A 0.9556 3.5 ! ALA interacting with ALA
P4A P5G 0.9556 3.5 ! ALA interacting with GLY
P4A NaP 0.9556 3.5 ! ALA interacting with PRO
P5G P5G 0.9556 3.5 ! GLY interacting with GLY
P5G NaP 0.9556 3.5 ! GLY interacting with PRO
NaP NaP 0.9556 3.5 ! PRO interacting with PRO
!
! backbone - side chains and side chains - side chains
!
! CYS
P5p C5C 17.9175 3.1 ! BN0 coil - SC CYS
Qdb C5C 17.9175 3.1 ! BN0 nter - SC CYS
Qab C5C 17.9175 3.1 ! BN0 cter - SC CYS
! VAL
P5p ACV 9999.9 2.65 ! BNO coil - SC VAL constrained
Qdb ACV 9999.9 2.65 ! BN0 nter - SC VAL constrained
Qab ACV 9999.9 2.65 ! BN0 cter - SC VAL constrained
! LEU
P5p ACL 17.9175 3.1 ! BN0 coil - SC LEU
Qdb ACL 17.9175 3.1 ! BN0 nter - SC LEU
Qab ACL 17.9175 3.1 ! BN0 cter - SC LEU
! ILE
P5p ACL 9999.9 3.1 ! BN0 coil - SC ILE constrained
Qdb ACL 9999.9 3.1 ! BN0 nter - SC ILE constrained
Qab ACL 9999.9 3.1 ! BN0 cter - SC ILE constrained
! MET
P5p C5M 5.9725 4.0 ! BN0 coil - SC MET
Qdb C5M 5.9725 4.0 ! BN0 nter - SC MET
Qab C5M 5.9725 4.0 ! BN0 cter - SC MET
! PRO
P5p ACP 17.9175 3.0 ! BN0 coil - SC PRO
Qdb ACP 17.9175 3.0 ! BN0 nter - SC PRO
Qab ACP 17.9175 3.0 ! BN0 cter - SC PRO
! ASN
P5p P5N 11.945 3.2 ! BN0 coil - SC ASN
Qdb P5N 11.945 3.2 ! BN0 nter - SC ASN
Qab P5N 11.945 3.2 ! BN0 cter - SC ASN
! GLN
P5p P4Q 11.945 4.0 ! BN0 coil - SC GLN
Qdb P4Q 11.945 4.0 ! BN0 nter - SC GLN
Qab P4Q 11.945 4.0 ! BN0 cter - SC GLN
! ASP
P5p QaD 17.9175 3.2 ! BN0 coil - SC ASP
Qdb QaD 17.9175 3.2 ! BN0 nter - SC ASP
Qab QaD 17.9175 3.2 ! BN0 cter - SC ASP
! GLU
P5p QaE 11.945 4.0 ! BN0 coil - SC GLU
Qdb QaE 11.945 4.0 ! BN0 nter - SC GLU
Qab QaE 11.945 4.0 ! BN0 cter - SC GLU
! THR
P5p P1T 9999.9 2.6 ! BN0 coil - SC THR constrained
Qdb P1T 9999.9 2.6 ! BN0 nter - SC THR constrained
Qab P1T 9999.9 2.6 ! BN0 cter - SC THR constrained
! SER
P5p P1S 17.9175 2.5 ! BN0 coil - SC SER
Qdb P1S 17.9175 2.5 ! BN0 nter - SC SER
Qab P1S 17.9175 2.5 ! BN0 cter - SC SER
! LYS
P5p C3p 11.945 3.3 ! BN0 coil - SC1 LYS
Qdb C3p 11.945 3.3 ! BN0 nter - SC1 LYS
Qab C3p 11.945 3.3 ! BN0 cter - SC1 LYS
C3p QdK 11.945 2.8 ! SC1 - SC2 LYS
! ARG
P5p N0p 11.945 3.3 ! BN0 coil - SC1 ARG
Qdb N0p 11.945 3.3 ! BN0 nter - SC1 ARG
Qab N0p 11.945 3.3 ! BN0 cter - SC1 ARG
N0p QdR 11.945 3.4 ! SC1 - SC2 ARG
! HIS
P5p SCp 17.9175 3.2 ! BN0 coil - SC1 HIS (ok also for PHE/TRP 3.1/3.0)
Qdb SCp 17.9175 3.2 ! BN0 nter - SC1 HIS (ok also for PHE/TRP 3.1/3.0)
Qab SCp 17.9175 3.2 ! BN0 cter - SC1 HIS (ok also for PHE/TRP 3.1/3.0)
SCp SPH 9999.9 2.7 ! SC1 - SC2/3 HIS constrained
SPH SPH 9999.9 2.7 ! SC2 - SC3 HIS constrained
! PHE
SCp SCF 9999.9 2.7 ! SC1 - SC2/3 PHE constrained
SCF SCF 9999.9 2.7 ! SC2 - SC3 PHE constrained (ok also for TYR/TRP)
! TYR
P5p SCF 11.945 3.2 ! BN0 coil - SC1/2 TYR
Qdb SCF 11.945 3.2 ! BN0 nter - SC1/2 TYR
Qab SCF 11.945 3.2 ! BN0 cter - SC1/2 TYR
SCF SPY 9999.9 2.7 ! SC1/2 - SC3 TYR constrained
! TRP
SCF SPW 9999.9 2.7 ! SC1/3/4 - SC2 TRP constrained
SCF SCW 9999.9 2.7 ! SC1 - SC2 TRP constrained
SPW SCW 9999.9 2.7 ! SC2 - SC3/4 TRP constrained
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
! backbone - side chains and side chains - side chains
!
