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par_lbm.prm
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>> LBM-CG Parameter File for Proteins version 1.1 <<
>> Mapping Martini CG-FF like <<
>> Backbone part obtained to mantain secondary structure elements <<
>> Bonded part obtained from Boltzmann inversion of UA-FF simulations <<
>> Non-bonded part extracted from Martini CG-FF <<
*>>>>>>>>>>>>>>>>>>>>>> September, 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the LBM EPFL web site
* parameter set discussion forum
*
* modified by Enrico 09-09-2011
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
! backbone
BUN BU 50.00 3.81 !
BUN BUC 50.00 3.81 !
BUN BA 50.00 3.81 !
BUN BAC 50.00 3.81 !
BU BU 50.00 3.81 !
BU BUC 50.00 3.81 !
BUC BU 50.00 3.81 !
BU BA 50.00 3.81 !
BU BAC 50.00 3.81 !
BAN BA 50.00 3.81 !
BA BA 50.00 3.81 !
BA BAC 50.00 3.81 !
!
! arginine
BUN SR1 30.53 3.25 ! fit Boltzmann inversion sim UA
BU SR1 30.53 3.25 ! fit Boltzmann inversion sim UA
BUC SR1 30.53 3.25 ! fit Boltzmann inversion sim UA
SR1 SR2 16.50 3.38 ! fit Boltzmann inversion sim UA
!
! asparagine
BUN SN 50.00 2.60 ! fit Boltzmann inversion sim UA
BU SN 50.00 2.60 ! fit Boltzmann inversion sim UA
BUC SN 50.00 2.60 ! fit Boltzmann inversion sim UA
!
! aspartate
BUN SD 50.00 2.58 ! fit Boltzmann inversion sim UA
BU SD 50.00 2.58 ! fit Boltzmann inversion sim UA
BUC SD 50.00 2.58 ! fit Boltzmann inversion sim UA
!
! cysteine
BUN SC1 50.00 2.42 ! fit Boltzmann inversion sim UA
BU SC1 50.00 2.42 ! fit Boltzmann inversion sim UA
BUC SC1 50.00 2.42 ! fit Boltzmann inversion sim UA
BUN SC2 50.00 2.42 ! fit Boltzmann inversion sim UA
BU SC2 50.00 2.42 ! fit Boltzmann inversion sim UA
BUC SC2 50.00 2.42 ! fit Boltzmann inversion sim UA
SC2 SC2 50.00 2.4 ! trial
SC1 SC1 50.00 2.4 ! trial
!
! glutamate
BUN SE 50.00 3.47 ! fit Boltzmann inversion sim UA
BU SE 50.00 3.47 ! fit Boltzmann inversion sim UA
BUC SE 50.00 3.47 ! fit Boltzmann inversion sim UA
!
! glutamine
BUN SQ 50.00 3.5 ! fit Boltzmann inversion sim UA
BU SQ 50.00 3.5 ! fit Boltzmann inversion sim UA
BUC SQ 50.00 3.5 ! fit Boltzmann inversion sim UA
!
! histidine
BUN SH1 50.00 1.92 ! fit Boltzmann inversion sim UA
BU SH1 50.00 1.92 ! fit Boltzmann inversion sim UA
BUC SH1 50.00 1.92 ! fit Boltzmann inversion sim UA
SH1 SH2 50.00 2.42 ! fit Boltzmann inversion sim UA
SH2 SH2 50.00 1.75 ! fit Boltzmann inversion sim UA
!
! isoleucine
BUN SI 10.00 2.22 ! fit Boltzmann inversion sim UA
BU SI 10.00 2.22 ! fit Boltzmann inversion sim UA
BUC SI 10.00 2.22 ! fit Boltzmann inversion sim UA
!
! leucine
BUN SL 50.00 2.64 ! fit Boltzmann inversion sim UA
BU SL 50.00 2.64 ! fit Boltzmann inversion sim UA
BUC SL 50.00 2.64 ! fit Boltzmann inversion sim UA
!
