lampiran komputasi

8/9/2019 Lampiran komputasi

1/19

55

LAMPIRAN

Lampiran 1. Tabel Panjang Ikatan ETQ

No AtomPanjang Ikatan (Å) Selisih Experimen – Hasil

Docking Experimen Hasil Docking 19 - ! " - " 1#$% 1#$% !#!!19 - $ " - " 1#$% 1#%9 !#1&$ - ' " - " 1#&! 1#%9 !#!1' - " - 1#%' 1#%' !#!!' - % " - " 1#&! 1#%9 !#!1% - 1 " - " 1#&! 1#%9 !#!11 - " - " 1#&! 1#%9 !#!1

- * " - "l 1# % 1# % !#!! - & " - " 1#%9 1#%9 !#!!

$ - & " - " 1#%9 1#%9 !#!!1 - 9 " - " 1#%' 1#%' !#!!9 - % " - " 1#&% 1#&% !#!!% - 1! " - " 1#$$ 1#%9 !#1'1! - " - 1# % 1# % !#!!1! - 11 " - N 1#%& 1#%& !#!!

11 - 1% N - " 1#&* 1#& !#!11% - 1& " - " 1#$% 1#$% !#!!1& - 1' " - " 1#$ 1#$ !#!!1' - 1* " - " 1#$ 1#$ !#!!1* - 1 " - " 1#$% 1#$ !#!11 - 1$ " - N 1#&* 1#& !#!11$ - 1& N - " 1#& 1#& !#!!1$ - 1 N- " 1#& 1#& !#!!

1 - " - " 1#$% 1#$% !#!! - &9 - H !#9' 1 -!#!&

11 - N - H 1#!1 1 !#!1


2/19

56

Lampiran 2. Tabel Sudut Ikat ETQ

no Atom S+,+t ikat ( ) Selisih Experimen -hasil ,o.kingExperimen Hasil Docking - 1-1$ " - " - N 11!#& 111 -!#'

1-1$-1 " - N - " 1!*# 1!9#$ -1#%1 -1$-1& " - N - " 1! # 1!& %#1$-1 -1* N - " - " 1!'#$ 1!& #$1 -1*-1' " - " - " 1! #9 1!& -1#11*-1&-1& " - " - " 1! #1 1!& -1#91$-1&-1' N - " - " 1!$#' 1!& 1#'1$-1&-1% N - " - " 11!# 111 -!#*1'-1&-1% " - " - " 1!9#$ 1!9#$ !#!1&-1%-11 " - " - N 111# 1!9#$ 1#1%-11-1' " - N - " 1 %#' 1 1#'11-1!-1 N - " - " 1 %#' 1 & -!#&1 -1!-% -" - " 1 !#' 1 1 -!#&1!-%-' " - " - " 119#1 1 ! -!#9'-%-1 " - " - " 119#1 1 ! -!#91-%-$ " - " - " 119#9 11$ %-$-19 -" - " 11*#9 11$ %#9$-19- ! " - " - " 1 ! 1 ! !$-19- ! " - " - " 111#' 1!9#$ #1$-&- " - " - " 1 !#$ 1 ! !#$&- -* " - " - "l 119#' 1 ! -!#&&- -1 " - " - " 1 !#$ 1 ! !#$*- -1 "l - " - " 119#* 1 ! -!#%-1- " - " - " 119#* 1 ! -!#%-1-9 " - " - 1 1#1 11$ '#1

-1-9 " - " - 119#1 11$ 1-9- % " - - " 1!*# 1!9#$ -!#*


3/19

57

Lampiran 3. Tabel Muatan ETQ

No#atom Atom

/+atan

selisih experimen -,o.kingExperimen Hasil Docking 1 " !#!1 !#!1 !

" !#!9& !#!9& !% " !#1!9 !#1!9 !& " -!#! -!#! !$ " !#!$1 !#!$1 !' " -!#!!* -!#!!* !