! legend
! bb = backbone ; sc = side chain
!
P5p P5p P5p 5.9725 127.00 ! bb-bb-bb
P5p P5p Qab 5.9725 127.00 ! bb-bb-bb
P5p P5p P4A 5.9725 127.00 ! bb-bb-bb
P5p P5p P5G 5.9725 127.00 ! bb-bb-bb
P5p P5p NaP 5.9725 127.00 ! bb-bb-bb
P5p P5p C5M 5.9725 100.00 ! bb-bb-sc all
P5p P5p P5N 5.9725 100.00 ! bb-bb-sc all
P5p P5p P4Q 5.9725 100.00 ! bb-bb-sc all
P5p P5p QaD 5.9725 100.00 ! bb-bb-sc all
P5p P5p QaE 5.9725 100.00 ! bb-bb-sc all
P5p P5p P1T 5.9725 100.00 ! bb-bb-sc all
P5p P5p P1S 5.9725 100.00 ! bb-bb-sc all
P5p P5p C3p 5.9725 100.00 ! bb-bb-sc all
P5p P5p SCF 5.9725 100.00 ! bb-bb-sc all
P5p P5p SPW 5.9725 100.00 ! bb-bb-sc all
P5p P5p C5C 5.9725 100.00 ! bb-bb-sc all
P5p P5p ACV 5.9725 100.00 ! bb-bb-sc all
P5p P5p ACL 5.9725 100.00 ! bb-bb-sc all
P5p P5p N0p 5.9725 100.00 ! bb-bb-sc all
P5p P5p SCp 5.9725 100.00 ! bb-bb-sc all
P5p P4A P5p 5.9725 127.00 ! bb-bb-bb
P5p P4A Qab 5.9725 127.00 ! bb-bb-bb
P5p P4A P4A 5.9725 127.00 ! bb-bb-bb
P5p P4A P5G 5.9725 127.00 ! bb-bb-bb
P5p P4A NaP 5.9725 127.00 ! bb-bb-bb
P5p P5G P5p 5.9725 127.00 ! bb-bb-bb
P5p P5G Qab 5.9725 127.00 ! bb-bb-bb
P5p P5G P4A 5.9725 127.00 ! bb-bb-bb
P5p P5G P5G 5.9725 127.00 ! bb-bb-bb
P5p P5G NaP 5.9725 127.00 ! bb-bb-bb
P5p NaP P5p 5.9725 127.00 ! bb-bb-bb
P5p NaP Qab 5.9725 127.00 ! bb-bb-bb
P5p NaP P4A 5.9725 127.00 ! bb-bb-bb
P5p NaP P5G 5.9725 127.00 ! bb-bb-bb
P5p NaP NaP 5.9725 127.00 ! bb-bb-bb
P5p C3p QdK 5.9725 180.00 ! bb-sc1-sc2 lys/arg
P5p SCF SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
P5p SCF SPY 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
P5p SCF SPW 11.945 90.00 ! bb-sc1-sc2 trp
P5p SPW SCF 11.945 90.00 ! bb-sc1-sc2 trp
P5p N0p QdR 5.9725 180.00 ! bb-sc1-sc2 lys/arg
P5p SCp SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
P5p SCp SPH 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qdb P5p P5p 5.9725 127.00 ! bb-bb-bb
Qdb P5p Qab 5.9725 127.00 ! bb-bb-bb
Qdb P5p P4A 5.9725 127.00 ! bb-bb-bb
Qdb P5p P5G 5.9725 127.00 ! bb-bb-bb
Qdb P5p NaP 5.9725 127.00 ! bb-bb-bb
Qdb P5p C5M 5.9725 100.00 ! bb-bb-sc all
Qdb P5p P5N 5.9725 100.00 ! bb-bb-sc all
Qdb P5p P4Q 5.9725 100.00 ! bb-bb-sc all
Qdb P5p QaD 5.9725 100.00 ! bb-bb-sc all
Qdb P5p QaE 5.9725 100.00 ! bb-bb-sc all
Qdb P5p P1T 5.9725 100.00 ! bb-bb-sc all
Qdb P5p P1S 5.9725 100.00 ! bb-bb-sc all
Qdb P5p C3p 5.9725 100.00 ! bb-bb-sc all
Qdb P5p SCF 5.9725 100.00 ! bb-bb-sc all
Qdb P5p SPW 5.9725 100.00 ! bb-bb-sc all
Qdb P5p C5C 5.9725 100.00 ! bb-bb-sc all
Qdb P5p ACV 5.9725 100.00 ! bb-bb-sc all
Qdb P5p ACL 5.9725 100.00 ! bb-bb-sc all