! lysine
BUN SK1 50.00 2.60 ! fit Boltzmann inversion sim UA
BU SK1 50.00 2.60 ! fit Boltzmann inversion sim UA
BUC SK1 50.00 2.60 ! fit Boltzmann inversion sim UA
SK1 SK2 50.00 3.25 ! fit Boltzmann inversion sim UA
!
! methionine
BUN SM 2.00 3.20 ! fit Boltzmann inversion sim UA
BU SM 2.00 3.20 ! fit Boltzmann inversion sim UA
BUC SM 2.00 3.20 ! fit Boltzmann inversion sim UA
!
! phenylalanine
BUN SF1 50.00 1.97 ! fit Boltzmann inversion sim UA
BU SF1 50.00 1.97 ! fit Boltzmann inversion sim UA
BUC SF1 50.00 1.97 ! fit Boltzmann inversion sim UA
SF1 SF2 50.00 2.57 ! fit Boltzmann inversion sim UA
SF2 SF2 50.00 2.31 ! fit Boltzmann inversion sim UA
!
! proline
BUN SP 50.00 1.86 ! fit Boltzmann inversion sim UA
BU SP 50.00 1.86 ! fit Boltzmann inversion sim UA
BUC SP 50.00 1.86 ! fit Boltzmann inversion sim UA
!
! serine
BUN SS 50.00 2.0 ! fit Boltzmann inversion sim UA
BU SS 50.00 2.0 ! fit Boltzmann inversion sim UA
BUC SS 50.00 2.0 ! fit Boltzmann inversion sim UA
!
! threonine
BUN ST 50.00 1.97 ! fit Boltzmann inversion sim UA
BU ST 50.00 1.97 ! fit Boltzmann inversion sim UA
BUC ST 50.00 1.97 ! fit Boltzmann inversion sim UA
!
! tryptophan
BUN SW1 50.00 1.96 ! fit Boltzmann inversion sim UA
BU SW1 50.00 1.96 ! fit Boltzmann inversion sim UA
BUC SW1 50.00 1.96 ! fit Boltzmann inversion sim UA
!
SW1 SW2 50.00 2.42 ! fit Boltzmann inversion sim UA
SW1 SW3 50.00 2.96 ! fit Boltzmann inversion sim UA
SW2 SW3 50.00 2.96 ! fit Boltzmann inversion sim UA
SW3 SW3 50.00 1.95 ! fit Boltzmann inversion sim UA
!
! tyrosine
BUN SY1 50.00 1.97 ! fit Boltzmann inversion sim UA
BU SY1 50.00 1.97 ! fit Boltzmann inversion sim UA
BUC SY1 50.00 1.97 ! fit Boltzmann inversion sim UA
SY1 SY2 82.00 2.74 ! fit Boltzmann inversion sim UA
SY2 SY2 100.00 2.23 ! fit Boltzmann inversion sim UA
!
! valine
BUN SV 50.00 1.97 ! fit Boltzmann inversion sim UA
BU SV 50.00 1.97 ! fit Boltzmann inversion sim UA
BUC SV 50.00 1.97 ! fit Boltzmann inversion sim UA
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 Theta0 Ktheta1 Ktheta2 Ktheta3
! backbone
BUN BU BU 132 256.2223 725.0207 512.8895 ! symmetric barrier of 8 kcal/mol with minima in alpha and beta
BUN BU BA 132 256.2223 725.0207 512.8895
BU BU BU 132 256.2223 725.0207 512.8895
BU BU BUC 132 256.2223 725.0207 512.8895
BU BA BU 132 256.2223 725.0207 512.8895
BU BA BA 132 256.2223 725.0207 512.8895
BU BU BA 132 256.2223 725.0207 512.8895
BU BA BUC 132 256.2223 725.0207 512.8895
BU BA BAC 132 256.2223 725.0207 512.8895
BU BU BAC 132 256.2223 725.0207 512.8895
BA BA BA 132 256.2223 725.0207 512.8895
BA BA BU 132 256.2223 725.0207 512.8895
BA BU BU 132 256.2223 725.0207 512.8895
BA BU BA 132 256.2223 725.0207 512.8895
BA BA BU 132 256.2223 725.0207 512.8895
BA BA BAC 132 256.2223 725.0207 512.8895
BA BA BUC 132 256.2223 725.0207 512.8895
BA BU BUC 132 256.2223 725.0207 512.8895
BA BU BAC 132 256.2223 725.0207 512.8895
BA BA BUC 132 256.2223 725.0207 512.8895
BAN BA BA 132 256.2223 725.0207 512.8895
!