-!# -!# !* "l -!#!&1 -!#!&1 !

9 -!# !* -!# !* !1! " !#!%$ !#%$' -!#% 111 N -!#1$1 !#1&* -!# 991 -!#$ -!#$ % !#!!11% " !#!1$ !#!$1 -!#!%'1& " !#! $ !#!1' !#!!91$ N -!# 99 !#!!* -!#%!1' " -!#!%$ !#!!' -!#!&11 " -!#!!1 -!#!11 !#!11* " -!#!%9 !#!! -!#!&119 " !#! * !#! * !

! " -!#!'1 -!#!'1 !1 " -!#!!& -!#!1& !#!1

" -!#!$ -!#!1' -!#!%'% " !#!$ !#119 -!#!'9& H0 -!#!!9 !#!!9$ H !#!'' !#!'' !' H !# '1 !# '1 !

H !#1% !#1% !* H !#!&9 !#!$& -!#!!$9 H !#!&9 !#!$& -!#!!$

%! H !#!&* !#1 -!#!$%1 H !#! * !#!%& -!#!!'% H !#! * !#!%& -!#!!'%% H !#!&% !#!9& -!#!$1%& H !#! * !#!9& -!#!''%$ H !#! * !#!%& -!#!!'


4/19

58

%' H !#! * !#!%& -!#!!'% H !#!% !#!% !

%* H !#! % !#!% -!#!!9%9 H !#!% !#! % !#!!9&! H !#! % !#! % !&1 H !#! % !#! % !& H !#!&% !#!9& -!#!$1&% H !#!&% !#!9& -!#!$1&& H !#! & !#!% -!#!!'&$ H !#!% !#!% !#!!&' H !#! & !#!% -!#!!'& H !#!'' !#!'' !

&* H !#!'' !#!'' !&9 H !#!'' !#!'' !


5/19

59

Lampiran . Tabel Panjang Ikatan Aripipra!"le

noAtom Atom

Panjang Ikatan ( Å) SelisihExperiment -

o.kingExperimenHasil

Docking %!-& " 2 1# 1# && -!#! &

-% " - 1#%' 1#%*!& -!#! !&1'-% " - 1#&% 1#&%$ -!#!!$1'-1$ " - " 1#$& 1#$19& !#! !'1$-1% " - " 1#$& 1#$1 ' !#! &1%-1 " - " 1#$& 1#$ * !#!11%%!- $ " - " 1#$1% 9 1#$1!9 !#!! *9

$- ! " - " 1#$%&9 1#$1% !#! 1!-19 " - " 1#$19' 1#&*'% !#!%%%

19- 1 " 2 " 1#%&'&& 1#& !9 -!#! &&'19- * " - " 1#&'$11 1#%91* !#! %%1

*- 9 " 2 " 1#%%9 9 1#%9%1 -!#!$%*19- " - " 1#&$*'$ 1#& !#!$*'$

- ' " 2 " 1#%%9$' 1#&!&1 -!#!'&$&'- 1 " - " 1#&'!* 1#&!' !#!$&11- " - N 1#% $ 9 1#%9* -!#! &1

%!- " - N 1#% !** 1#%91% -!#! !&%1 - H - N 1#!1 !#99999 !#!1!!11 - $ " - N 1#& 1#&& !#! *$ - 9 N - " 1#& 1& 1#&&9$ !#! 19$ - * N - " 1#& 1$1 1#&&9& !#! 11* - 1! " - " 1#$&!1 1#$&& -!#!!&'11 - 9 " - " 1#$&!!& 1#$&$ -!#!!$''11 - ' " - N 1#&'*%& 1#&$'' !#!11 &' - 1! N - " 1#&'*%* 1#&$&1 !#!1& *1& - ' " - N 1#% 1#& '& -!#1!'&1& - 1* " - " 1#&'!! 1#&!9 !#!$1!