Qdb P5p N0p 5.9725 100.00 ! bb-bb-sc all
Qdb P5p SCp 5.9725 100.00 ! bb-bb-sc all
Qdb P4A P5p 5.9725 127.00 ! bb-bb-bb
Qdb P4A Qab 5.9725 127.00 ! bb-bb-bb
Qdb P4A P4A 5.9725 127.00 ! bb-bb-bb
Qdb P4A P5G 5.9725 127.00 ! bb-bb-bb
Qdb P4A NaP 5.9725 127.00 ! bb-bb-bb
Qdb P5G P5p 5.9725 127.00 ! bb-bb-bb
Qdb P5G Qab 5.9725 127.00 ! bb-bb-bb
Qdb P5G P4A 5.9725 127.00 ! bb-bb-bb
Qdb P5G P5G 5.9725 127.00 ! bb-bb-bb
Qdb P5G NaP 5.9725 127.00 ! bb-bb-bb
Qdb NaP P5p 5.9725 127.00 ! bb-bb-bb
Qdb NaP Qab 5.9725 127.00 ! bb-bb-bb
Qdb NaP P4A 5.9725 127.00 ! bb-bb-bb
Qdb NaP P5G 5.9725 127.00 ! bb-bb-bb
Qdb NaP NaP 5.9725 127.00 ! bb-bb-bb
Qdb NaP ACP 5.9725 100.00 ! bb-bb-sc all
Qdb C3p QdK 5.9725 180.00 ! bb-sc1-sc2 lys/arg
Qdb SCF SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qdb SCF SPY 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qdb SCF SPW 11.945 90.00 ! bb-sc1-sc2 trp
Qdb SPW SCF 11.945 90.00 ! bb-sc1-sc2 trp
Qdb N0p QdR 5.9725 180.00 ! bb-sc1-sc2 lys/arg
Qdb SCp SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qab C3p QdK 5.9725 180.00 ! bb-sc1-sc2 lys/arg
Qab SCF SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qab SCF SPY 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qab SCF SPW 11.945 90.00 ! bb-sc1-sc2 trp
Qab SPW SCF 11.945 90.00 ! bb-sc1-sc2 trp
Qab N0p QdR 5.9725 180.00 ! bb-sc1-sc2 lys/arg
Qab SCp SCF 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
Qab SCp SPH 11.945 150.00 ! bb-sc1-sc2 his/phe/tyr
P4A P5p Qab 5.9725 127.00 ! bb-bb-bb
P4A P5p P4A 5.9725 127.00 ! bb-bb-bb
P4A P5p P5G 5.9725 127.00 ! bb-bb-bb
P4A P5p NaP 5.9725 127.00 ! bb-bb-bb
P4A P5p C5M 5.9725 100.00 ! bb-bb-sc all
P4A P5p P5N 5.9725 100.00 ! bb-bb-sc all
P4A P5p P4Q 5.9725 100.00 ! bb-bb-sc all
P4A P5p QaD 5.9725 100.00 ! bb-bb-sc all
P4A P5p QaE 5.9725 100.00 ! bb-bb-sc all
P4A P5p P1T 5.9725 100.00 ! bb-bb-sc all
P4A P5p P1S 5.9725 100.00 ! bb-bb-sc all
P4A P5p C3p 5.9725 100.00 ! bb-bb-sc all
P4A P5p SCF 5.9725 100.00 ! bb-bb-sc all
P4A P5p SPW 5.9725 100.00 ! bb-bb-sc all
P4A P5p C5C 5.9725 100.00 ! bb-bb-sc all
P4A P5p ACV 5.9725 100.00 ! bb-bb-sc all
P4A P5p ACL 5.9725 100.00 ! bb-bb-sc all
P4A P5p N0p 5.9725 100.00 ! bb-bb-sc all
P4A P5p SCp 5.9725 100.00 ! bb-bb-sc all
P4A Qab C5M 5.9725 100.00 ! bb-bb-sc all
P4A Qab P5N 5.9725 100.00 ! bb-bb-sc all
P4A Qab P4Q 5.9725 100.00 ! bb-bb-sc all
P4A Qab QaD 5.9725 100.00 ! bb-bb-sc all
P4A Qab QaE 5.9725 100.00 ! bb-bb-sc all
P4A Qab P1T 5.9725 100.00 ! bb-bb-sc all
P4A Qab P1S 5.9725 100.00 ! bb-bb-sc all