! arginine
BU BU SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SR1 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SR1 BUN BU 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
SR1 BUN BA 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
SR1 BU BU 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
SR1 BU BUC 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
SR1 BU BAC 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
SR1 BU BA 120.00 2.62 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BUN SR1 SR2 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SR1 SR2 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SR1 SR2 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
SR2 SR1 BU 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
SR2 SR1 BUN 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
SR2 SR1 BUC 154.00 2.95 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! asparagine
SN BU BU 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA (prov)
SN BU BUC 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
SN BU BA 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
SN BU BAC 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
SN BUN BU 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
SN BUN BA 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BU BU SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BUN BU SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BA BU SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BAN BU SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BU BUC SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
BA BUC SN 145.0 29.629 65.843 36.579 ! fit Boltzmann inversion sim UA
!
! aspartate
SD BUN BU 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA (prov)
SD BUN BA 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SD BU BU 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SD BU BUC 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SD BU BA 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SD BU BAC 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BU SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BUN BU SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BU SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BAN BU SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BUC SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BUC SD 145.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
!
! cysteine
! 1
SC1 BUN BU 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SC1 BUN BA 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SC1 BU BU 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SC1 BU BUC 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SC1 BU BA 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
SC1 BU BAC 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BU SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BUN BU SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BU SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BAN BU SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BUC SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BUC SC1 143.0 42.666 113.777 75.851 ! fit Boltzmann inversion sim UA
! 2
SC2 BUN BU 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
SC2 BUN BA 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
SC2 BU BU 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
SC2 BU BUC 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
SC2 BU BA 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
SC2 BU BAC 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BU SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BUN BU SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BU SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BAN BU SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BU BUC SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
BA BUC SC2 143.0 10.0 113.777 75.851 ! fit Boltzmann inversion sim UA
!
SC2 SC2 BUN 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
SC2 SC2 BU 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
SC2 SC2 BUC 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
SC1 SC1 BUN 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
SC1 SC1 BU 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
SC1 SC1 BUC 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BUN SC2 SC2 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BU SC2 SC2 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BUC SC2 SC2 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BUN SC1 SC1 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BU SC1 SC1 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
BUC SC1 SC1 116.0 2.2 0.0 0.0 ! fit Boltzmann inversion sim UA Protein with S-bridge
!
! glutamate
SE BUN BU 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
SE BUN BA 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
SE BU BU 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
SE BU BUC 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
SE BU BA 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
SE BU BAC 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SE 121.0 2.53 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! glutamine
SQ BUN BU 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
SQ BUN BA 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
SQ BU BU 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
SQ BU BUC 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
SQ BU BA 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
SQ BU BAC 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SQ 117.0 1.16 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! histidine
SH1 BUN BU 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH1 BUN BA 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH1 BU BU 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH1 BU BUC 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH1 BU BA 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH1 BU BAC 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BU SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SH1 116.0 3.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BUN SH1 SH2 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SH1 SH2 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SH1 SH2 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SH2 SH1 BUN 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH2 SH1 BU 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH2 SH1 BUC 129.0 6.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SH1 SH2 SH2 69.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SH2 SH1 SH2 42.5 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! isoleucine
SI BUN BU 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
SI BUN BA 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
SI BU BU 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
SI BU BUC 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
SI BU BA 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
SI BU BAC 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SI 113.0 8.58 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! leucine
SL BUN BU 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
SL BUN BA 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
SL BU BU 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
SL BU BUC 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