1* - & " 2 " 1#%& 1#%9!* -!#!$!*& - " - " 1#&$99 1#%91 !#!'*

- % " 2 " 1#%& 1#%9 ' -!#!$ '% - 1 " - " 1#&' 1#&!% !#!$% - " - "l 1# ' 1#'991 !#!'!9

1 - 1 "- "l 1# ' 1#'9' !#!'%%


6/19

60

Lampiran #. Sudut Ikat Aripipra!"le

N" At"m At"m Sudut $%& Seli'i(E)perimen *+",kingE)perimen

-a'il Docking

& - %! - - " - N 1 !#1'% 11*#9%' 1#& - %! - $ - " - " 1 !#1' 1 #'& - #&*$%1 - - %! H - N - " 11*#9$ 11*#*&& !#1!'%1 - - 1 H - N - " 11*#9$ 11*#*&1 !#1!9

- 1 -19 N - " 2 " 1 1# 1 !#! $ 1#' $1 - 19 - ! " 2 " - " 1 !# 1' 119# &$ !#9 1

19- !- $ " - " - " 1!*#'9% 11 #''1 -%#9'*! - $ - $% " - " - H 1!9# 9* 1!$#9*9 %#*!91 - $ - $ " - " - H 1!9#** 1!*#&9' 1#%*&

$& - ' - 1 H - " - " 119# 9$ 1 !#%$$ -!#$'$& - ' - H - " 2 " 119# 9$ 1 !#%$$ -!#$'

- '- 1 " 2 " - " 1 !#&1 119# 9 1#1 - 9 - * " - " 2 " 1 ! 11*#9$* 1#!&

19 - * - 9 " 2 " - " 1 !#!91 1 1#& 1 -1#%*19 - * - $' " - " - H 1 !#!$% 119# '& !# *9

*- 9-$ " 2 " - H 1 ! 1 !#$19 -!#$19-%-1' " - - " 1!9#& 1 11$#9! -'#&%'

%- - ' - " 2 " 1 ! 11 && $# $'% - - 9 - " - " 1 ! 1 $** -$**%- 1' - 1$ -" - " 1!9#& 1 1!'#%&$ %#1 '1'-1$-1% " - " - " 1!9#& 1 11%#!9' -%#' $1$-1%-1 " - " - " 1!9#& 1 111#'%1 - #1'9-$-1 " - N - " 1!9#& 1 11$#*99 -'#& *1 - $ -* " - N - " 1!9#&1 11'# !9 -'# 9*-1!-' " - " - N 1!9#! * 11 #11 -%#!%&9 -11 -' " - " - N 1!9#! 9 111#'% - #$$*1& - ' - 11 " - N - " 1 !#$&' 11$#! $#$ '1& - ' - 1! " - N - " 1 !#$&' 11%#*&9 '#'91 -1&-' " 2 " -N 1 ! 11*#*'% 1#1%1*-1&-' " 2 " -N 1 ! 1 # % - # %

& - 1* -&* " 2 " - H 1 ! 119#&* !#$1*$1- &- H - " - " 1 ! 119# %* !# '

& - -$$ " - " - H 1 ! 1 !# & -!# & - % " 2 " - "l 1 ! 11*#&& 1#$$%


7/19

61

1&-1 -1 " 2 " - "l 1 ! 1 !#$ $ -!#$ $1 - %- " - " - "l 119#99 1 !#* & -!#*%&

%-1 -1 " - " - "l 1 ! 119#'! !#%9%


8/19

62

Lampiran . Tabel muatan aripipra!"le

N" at"m At"m

Muatan at"m 'eli'i(

E)perimen * Docking

E)perimen -a'il Docking

1 "l -!#! 1 -!#!'$ -!#!!'2 "l -!#! % -!#!'& -!#!!93 -!# & -!#19 -!#!&%

-!#& ' -!# 1* !# &# N -!#%!1 -!# ** -!#!1%

N -!#1 !#!19 -!#1%9/ N -!#! & !#!19 -!#!9%0 " !#!11 !#11' -!#1!$

" !#!11 !#11' -!#1!$1 " !#!1' !#11' -!#111 " !#!1' !#11' -!#112 " -!#!! !#11' -!#11*13 " -!#!%* !#11' -!#1$&1 " !#!!' !#11 -!#1111# " -!#! ' !#11' -!#1&1 " !#!$$ !# 1 -!# 1'1/ " !#!!' -!#!% !#!&%10 " -!#!$ -!#! % -!#!%&