P4A Qab C3p 5.9725 100.00 ! bb-bb-sc all
P4A Qab SCF 5.9725 100.00 ! bb-bb-sc all
P4A Qab SPW 5.9725 100.00 ! bb-bb-sc all
P4A Qab C5C 5.9725 100.00 ! bb-bb-sc all
P4A Qab ACV 5.9725 100.00 ! bb-bb-sc all
P4A Qab ACL 5.9725 100.00 ! bb-bb-sc all
P4A Qab N0p 5.9725 100.00 ! bb-bb-sc all
P4A Qab SCp 5.9725 100.00 ! bb-bb-sc all
P4A P4A Qab 5.9725 127.00 ! bb-bb-bb
P4A P4A P4A 5.9725 127.00 ! bb-bb-bb
P4A P4A P5G 5.9725 127.00 ! bb-bb-bb
P4A P4A NaP 5.9725 127.00 ! bb-bb-bb
P4A P5G Qab 5.9725 127.00 ! bb-bb-bb
P4A P5G P4A 5.9725 127.00 ! bb-bb-bb
P4A P5G P5G 5.9725 127.00 ! bb-bb-bb
P4A P5G NaP 5.9725 127.00 ! bb-bb-bb
P4A NaP Qab 5.9725 127.00 ! bb-bb-bb
P4A NaP P4A 5.9725 127.00 ! bb-bb-bb
P4A NaP P5G 5.9725 127.00 ! bb-bb-bb
P4A NaP NaP 5.9725 127.00 ! bb-bb-bb
P4A NaP ACP 5.9725 100.00 ! bb-bb-sc all
P5G P5p Qab 5.9725 127.00 ! bb-bb-bb
P5G P5p P5G 5.9725 127.00 ! bb-bb-bb
P5G P5p NaP 5.9725 127.00 ! bb-bb-bb
P5G P5p C5M 5.9725 100.00 ! bb-bb-sc all
P5G P5p P5N 5.9725 100.00 ! bb-bb-sc all
P5G P5p P4Q 5.9725 100.00 ! bb-bb-sc all
P5G P5p QaD 5.9725 100.00 ! bb-bb-sc all
P5G P5p QaE 5.9725 100.00 ! bb-bb-sc all
P5G P5p P1T 5.9725 100.00 ! bb-bb-sc all
P5G P5p P1S 5.9725 100.00 ! bb-bb-sc all
P5G P5p C3p 5.9725 100.00 ! bb-bb-sc all
P5G P5p SCF 5.9725 100.00 ! bb-bb-sc all
P5G P5p SPW 5.9725 100.00 ! bb-bb-sc all
P5G P5p C5C 5.9725 100.00 ! bb-bb-sc all
P5G P5p ACV 5.9725 100.00 ! bb-bb-sc all
P5G P5p ACL 5.9725 100.00 ! bb-bb-sc all
P5G P5p N0p 5.9725 100.00 ! bb-bb-sc all
P5G P5p SCp 5.9725 100.00 ! bb-bb-sc all
P5G Qab C5M 5.9725 100.00 ! bb-bb-sc all
P5G Qab ACP 5.9725 100.00 ! bb-bb-sc all
P5G Qab P5N 5.9725 100.00 ! bb-bb-sc all
P5G Qab P4Q 5.9725 100.00 ! bb-bb-sc all
P5G Qab QaD 5.9725 100.00 ! bb-bb-sc all
P5G Qab QaE 5.9725 100.00 ! bb-bb-sc all
P5G Qab P1T 5.9725 100.00 ! bb-bb-sc all
P5G Qab P1S 5.9725 100.00 ! bb-bb-sc all
P5G Qab C3p 5.9725 100.00 ! bb-bb-sc all
P5G Qab SCF 5.9725 100.00 ! bb-bb-sc all
P5G Qab SPW 5.9725 100.00 ! bb-bb-sc all
P5G Qab C5C 5.9725 100.00 ! bb-bb-sc all
P5G Qab ACV 5.9725 100.00 ! bb-bb-sc all
P5G Qab ACL 5.9725 100.00 ! bb-bb-sc all
P5G Qab N0p 5.9725 100.00 ! bb-bb-sc all
P5G Qab SCp 5.9725 100.00 ! bb-bb-sc all
P5G P4A Qab 5.9725 127.00 ! bb-bb-bb
P5G P4A P5G 5.9725 127.00 ! bb-bb-bb
P5G P4A NaP 5.9725 127.00 ! bb-bb-bb
P5G P5G Qab 5.9725 127.00 ! bb-bb-bb
P5G P5G P5G 5.9725 127.00 ! bb-bb-bb
P5G P5G NaP 5.9725 127.00 ! bb-bb-bb
P5G NaP Qab 5.9725 127.00 ! bb-bb-bb
P5G NaP P5G 5.9725 127.00 ! bb-bb-bb
P5G NaP NaP 5.9725 127.00 ! bb-bb-bb