SL BU BA 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
SL BU BAC 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SL 118.0 1.9 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! lysine
SK1 BUN BU 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
SK1 BUN BA 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
SK1 BU BU 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
SK1 BU BUC 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
SK1 BU BA 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
SK1 BU BAC 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SK1 120.0 3.14 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BUN SK1 SK2 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SK1 SK2 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SK1 SK2 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SK2 SK1 BU 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SK2 SK1 BUN 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SK2 SK1 BUC 155.0 3.8 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! methionine
SM BUN BU 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SM BUN BA 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SM BU BU 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SM BU BUC 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SM BU BA 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SM BU BAC 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BU SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SM 117.0 1.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! phenylalanine
SF1 BUN BU 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
SF1 BUN BA 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
SF1 BU BU 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
SF1 BU BUC 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
SF1 BU BA 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
SF1 BU BAC 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BU SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SF1 117.0 2.3 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BUN SF1 SF2 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SF1 SF2 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SF1 SF2 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SF2 SF1 BUN 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SF2 SF1 BU 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SF2 SF1 BUC 128.6 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SF1 SF2 SF2 63.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SF2 SF1 SF2 53.0 10.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! proline
SP BUN BU 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
SP BUN BA 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
SP BU BU 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
SP BU BUC 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
SP BU BA 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
SP BU BAC 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BU BU SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BUN BU SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BA BU SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BAN BU SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BU BUC SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
BA BUC SP 143.0 264.462 480.841 218.564 ! fit Boltzmann inversion sim UA
!
! serine
SS BUN BU 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
SS BUN BA 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
SS BU BU 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
SS BU BUC 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
SS BU BA 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
SS BU BAC 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SS 113.5 2.7 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! threonine
ST BUN BU 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
ST BUN BA 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
ST BU BU 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
ST BU BUC 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
ST BU BA 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
ST BU BAC 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BU ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC ST 112.0 14.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! tryptophan
SW1 BUN BU 136.0 66.66 222.22 185.185 ! provvisorio
SW1 BUN BA 136.0 66.66 222.22 185.185
SW1 BU BU 136.0 66.66 222.22 185.185
SW1 BU BUC 136.0 66.66 222.22 185.185
SW1 BU BA 136.0 66.66 222.22 185.185
SW1 BU BAC 136.0 66.66 222.22 185.185
!
BU BU SW1 136.0 66.66 222.22 185.185
BUN BU SW1 136.0 66.66 222.22 185.185
BA BU SW1 136.0 66.66 222.22 185.185
BAN BU SW1 136.0 66.66 222.22 185.185
BU BUC SW1 136.0 66.66 222.22 185.185
BA BUC SW1 136.0 66.66 222.22 185.185
!
BUN SW1 SW2 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SW1 SW2 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SW1 SW2 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
SW2 SW1 BUN 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
SW2 SW1 BU 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
SW2 SW1 BUC 130.0 11.4 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BUN SW1 SW3 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SW1 SW3 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SW1 SW3 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW1 BUN 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW1 BU 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW1 BUC 116.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SW1 SW2 SW3 94.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW2 SW1 94.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SW1 SW3 SW3 106.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW3 SW1 106.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SW2 SW3 SW3 83.4 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW3 SW2 83.4 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SW2 SW1 SW3 76.2 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SW3 SW1 SW2 76.2 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! tyrosine
SY1 BUN BU 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
SY1 BUN BA 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
SY1 BU BU 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
SY1 BU BUC 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
SY1 BU BA 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
SY1 BU BAC 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BU BU SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BUN BU SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BA BU SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BAN BU SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BU BUC SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
BA BUC SY1 140.0 53.464 159.594 119.1 ! fit Boltzmann inversion sim UA
!
BUN SY1 SY2 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BU SY1 SY2 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
BUC SY1 SY2 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SY2 SY1 BUN 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SY2 SY1 BU 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SY2 SY1 BUC 131.0 11.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
SY1 SY2 SY2 65.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
SY2 SY1 SY2 46.0 50.0 0.0 0.0 ! fit Boltzmann inversion sim UA
!