1 " -!#! % -!#!% !#!1&2 " -!#!!& !#11' -!#121 " !#!1$ !#11 -!#1!22 " !#! * !#11 -!#!*923 " !#!1 -!#!% !#!&2 " -!#!$% -!#! % -!#!%2# " !#!1 !#11' -!#1!'2 " !#!1% -!#! !#!%$2/ " -!#!$1 -!#! % -!#! *20 " -!#!19 -!#! % !#!!&2 " -!#!1$ -!#! % !#!!*3 " !#!*& !# $& -!#131 H !#1$9 -!#!1& !#1 %32 H !#!&& -!#! !#!'&33 H !#!&& -!#! 1 !#!'$3 H !#!&& -!#! 1 !#!'$3# H !#!&& -!#! 1 !#!'$


9/19

63

3 H !#!&$ -!#! 1 !#!''3/ H !#!&$ -!#! 1 !#!''30 H !#!&$ -!#! 1 !#!''3 H !#!&$ -!#! 1 !#!''

H !#!&% -!#! 1 !#!'&1 H !#!&% -!#! 1 !#!'&2 H !#! * -!#! 1 !#!&93 H !#! * -!#! !#!&*

H !#! 9 -!#! 1 !#!$# H !#! 9 -!#! 1 !#!$

H !#!' -!#! 1 !#!*1/ H !#!' -!#! 1 !#!*1

0 H !#!'& !#!!9 !#!$$H !#!%% -!#! 1 !#!$&# H !#!%% -!#! 1 !#!$&#1 H !#!' !#!!9 !#!$%#2 H !#!% -!#! 1 !#!$1#3 H !#!% -!#! 1 !#!$1# H !#! !#!!9 !#!'%## H !#!'& !#!!9 !#!$$# H !#!' !#!!9 !#!$*#/ H !#! !#!!9 !#!'1


10/19

64

Lampiran /. l"g ile penamba(an missing atom dan reconstructing sidechain'4i''pdb5ie4er

34 A P 5 log 6ile 6or A78"I :SS8lesson to ;e a.hemist8er !/issing Atom7 ? 6or resi,+e SE 1&$ o6 .hain @5@/issing Atom7 "? 6or resi,+e A ? 1&9 o6 .hain @5@/issing Atom7 " 6or resi,+e A ? 1&9 o6 .hain @5@/issing Atom7 NE 6or resi,+e A ? 1&9 o6 .hain @5@/issing Atom7 " 6or resi,+e A ? 1&9 o6 .hain @5@/issing Atom7 NH1 6or resi,+e A ? 1&9 o6 .hain @5@

/issing Atom7 NH 6or resi,+e A ? 1&9 o6 .hain @5@/issing Atom7 "? 6or resi,+e ASN 1!&! o6 .hain @5@/issing Atom7 1 6or resi,+e ASN 1!&! o6 .hain @5@/issing Atom7 N 6or resi,+e ASN 1!&! o6 .hain @5@/issing Atom7 "? 6or resi,+e ASN 1!$% o6 .hain @5@/issing Atom7 1 6or resi,+e ASN 1!$% o6 .hain @5@/issing Atom7 N 6or resi,+e ASN 1!$% o6 .hain @5@/issing Atom7 "? 6or resi,+e ASN 1!$$ o6 .hain @5@/issing Atom7 1 6or resi,+e ASN 1!$$ o6 .hain @5@/issing Atom7 N 6or resi,+e ASN 1!$$ o6 .hain @5@/issing Atom7 "? 6or resi,+e A ? 1!*! o6 .hain @5@