P5G NaP ACP 5.9725 100.00 ! bb-bb-sc all
NaP P5p Qab 5.9725 127.00 ! bb-bb-bb
NaP P5p NaP 5.9725 127.00 ! bb-bb-bb
NaP P5p C5M 5.9725 100.00 ! bb-bb-sc all
NaP P5p P5N 5.9725 100.00 ! bb-bb-sc all
NaP P5p P4Q 5.9725 100.00 ! bb-bb-sc all
NaP P5p QaD 5.9725 100.00 ! bb-bb-sc all
NaP P5p QaE 5.9725 100.00 ! bb-bb-sc all
NaP P5p P1T 5.9725 100.00 ! bb-bb-sc all
NaP P5p P1S 5.9725 100.00 ! bb-bb-sc all
NaP P5p C3p 5.9725 100.00 ! bb-bb-sc all
NaP P5p SCF 5.9725 100.00 ! bb-bb-sc all
NaP P5p SPW 5.9725 100.00 ! bb-bb-sc all
NaP P5p C5C 5.9725 100.00 ! bb-bb-sc all
NaP P5p ACV 5.9725 100.00 ! bb-bb-sc all
NaP P5p ACL 5.9725 100.00 ! bb-bb-sc all
NaP P5p N0p 5.9725 100.00 ! bb-bb-sc all
NaP P5p SCp 5.9725 100.00 ! bb-bb-sc all
NaP Qab C5M 5.9725 100.00 ! bb-bb-sc all
NaP Qab ACP 5.9725 100.00 ! bb-bb-sc all
NaP Qab P5N 5.9725 100.00 ! bb-bb-sc all
NaP Qab P4Q 5.9725 100.00 ! bb-bb-sc all
NaP Qab QaD 5.9725 100.00 ! bb-bb-sc all
NaP Qab QaE 5.9725 100.00 ! bb-bb-sc all
NaP Qab P1T 5.9725 100.00 ! bb-bb-sc all
NaP Qab P1S 5.9725 100.00 ! bb-bb-sc all
NaP Qab C3p 5.9725 100.00 ! bb-bb-sc all
NaP Qab SCF 5.9725 100.00 ! bb-bb-sc all
NaP Qab SPW 5.9725 100.00 ! bb-bb-sc all
NaP Qab C5C 5.9725 100.00 ! bb-bb-sc all
NaP Qab ACV 5.9725 100.00 ! bb-bb-sc all
NaP Qab ACL 5.9725 100.00 ! bb-bb-sc all
NaP Qab N0p 5.9725 100.00 ! bb-bb-sc all
NaP Qab SCp 5.9725 100.00 ! bb-bb-sc all
NaP P4A Qab 5.9725 127.00 ! bb-bb-bb
NaP P4A NaP 5.9725 127.00 ! bb-bb-bb
NaP P5G Qab 5.9725 127.00 ! bb-bb-bb
NaP P5G NaP 5.9725 127.00 ! bb-bb-bb
NaP NaP NaP 5.9725 127.00 ! bb-bb-bb
C5M P5p Qab 5.9725 100.00 ! bb-bb-sc all
ACP Qdb P5p 5.9725 100.00 ! bb-bb-sc all
ACP Qdb P5G 5.9725 100.00 ! bb-bb-sc all
ACP Qdb NaP 5.9725 100.00 ! bb-bb-sc all
ACP Qdb P4A 5.9725 100.00 ! bb-bb-sc all
ACP NaP P5p 5.9725 100.00 ! bb-bb-sc all
ACP NaP Qab 5.9725 100.00 ! bb-bb-sc all
ACP NaP NaP 5.9725 100.00 ! bb-bb-sc all
P5N P5p Qab 5.9725 100.00 ! bb-bb-sc all
P5N Qdb Qab 5.9725 100.00 ! bb-bb-sc all
P5N Qdb P4A 5.9725 100.00 ! bb-bb-sc all
P5N Qdb P5G 5.9725 100.00 ! bb-bb-sc all
P5N Qdb NaP 5.9725 100.00 ! bb-bb-sc all
P5N Qab Qdb 5.9725 100.00 ! bb-bb-sc all
P4Q P5p Qab 5.9725 100.00 ! bb-bb-sc all
P4Q Qdb P5p 5.9725 100.00 ! bb-bb-sc all
P4Q Qdb Qab 5.9725 100.00 ! bb-bb-sc all
P4Q Qdb P4A 5.9725 100.00 ! bb-bb-sc all
P4Q Qdb P5G 5.9725 100.00 ! bb-bb-sc all
P4Q Qdb NaP 5.9725 100.00 ! bb-bb-sc all
P4Q Qab P5p 5.9725 100.00 ! bb-bb-sc all
QaD P5p Qab 5.9725 100.00 ! bb-bb-sc all
QaD Qdb P5p 5.9725 100.00 ! bb-bb-sc all
QaD Qdb Qab 5.9725 100.00 ! bb-bb-sc all