! valine
SV BUN BU 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SV BUN BA 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SV BU BU 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SV BU BUC 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SV BU BA 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
SV BU BAC 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
!
BU BU SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BUN BU SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BU SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BAN BU SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BU BUC SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
BA BUC SV 119.0 7.8 0.0 0.0 ! fit Boltzmann inversion sim UA
!
DIHEDRALS
! in this version we are dealing with the charmm class
! modified by Davide Alemani in Lammps
! k1 k2 k3 theta1 theta2 theta3
! backbone
BU BU BU BU 0.0 0.0 4.0 0.0 0.0 10 ! symmetric barrier with a barrier of 8 kcal/mol
BA BU BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BU BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BUN BU BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BU BUC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BU BU 0.0 0.0 4.0 0.0 0.0 10
BA BU BU BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BU BU BU BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BAC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BAC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BAC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BUC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BUC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BUC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BU BAC 0.0 0.0 4.0 0.0 0.0 10
BUN BU BU BA 0.0 0.0 4.0 0.0 0.0 10
BU BU BU BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BU BU 0.0 0.0 4.0 0.0 0.0 10
BA BU BU BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BU BU 0.0 0.0 4.0 0.0 0.0 10
BU BA BU BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BU BA BU 0.0 0.0 4.0 0.0 0.0 10
BU BU BA BUC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BA BU 0.0 0.0 4.0 0.0 0.0 10
BA BA BA BUC 0.0 0.0 4.0 0.0 0.0 10
BUN BA BA BA 0.0 0.0 4.0 0.0 0.0 10
BU BA BA BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BU BA BA 0.0 0.0 4.0 0.0 0.0 10
BA BU BA BAC 0.0 0.0 4.0 0.0 0.0 10
BAN BA BU BA 0.0 0.0 4.0 0.0 0.0 10
BA BA BU BAC 0.0 0.0 4.0 0.0 0.0 10
! side chains
!
! arginine
SR2 SR1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
SR2 SR1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SR2 SR1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
!
BU BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BA BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BAC BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUC SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BA BUC SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BA BUN SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
BAN BU SR1 SR2 0.0 0.0 1.0 0.0 0.0 0.0
! cysteine
BU SC2 SC2 BU 0.0 0.0 2.0 0.0 0.0 0.0
BU SC1 SC1 BU 0.0 0.0 2.0 0.0 0.0 0.0
!
! histidine
SH2 SH1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
SH2 SH1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SH2 SH1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
BU BU SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUC SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BU BA SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAC SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BA SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BA SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAN SH1 SH2 0.0 0.0 1.0 0.0 0.0 0.0
!
! lysine
SK2 SK1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
SK2 SK1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SK2 SK1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
!
BU BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BA BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BAC BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUC SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BA BUC SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BA BUN SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
BAN BU SK1 SK2 0.0 0.0 1.0 0.0 0.0 0.0
!
! phenylalanine
SF2 SF1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
SF2 SF1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SF2 SF1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
BU BU SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUC SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BU BA SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAC SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BA SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BA SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAN SF1 SF2 0.0 0.0 1.0 0.0 0.0 0.0
!
! tryptophan
SW3 SW1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
SW3 SW1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SW3 SW1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
BU BU SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BU BUC SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BU BA SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BU BAC SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BUC BA SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BUN BA SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
BU BAN SW1 SW3 0.0 0.0 1.0 0.0 0.0 0.0
!
! tyrosine
BU BU SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0 ! provvisorio
BU BUC SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BU BA SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAC SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BU SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BUC BA SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BU SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BUN BA SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BU BUN SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
BU BAN SY1 SY2 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BU 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BUC 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BA 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BAC 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BUC BU 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BUC BA 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BUN BU 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BUN BA 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BUN 0.0 0.0 1.0 0.0 0.0 0.0
SY2 SY1 BU BAN 0.0 0.0 1.0 0.0 0.0 0.0
IMPROPER
!