/issing Atom7 " 6or resi,+e A ? 1!*! o6 .hain @5@/issing Atom7 NE 6or resi,+e A ? 1!*! o6 .hain @5@/issing Atom7 " 6or resi,+e A ? 1!*! o6 .hain @5@/issing Atom7 NH1 6or resi,+e A ? 1!*! o6 .hain @5@/issing Atom7 NH 6or resi,+e A ? 1!*! o6 .hain @5@

e.onstr+.ting Si,e.hain o6 resi,+e S 1&$ o6 .hain @[email protected]+.ting Si,e.hain o6 resi,+e 1&9 o6 .hain @[email protected]+.ting Si,e.hain o6 resi,+e N 1!&! o6 .hain @[email protected]+.ting Si,e.hain o6 resi,+e N 1!$% o6 .hain @[email protected]+.ting Si,e.hain o6 resi,+e N 1!$$ o6 .hain @[email protected]+.ting Si,e.hain o6 resi,+e 1!*! o6 .hain @5@

3,one loa,ing la>er !7%P54.hain;3-------------------------------------------------------


11/19

65

Lampiran 0. 6ile input pr"t"k"l 'imula'i energi minimi'a'i steep descent

B +n .ontrolintegrator 2 steepnsteps 2 $!!!B E/ .riteria an, other st+66 emtol 2 1!!emstep 2 !#!1niter 2 !n;6gs.orr 2 1!B +tp+t .ontrolnstlog 2 1nstenerg> 2 1B Neigh;orsear.hing an, short-range non;on,e, intera.tionsnstlist 2 1nsCt>pe 2 gri, p;. 2 x>Drlist 2 1B Ele.trostati.s.o+lom;t>pe 2 P/Er.o+lom; 2 1#!B an ,er Faals

,=-t>pe 2 s=it.hr ,=-s=it.h 2 !#*r ,= 2 !#9B Appl> long range ,ispersion .orre.tions 6or Energ> an, Press+re

isp"orr 2 EnerPresB Spa.ing 6or the P/E3PPP/ GG< gri,6o+rierspa.ing 2 !#1B EFA4 3P/E3PPP/ parameters pmeCor,er 2 'e=al,Crtol 2 1e-!'epsilonCs+r6a.e 2 !optimiDeC66t 2 noB


12/19

66

Lampiran . 6ile input pr"t"k"l 'imula'i energi minimi'a'i L*768S

B +n .ontrolintegrator 2 l-;6gsnsteps 2 $!!!,e6ine 2 - G4E I54EB E/ .riteria an, other st+66 emtol 2 1!!emstep 2 !#!1niter 2 !n;6gs.orr 2 1!B +tp+t .ontrolnstlog 2 1nstenerg> 2 1B Neigh;orsear.hing an, short-range non;on,e, intera.tionsnstlist 2 1nsCt>pe 2 gri, p;. 2 x>Drlist 2 1#!B Ele.trostati.s.o+lom;t>pe 2 P/Er.o+lom; 2 1#!B an ,er Faals

,=-t>pe 2 s=it.hr ,=-s=it.h 2 !#*r ,= 2 !#9B Appl> long range ,ispersion .orre.tions 6or Energ> an, Press+re

isp"orr 2 EnerPresB Spa.ing 6or the P/E3PPP/ GG< gri,6o+rierspa.ing 2 !#1B EFA4 3P/E3PPP/ parameters pmeCor,er 2 'e=al,Crtol 2 1e-!'epsilonCs+r6a.e 2 !optimiDeC66t 2 noB