QaD Qdb P4A 5.9725 100.00 ! bb-bb-sc all
QaD Qdb P5G 5.9725 100.00 ! bb-bb-sc all
QaD Qdb NaP 5.9725 100.00 ! bb-bb-sc all
QaD Qab P5p 5.9725 100.00 ! bb-bb-sc all
QaD Qab Qdb 5.9725 100.00 ! bb-bb-sc all
QaE P5p Qab 5.9725 100.00 ! bb-bb-sc all
QaE Qdb P5p 5.9725 100.00 ! bb-bb-sc all
QaE Qdb Qab 5.9725 100.00 ! bb-bb-sc all
QaE Qdb P4A 5.9725 100.00 ! bb-bb-sc all
QaE Qdb P5G 5.9725 100.00 ! bb-bb-sc all
QaE Qdb NaP 5.9725 100.00 ! bb-bb-sc all
QaE Qab P5p 5.9725 100.00 ! bb-bb-sc all
QaE Qab Qdb 5.9725 100.00 ! bb-bb-sc all
P1T P5p Qab 5.9725 100.00 ! bb-bb-sc all
P1T Qdb P5p 5.9725 100.00 ! bb-bb-sc all
P1T Qdb Qab 5.9725 100.00 ! bb-bb-sc all
P1T Qdb P4A 5.9725 100.00 ! bb-bb-sc all
P1T Qdb P5G 5.9725 100.00 ! bb-bb-sc all
P1T Qdb NaP 5.9725 100.00 ! bb-bb-sc all
P1T Qab P5p 5.9725 100.00 ! bb-bb-sc all
P1T Qab Qdb 5.9725 100.00 ! bb-bb-sc all
P1S P5p Qab 5.9725 100.00 ! bb-bb-sc all
P1S Qdb P5p 5.9725 100.00 ! bb-bb-sc all
P1S Qdb Qab 5.9725 100.00 ! bb-bb-sc all
P1S Qdb P4A 5.9725 100.00 ! bb-bb-sc all
P1S Qdb P5G 5.9725 100.00 ! bb-bb-sc all
P1S Qdb NaP 5.9725 100.00 ! bb-bb-sc all
P1S Qab P5p 5.9725 100.00 ! bb-bb-sc all
P1S Qab Qdb 5.9725 100.00 ! bb-bb-sc all
C3p P5p Qab 5.9725 100.00 ! bb-bb-sc all
C3p Qdb P5p 5.9725 100.00 ! bb-bb-sc all
C3p Qdb Qab 5.9725 100.00 ! bb-bb-sc all
C3p Qdb P4A 5.9725 100.00 ! bb-bb-sc all
C3p Qdb P5G 5.9725 100.00 ! bb-bb-sc all
C3p Qdb NaP 5.9725 100.00 ! bb-bb-sc all
C3p Qab P5p 5.9725 100.00 ! bb-bb-sc all
C3p Qab Qdb 5.9725 100.00 ! bb-bb-sc all
SCF P5p Qab 5.9725 100.00 ! bb-bb-sc all
! devo metterlo?
!SCF P5p SCF
SCF P5p SPW 11.945 90.00 ! bb-sc1-sc2 trp
SCF Qdb P5p 5.9725 100.00 ! bb-bb-sc all
SCF Qdb Qab 5.9725 100.00 ! bb-bb-sc all
SCF Qdb P4A 5.9725 100.00 ! bb-bb-sc all
SCF Qdb P5G 5.9725 100.00 ! bb-bb-sc all
SCF Qdb NaP 5.9725 100.00 ! bb-bb-sc all
! devo metterlo?
!SCF Qdb SCF
SCF Qdb SPW 11.945 90.00 ! bb-sc1-sc2 trp
SCF Qab P5p 5.9725 100.00 ! bb-bb-sc all
SCF Qab Qdb 5.9725 100.00 ! bb-bb-sc all
! devo metterlo?
!SCF Qab SCF
SCF Qab SPW 11.945 90.00 ! bb-sc1-sc2 trp
! devo metterli?
!SCF SCF SCF
!SCF SCF SPW
!SCF SPY SCF
!SCF SPY SPY
!SCF SPW SCF
!SCF SCp SCF
SPW P5p Qab 5.9725 100.00 ! bb-bb-sc all
SPW P5p SCF 11.945 90.00 ! bb-sc1-sc2 trp
SPW Qdb P5p 5.9725 100.00 ! bb-bb-sc all
SPW Qdb Qab 5.9725 100.00 ! bb-bb-sc all
SPW Qdb P4A 5.9725 100.00 ! bb-bb-sc all
SPW Qdb P5G 5.9725 100.00 ! bb-bb-sc all
SPW Qdb NaP 5.9725 100.00 ! bb-bb-sc all
SPW Qab P5p 5.9725 100.00 ! bb-bb-sc all
SPW Qab Qdb 5.9725 100.00 ! bb-bb-sc all
! devo metterlo?