!atom types Ktheta2 Ktheta3 Ktheta4 phi0
X BU X SR1 1.3 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SN 2.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SD 1.6 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SC1 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SC2 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SE 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SQ 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SH1 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
BUN SH2 SH2 SH1 55.36 162.82 119.72 20 ! fit Boltzmann inversion sim UA
BU SH2 SH2 SH1 55.36 162.82 119.72 20 ! fit Boltzmann inversion sim UA
BUC SH2 SH2 SH1 55.36 162.82 119.72 20 ! fit Boltzmann inversion sim UA
X BU X SI 1.6 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SL 4.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SK1 1.4 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SM 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SF1 29.0 0.0 0.0 180
BUN SF2 SF2 SF1 75.42 215.5 153.92 20
BU SF2 SF2 SF1 75.42 215.5 153.92 20
BUC SF2 SF2 SF1 75.42 215.5 153.92 20
X BU X SP 4.0 0.0 0.0 82 ! fit Boltzmann inversion sim UA
X BU X SS 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X ST 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
X BU X SW1 1.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
SW1 SW2 SW3 SW3 40.0 0.0 0.0 0 ! fit Boltzmann inversion sim UA
BUN SW2 SW3 SW1 40.0 100.0 62.5 23 ! fit Boltzmann inversion sim UA
BU SW2 SW3 SW1 40.0 100.0 62.5 23 ! fit Boltzmann inversion sim UA
BUC SW2 SW3 SW1 40.0 100.0 62.5 23 ! fit Boltzmann inversion sim UA
X BU X SY1 2.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
BUN SY2 SY2 SY1 71.0 197.0 136.86 20 ! fit Boltzmann inversion sim UA
BU SY2 SY2 SY1 71.0 197.0 136.86 20 ! fit Boltzmann inversion sim UA
BUC SY2 SY2 SY1 71.0 197.0 136.86 20 ! fit Boltzmann inversion sim UA
X BU X SV 2.0 0.0 0.0 180 ! fit Boltzmann inversion sim UA
NONBONDED
!atom ignored epsilon sigma
BAN 0.0 1.3 4.5
BA 0.0 1.3 4.5
BAC 0.0 1.3 4.5
BUN 0.0 1.3 4.5
BU 0.0 1.3 4.5
BUC 0.0 1.3 4.5
SR1 0.0 1.3 4.5
SR2 0.0 1.3 4.5
SN 0.0 1.3 4.5
SD 0.0 1.3 4.5
SC1 0.0 1.3 4.5
SC2 0.0 1.3 4.5
SE 0.0 1.3 4.5
SQ 0.0 1.3 4.5
SH1 0.0 1.3 4.5
SH2 0.0 1.3 4.5
SI 0.0 1.3 4.5
SL 0.0 1.3 4.5
SK1 0.0 1.3 4.5
SK2 0.0 1.3 4.5
SM 0.0 1.3 4.5
SF1 0.0 1.3 4.5
SF2 0.0 1.3 4.5
SP 0.0 1.3 4.5
SS 0.0 1.3 4.5
ST 0.0 1.3 4.5
SW1 0.0 1.3 4.5
SW2 0.0 1.3 4.5
SW3 0.0 1.3 4.5
SY1 0.0 1.3 4.5
SY2 0.0 1.3 4.5
SV 0.0 1.3 4.5
ELLIPSOID
!atom sx sy sz q0 q1 q2 q3
SN 1.0 1.0 1.0 0.0 0.0 0.0 0.0
SQ 1.0 1.0 1.0 0.0 0.0 0.0 0.0
SS 1.0 1.0 1.0 0.0 0.0 0.0 0.0
ST 1.0 1.0 1.0 0.0 0.0 0.0 0.0
SW2 1.0 1.0 1.0 0.0 0.0 0.0 0.0
SY2 1.0 1.0 1.0 0.0 0.0 0.0 0.0
DIPOLE
!atom dx dy dz
SN 1.0 1.0 1.0
SQ 1.0 1.0 1.0
SS 1.0 1.0 1.0
ST 1.0 1.0 1.0
SW2 1.0 1.0 1.0
SY2 1.0 1.0 1.0
END
END