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1 !"# $! % &'(

2 !)'*! '! " # #" $ % & #" & " $ & " " #" & " # #! # "! #" & ' #" # #" $ % &! ( # "! $ %&& ' $ & % # $ #" )* #" $ +$,-."// +#//- +$01 2 # 3$ "! $ +$,-."// #551 " #" & #"!"#$$%$$" &'( )'&* +((!"#$$%* +((* ++(, % 6 +7" "%!$ " $%&

3 +,-$./-0.*'&1,&/& 5 8+9' :6+;2:<9286(+63(6 / 5 ( #" / #" - / #", / +696+( 3448' 55 /5 55 /5 &! && " 5= - >6+9' $! # 5, -.! & " 51 -/ $ - 6?& -= (# #! # 6( ?& / / 3 # (>' = /5 0 $ 0 / 0 5 $ 1 // 5 $ / = '(((98 // =5 (>' /- = 9$ / (98 /, (+6 / / / -= , 234 = -1

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

6 5!#&'6/#$./+,&'&*!& # (>' 3:"B 3:"6 $ # 6 # " # "! & 3:"6B & J 52 # 3:"6 & & & C3:"6D C"3:"6D )! '! # & 3:"6 3:" $ A# "& ' " % >' 3:"6 C+3:"6D &# & & J $ +3:"6 # "! & >' GO / 6## 5H & G4&# 511H " " # & A# # "& G H ( 3:"6 " " > +3:"6 "3:"6 0P 0P " > +3:"6 3:"6,P 0P " G 5110H ' 3:"6B 4 " A# $ # " & # +3:"6 " # +3:"6 & ( 5115"! & 3:"6B!)! 6A# $ &! $ " QJR G( 5115H 3:"6 & /0 # A# " " % & $"$" # C.D & :) " 3:"6 3:"6 &#. " $"$"$ : G( K 51,0H $ & & (! 5 R)" 5- Q)"E ' S #& A# # $ & G( 5115H &&! 3:"6 # # CD 2 $ >' G<$"# 511=H.' 3:6 " (:. '

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

8 /H '! $ 3:"6 " $ - +3:"6 ' +#//0 3:"6."// +3:" :"6B & 3D # (/ C(D 4//- C4/0D <--0 C<--D D 3:"B # 4#55 C4#55,D 4#5 C4#551D (/ C(D 3:"6 :D 3:"B $ +$,= C+$,-D 4 C4511D +#//0 C."//D 3:"6 3 3:"6 +3:"6 $ 3 +$,- $ & 3:" ' " >" )> C D 5- > M#$ 3:"6 "" 1 > 1- > V,-6 V,-3 3:"6 V,- 3:"6, > " # $,- G9" 511H 3:" I # # E# "#E#$$ $ ( & $ &# & 3:" <-- #J& # $ & & 3:" ( <-- $ " C<OD " # 3:"6 G K V 51,-H % # #$$ 3:" & &#$$ <-- $ & & # C:9 ) W < W D <-- $ "#E#$$ $ ( " 3:"6 & $ G T 51,0H 058 O X )9):< ):< )8 W C:< / D / I X :< / I<O X " <9):< ):< )8 W C:< / D / I:9 ) W < W X # 3:" 5D 3# D ' # G T 51,0H

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

10 ' $ 3:"6 " # ' $" # # 4, 40, 3$, 3$/- 3$/5 3$/, 3$/,5 0! & " & G8 51, ( 511/ $ 511/ /H $ $" Q)"E $ # 3$0 $ " % / 4--! # G 5110H > " 3$0 & " "& G+ 511,H 3 " $ # # " $ "## ) & G(" 511-H M # 3:"6 " # " " &# # G3MA 511H ' " # $ $ & J G3MA V 5110& 5111 (" 511-H.& & % # G( 511/H! & J # ' # & & J $ & G$ 511/H ' # & J G( 511/H +#$ "! & J &! )* " & J $! *)# G'"# 511=H *)* " $ " G# K. 51,H 6 & "% # & A# ' # +$,- 51 4#--5 # $ $ " & A# ' & # +$,- " $$ & $ " & " $$ " & $ & J $ 6 & $ " & " G4 511-H 3:"6 $ "& " " # " $ # $ & G H ' & J # 3:"6 & J $ GO /H '! # 3:"6 " & # $ & & J + & 5 #!

11 ' 52! 0 ( ' # 3:"6 4/0 3 "## 3:" <-- +$,- ' )* 3:" & 3:"6B &."// ' )* 3:" & +#55 " 3:"6 +#55 +#0 +$55- +#5/ +$/ +$01.",,."1."//5 +#//- +$-/ +#-- 4#55, 4# , 40, 3$, 3$/- 3$/5 3$/, 3$/, $0 4--/ #--5 '."// " 3:"6 ' # +$,- +#55."// % # Y- P >! $ 3:" 8 "! $ # E# " & 3:" & "## ' $ 3:"6 "! & & J ' 3:" & ) 8 #! & J ' +$,- 3:"6B & # $ 5+ ( & " >' & 3:" & # +$,-."// )* 4511 ) 6 "#& &# E# $ 3:" 8< "! $ 4#55, 4#551 G9" 511 H ' 3:" & 3:"6 " # (>' 3:"6 " 3:" &! "& "& G & " K < -HI& $& & & $& & # & "&! $& "& % $ & J & "& 3:"6! # & % $ & J G : $ K >ZA)+ H