!SPW SCF SCF
C5C P5p Qab 5.9725 100.00 ! bb-bb-sc all
C5C Qdb P5p 5.9725 100.00 ! bb-bb-sc all
C5C Qdb Qab 5.9725 100.00 ! bb-bb-sc all
C5C Qdb P4A 5.9725 100.00 ! bb-bb-sc all
C5C Qdb P5G 5.9725 100.00 ! bb-bb-sc all
C5C Qdb NaP 5.9725 100.00 ! bb-bb-sc all
C5C Qab P5p 5.9725 100.00 ! bb-bb-sc all
C5C Qab Qdb 5.9725 100.00 ! bb-bb-sc all
ACV P5p Qab 5.9725 100.00 ! bb-bb-sc all
ACV Qdb P5p 5.9725 100.00 ! bb-bb-sc all
ACV Qdb Qab 5.9725 100.00 ! bb-bb-sc all
ACV Qdb P4A 5.9725 100.00 ! bb-bb-sc all
ACV Qdb P5G 5.9725 100.00 ! bb-bb-sc all
ACV Qdb NaP 5.9725 100.00 ! bb-bb-sc all
ACV Qab P5p 5.9725 100.00 ! bb-bb-sc all
ACV Qab Qdb 5.9725 100.00 ! bb-bb-sc all
ACL P5p Qab 5.9725 100.00 ! bb-bb-sc all
ACL Qdb P5p 5.9725 100.00 ! bb-bb-sc all
ACL Qdb Qdb 5.9725 100.00 ! bb-bb-sc all
ACL Qdb Qab 5.9725 100.00 ! bb-bb-sc all
ACL Qdb P4A 5.9725 100.00 ! bb-bb-sc all
ACL Qdb P5G 5.9725 100.00 ! bb-bb-sc all
ACL Qdb NaP 5.9725 100.00 ! bb-bb-sc all
ACL Qab P5p 5.9725 100.00 ! bb-bb-sc all
ACL Qab Qdb 5.9725 100.00 ! bb-bb-sc all
N0p P5p Qab 5.9725 100.00 ! bb-bb-sc all
N0p Qdb P5p 5.9725 100.00 ! bb-bb-sc all
N0p Qdb Qab 5.9725 100.00 ! bb-bb-sc all
N0p Qdb P4A 5.9725 100.00 ! bb-bb-sc all
N0p Qdb P5G 5.9725 100.00 ! bb-bb-sc all
N0p Qdb NaP 5.9725 100.00 ! bb-bb-sc all
N0p Qab P5p 5.9725 100.00 ! bb-bb-sc all
N0p Qab Qdb 5.9725 100.00 ! bb-bb-sc all
SCp P5p Qab 5.9725 100.00 ! bb-bb-sc all
SCp Qdb P5p 5.9725 100.00 ! bb-bb-sc all
SCp Qdb Qab 5.9725 100.00 ! bb-bb-sc all
SCp Qdb P4A 5.9725 100.00 ! bb-bb-sc all
SCp Qdb P5G 5.9725 100.00 ! bb-bb-sc all
SCp Qdb NaP 5.9725 100.00 ! bb-bb-sc all
SCp Qab P5p 5.9725 100.00 ! bb-bb-sc all
SCp Qab Qdb 5.9725 100.00 ! bb-bb-sc all
! devo metterli?
!SCp SCF SCF
!SCp SPH SPH
!SPH SCp Qdb
!SPH SCp SPH
!SPH SPH SCp
! aggiunte per TRP
! bb-bb-sc1
P5p P5p SCW 5.9725 100.00 ! bb-bb-sc all
P5p Qdb SCW 5.9725 100.00 ! bb-bb-sc all
P5p Qab SCW 5.9725 100.00 ! bb-bb-sc all
P4A P5p SCW 5.9725 100.00 ! bb-bb-sc all
P4A Qdb SCW 5.9725 100.00 ! bb-bb-sc all
P4A Qab SCW 5.9725 100.00 ! bb-bb-sc all
P5G P5p SCW 5.9725 100.00 ! bb-bb-sc all
P5G Qdb SCW 5.9725 100.00 ! bb-bb-sc all
P5G Qab SCW 5.9725 100.00 ! bb-bb-sc all
NaP P5p SCW 5.9725 100.00 ! bb-bb-sc all
NaP Qdb SCW 5.9725 100.00 ! bb-bb-sc all
NaP Qab SCW 5.9725 100.00 ! bb-bb-sc all
Qdb P5p SCW 5.9725 100.00 ! bb-bb-sc all
Qdb Qab SCW 5.9725 100.00 ! bb-bb-sc all
Qab P5p SCW 5.9725 100.00 ! bb-bb-sc all
Qab Qdb SCW 5.9725 100.00 ! bb-bb-sc all
! bb-sc
SCW P5p SPW 11.945 210.00 ! bb-sc1-sc2 trp
SCW Qab SPW 11.945 210.00 ! bb-sc1-sc2 trp
SCW Qdb SPW 11.945 210.00 ! bb-sc1-sc2 trp
SCW SPW P5p 11.945 210.00 ! bb-sc1-sc2 trp
SCW SPW Qab 11.945 210.00 ! bb-sc1-sc2 trp
SCW SPW Qdb 11.945 210.00 ! bb-sc1-sc2 trp
! devo metterlo?