13/19

67

Lampiran 1 . 6ile input pr"t"k"l 'imula'i k"ndi'i N9T

title 2 N < eJ+ilB +n parametersintegrator 2 m, B leap-6rog integrator Bnsteps 2 $!!!! B K $!!!! 2 1!! psnsteps 2 $!!!! B K $!! 2 1 ps,t 2 !#!! B 6sB +tp+t .ontrolnstxo+t 2 1!!! B sa e .oor,inates e er> !# psnst o+t 2 1!!! B sa e elo.ities e er> !# psnstxt.o+t 2 1!!!nstenerg> 2 1!! B sa e energies e er> !# psnstlog 2 1!! B +p,ate log 6ile e er> !# psB 5on, parameters.ontin+ation 2 no B 6irst ,>nami.s r+n.onstraintCalgorithm 2 lin.s B holonomi. .onstraints.onstraints 2 all-;on,s B all ;on,s (e en hea > atom-H ;on,s) .onstraine,lin.sCiter 2 1 B a..+ra.> o6 4IN"Slin.sCor,er 2 & B also relate, to a..+ra.>B Neigh;orsear.hing

,=Ct>pe 2 .+t-o66 B sear.h neigh;oring gri, .ellsnstlist 2 1! B 1! 6srlist 2 1#! B short-range neigh;orlist .+to66 (in nm)r.o+lom; 2 1#! B short-range ele.trostati. .+to66 (in nm)r ,= 2 1#! B short-range an ,er Faals .+to66 (in nm)B Ele.trostati.s.o+lom;t>pe 2 P/E B Parti.le /esh E=al, 6or long-range ele.trostati.s pmeCor,er 2 & B .+;i. interpolation6o+rierspa.ing 2 !#1' B gri, spa.ing 6or GG<B stem B t=o .o+pling gro+ps - more a..+rateta+Ct 2 !# B time .onstantL in psre6Ct 2 %!! B re6eren.e temperat+reL one 6or ea.h gro+pL in M B Press+re .o+pling is o66 p.o+pl 2 no B no press+re .o+pling in N <B Perio,i. ;o+n,ar> .on,itions p;. 2 x>D B %- P5"B ispersion .orre.tion

isp"orr 2 EnerPres B a..o+nt 6or .+t-o66 ,F s.hemeB elo.it> generationgenC el 2 >es B assign elo.ities 6rom /ax=ell ,istri;+tion


14/19

68

genCtemp 2 %!! B temperat+re 6or /ax=ell ,istri;+tiongenCsee, 2 -1 B generate a ran,om see,


15/19

'9

Lampiran 11. 6ile input pr"t"k"l 'imula'i k"ndi'i NPT

B +n parametersintegrator 2 m, B leap-6rog integrator Bnsteps 2 $!!!! B K $!!!! 2 1!! psnsteps 2 $!!!! B K $!! 2 1 ps,t 2 !#!! B 6sB +tp+t .ontrolnstxo+t 2 1!!! B sa e .oor,inates e er> !# psnst o+t 2 1!!! B sa e elo.ities e er> !# psnstxt.o+t 2 1!!!nstenerg> 2 1!! B sa e energies e er> !# psnstlog 2 1!! B +p,ate log 6ile e er> !# psB 5on, parameters.ontin+ation 2 >es B estarting a6ter N <.onstraintCalgorithm 2 lin.s B holonomi. .onstraints.onstraints 2 all-;on,s B all ;on,s (e en hea > atom-H ;on,s) .onstraine,lin.sCiter 2 1 B a..+ra.> o6 4IN"Slin.sCor,er 2 & B also relate, to a..+ra.>B Neigh;orsear.hingnsCt>pe 2 gri, B sear.h neigh;oring gri, .ellsnstlist 2 1! B 1! 6srlist 2 1#! B short-range neigh;orlist .+to66 (in nm)r.o+lom; 2 1#! B short-range ele.trostati. .+to66 (in nm)r ,= 2 1#! B short-range an ,er Faals .+to66 (in nm)B Ele.trostati.s.o+lom;t>pe 2 P/E B Parti.le /esh E=al, 6or long-range ele.trostati.s pmeCor,er 2 & B .+;i. interpolation6o+rierspa.ing 2 !#1' B gri, spa.ing 6or GG<B stem B t=o .o+pling gro+ps - more a..+rateta+Ct 2 !# B time .onstantL in psre6Ct 2 %!! B re6eren.e temperat+reL one 6or ea.h gro+pL in M B Press+re .o+pling is on p.o+pl 2 Parrinello- ahman B Press+re .o+pling on in NP< p.o+plt>pe 2 isotropi. B +ni6orm s.aling o6 ;ox e.torsta+Cp 2 $#! B time .onstantL in psre6Cp 2 1#! B re6eren.e press+reL in ;ar .ompressi;ilit> 2 $e-$ B isothermal .ompressi;ilit> o6 =aterL ;ar -1re6.oor,Cs.aling 2 .omB Perio,i. ;o+n,ar> .on,itions