!SPW SCW SCF
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
! backbone - backbone standard and backbone - gly/ala/pro
! template
!
P5p P5p P5p P5p 0.0000 1 0.00
Qdb P5p P5p P5p 0.0000 1 0.00
P5p P5p P5p Qab 0.0000 1 0.00
Qdb P5p P5p Qab 0.0000 1 0.00
P5p P5p P5p P4A 0.0000 1 0.00
P5p P5p P4A P4A 0.0000 1 0.00
P5p P4A P4A P4A 0.0000 1 0.00
P5p P5p P5p P5G 0.0000 1 0.00
P5p P5p P5G P5G 0.0000 1 0.00
P5p P5G P5G P5G 0.0000 1 0.00
Qdb P5G P5G P5G 0.0000 1 0.00
Qdb P4A P4A P4A 0.0000 1 0.00
Qab P5G P5G P5G 0.0000 1 0.00
Qab P4A P4A P4A 0.0000 1 0.00
NaP NaP NaP NaP 0.0000 1 0.00
NaP NaP NaP P5p 0.0000 1 0.00
NaP NaP P5p P5p 0.0000 1 0.00
NaP P5p P5p P5p 0.0000 1 0.00
P5p NaP P5p P5p 0.0000 1 0.00
P5p NaP P5p NaP 0.0000 1 0.00
X P5p P5G X 0.0000 1 0.00
X P5p P4A X 0.0000 1 0.00
! gly and ala
! considerare se metterli in questa forma
! o se possiamo mettere X e diminuire il
! numero di quadruplette
!P5G P5G P5G P5G 0.0000 1 0.00
!P5G P5G P5G P4A 0.0000 1 0.00
!P5G P5G P4A P4A 0.0000 1 0.00
!P5G P4A P4A P4A 0.0000 1 0.00
!P4A P4A P4A P4A 0.0000 1 0.00
!P5G P4A P4A P5G 0.0000 1 0.00
!P4A P5G P5G P4A 0.0000 1 0.00
!P4A P5G P4A P5G 0.0000 1 0.00
!P5G P4A P5G P4A 0.0000 1 0.00
!P5G P5G P4A P5G 0.0000 1 0.00
!P4A P4A P5G P4A 0.0000 1 0.00
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
! phe
P5p SCF SCF SCp 11.945 0 0.0000
! tyr
P5p SCF SPY SCF 11.945 0 0.0000
! his
P5p SPH SPH SCp 11.945 0 0.0000
! trp
P5p SCF SCF SCF 11.945 0 0.0000
P5p SCF SCF SPW 47.78 0 0.0000
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
! template
!CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! P5
P5N 0.000000 -1.33784 2.637785
P5p 0.000000 -1.33784 2.637785
P5G 0.000000 -1.33784 2.637785
! P4
P4Q 0.000000 -1.194500 2.637785
P4R 0.000000 -1.194500 2.637785
P4A 0.000000 -1.194500 2.637785
! P1
P1T 0.000000 -1.07505 2.637785
P1S 0.000000 -1.07505 2.637785
! Na
NaP 0.000000 -0.9556 2.637785
! N0
N0p 0.000000 -0.83615 2.637785
! C5
C5M 0.000000 -0.83615 2.637785
C5C 0.000000 -0.83615 2.637785
! C3
C3p 0.000000 -0.83615 2.637785
! C1
C13 0.000000 -0.83615 2.637785
C14 0.000000 -0.83615 2.637785
! Qd
Qdb 0.000000 -1.1945 2.637785
QdR 0.000000 -1.1945 2.637785
QdK 0.000000 -1.1945 2.637785
! Qa
Qab 0.000000 -1.1945 2.637785
QaD 0.000000 -1.1945 2.637785
QaE 0.000000 -1.1945 2.637785
! S*
SPW 0.000000 -0.80628 2.413293
SPY 0.000000 -0.80628 2.413293
SPH 0.000000 -0.80628 2.413293
SCF 0.000000 -0.62711 2.413293
SCp 0.000000 -0.62711 2.413293
SCW 0.000000 -0.62711 2.413293
! A*
ACP 0.000000 -0.83615 2.637785
ACV 0.000000 -0.83615 2.637785
ACL 0.000000 -0.83615 2.637785
! Water
P4 0.000000 -1.1945 2.637785
! Water anti freeze
BP4 0.000000 -1.33784 3.199068
! Water 1 molecule
W1 0.0000000 -0.7641 3.23
END