16/19

'9

p;. 2 x>D B %- P5"B ispersion .orre.tion

isp"orr 2 EnerPres B a..o+nt 6or .+t-o66 ,F s.hemeB elo.it> generationgenC el 2 no B elo.it> generation is o66


17/19

1

Lampiran 12. 6ile input pr"t"k"l 'imula'i per(itungan Free Energy

Pertubastion pembuatan lambdaB =e@ll +se the s, integrator =ith '!!!!! time steps (1 !!ps)integrator 2 s,nsteps 2 '!!!!!,t 2 !#!!nstenerg> 2 1!!!nstlog 2 $!!!B t+rn o66 traje.tor> =ritingnstxo+t 2 1!!!nst o+t 2 1!!!nstxt.o+t 2 1!!!B Fe +se the ol, gro+p s.heme ;e.a+se as o6 =ritingL the erlet s.hemeB ,oes not s+pport 6ree energ> .al.+lations =ith .o+ple, mole.+les#.+to66-s.heme 2 gro+pB .+t-o66s at 1#!nmrlist 2 1#!,isp.orr 2 EnerPres

,=-t>pe 2 .+t-o66 r ,= 2 1B "o+lom; intera.tions.o+lom;t>pe 2 pmer.o+lom; 2 1#!6o+rierspa.ing 2 !#1B "onstraints.onstraints 2 all-;on,sB set temperat+re to %!!M t.o+pl 2 -res.alet.-grps 2 s>stemta+-t 2 !#re6-t 2 %!!B set press+re to 1 ;ar =ith a thermostat that gi es a .orre.tB thermo,>nami. ensem;le p.o+pl 2 parrinello-rahmanre6-p 2 1.ompressi;ilit> 2 $e-$ta+-p 2 $

B an, set the 6ree energ> parameters6ree-energ> 2 >es.o+ple-molt>pe 2 P 5


18/19

1

B these @so6t-.ore@ parameters make s+re =e ne er get o erlappingB .harges as lam;,a goes to !

s.-po=er 2 1s.-sigma 2 !#%s.-alpha 2 1#!B =e still =ant the mole.+le to intera.t =ith itsel6 at lam;,a2!.o+ple-intramol 2 no.o+ple-lam;,a1 2 ,=J.o+ple-lam;,a! 2 noneinit-lam;,a-state 2 O4A/5 AO6ep-lam;,as 2 !#! !#1 !# !#% !#& !#$ !#' !# !#* !#9 1#!


19/19

1

Lampiran 13. +a tar 'ingkatan a'am amin"

Alanin (Ala)Arginin (Arg)Asam aspartat (Asp)Asam gl+tamat (?l+)Asparagin (Asn)Genilalanin (Phe)?lisin (?l>)?l+tamin (?ln)Histi,in (His)Isole+sin (Ile)

4e+sin (4e+)4isin (4>s)/etionin (/et)Prolin (Pro)Serin (Ser)Sistein (">s)

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