12 ' & "& & & "& 3:"6 # # A# & 3:"6 <$A 3 $ $ & "& G : $ K >ZA)+ H, 05; ( & "& <$A 3 G 5110H <$A 3 3:"6 $$ $ # $< )* $ +$,-."// : &# E# $ <$A 3 "#& "#E#$$ $ +#5/ 6 &! "# "#$$ E# "! $ <-- " # $ :< [ 9 "#& G 5110 V " K ( 5110H 1 05< <$A 3B 3:"6 ' $ $$ )* +$,-."// &# E# "#& "# $ +#5/B "#E#$$ ' "#& "# "#$$ <$A 3 E# "! $ <-- G 5110H O / " (>'! " # <$A 3 " $ 3:"6 ' 3$0 $ <$A 3 # $ ' )* $! $ "#& ' " # $ %

13 3:" " <$A 3 $ $$ &#$$ " & # & O /B $ $! $$

14 '&.*&'+ )!11*3,- >' &# $ & # " " $$ $ $) # 2 " $ & & "! R # &! $! 6 $ $ ' $ # & X \ & W \ & & & & 3 & & & " $$ " & 5 &!& " & X & C ] D " & CNJJS D & 5 CSD! /5 N & % &!! 02 " $ & &!& E) &! "! #) & & < 2 & # & " U binding = L i= 1 k binding, i ( ri r0, i ) 2

15 3 &%& " ^ X ^ C^ ] ^D " ^ CNJJ D ^ 5/ C D ^! / 05 " $ & &%& E) " ^! #) ^ < > # ^ " U θ = M i= 1 k, ( θ θ 0, ) θ i i i 2 / 3 " % & )/ # & 5))/)- // _ X ` _ C5 W C_ ] a DD " _ " CNJD $ C" D a C D '% & )/ " $ $ /=. & $ 0 6 " % & )/ # & 5))/)- < 8 " # _ " U Φ = N i= 1 (½ kφ, i (1 + cos( nφ γ n ))

16 - $$ " ) )$ " $ & $ $ "#& G + K > # H 6 " b X b Cb ] b D " b CNJJ D b $$ 5))/)- C D b! $$ < 8 $$ # b " U ϕ = N i= 1 kϕ, i ( ϕi ϕ0, i ) 2 & & & ' &! ) #! & " $ $ V CVD $@ 5 :& $ $$ &" # $ :& $ & $ $ /- +! $ " $ X q i 4πε q 0 j r ij "? $ C:&D c % CD /- 07 3? %? % 3 % < % $ $ # " U e = ij par q q i, j 0 ij i j 4πε r 3 V &! C D C D / # X 5 k " m r # $ " $ 3Iα i α j X ) " $ Q $ & 6 4r

17 # $!! #$ 5 " & 2 )N $ r U vdw = ε ij r m, ij ij 12 r 2 r m, ij ij 6 < c % #& & / % % 08 6 V 2 )N $ 6 & $)! & &#& c % E) #) V M 2 )N $ &.!! " $! $ " +! # $ $! " $ $! $ " 2! d " $ / ( & # k 2 2 Φ, i U ( R) = kbinding ( r r ) + kθ ( θ θ 0 ) + (1 + cos( nφ γ n )) + kϕ ( ϕ ϕ ) bindinger vinkler dihedral improper 12 6 r m, ij rm, ij qiq j + ε ij 2 rij rij 4πε 0r ubundne ij ' $ & $ #$ $ & /5 " $ ' &! $ " #$ $ " " &

18 ' 2 '" $$ V A & C D C!!D ^ C D ^ C!D _ C D C$D a C D b C D b C!! D c % C&#&D % C D ' $ & ' & $ $ ' " $ &! $ & $! #$ & & & $$ $ $ $"! ' $ & $ # > $ $ $ "! G > -H ' $ 5- &! $ &! &! $ " & 8MB &!@ X " $ B B & $ "#! $ " "! X ) J " B $ 8 $ " # & " " & " "@ X J 8MB &!! ' # # & ( # $ " " > EM)A $ 3 $ C CDD & $ W e C C W edd! C W ed X CD ] C ] ed W e J CD < " &@ CD X r ( t i + t ) r 2 t i ( t t ) $ $

19 >' $ " $ " " # $ 25 8% " & &! & # & $$!! $ > " " $ #!! " # " & & #! <#& & :<3>> &# &" $ & $ & V) ' :& $ /5 & $ ' &" $ & $. & $! $ #! $ ' &# $ $$ " &" "#& $ % " G > -H 3:" $ "! 3:"6! "#& $ ) )* ) $ 8 W $ 3:" 3:"6 4 3$ :<3>>! &" $! $ )* $ 3:" 3:"6 " *) # +$ +#." & :<3>>! )* ' # )* & ' '"# 511= )* & & ) $! &" $ & $ :<3>> ' K V 511, " :<3>> $ & W # $ :<3>> ) W 3$ " )* % " &." +$ ' & " $ & #!! )*.& &! " "! &!! &. & :<3>> && (>' 4 & " J&# 3:"! & 3:"6 ' & &J! '! & $$ # ) $ $ $! $

20 7&'.-& ' " >' 3:"6 <$ $ & "& "& $ $ "& G' V ## 5 : $.$ 5110 (" -H & " $ 3:" & " & " # 3:"6)3:" $ $ 3:" $ & ' &# " 3:" " " $ % " 3:" 3:"6! " % 3:" $ 3:"B $ $ $ " $ 3:" (>' (>' & $) I) "! &) $ "& > (>' "!! $ " &# $! >' 3:"6 "!! $ " "! & " # $ ( I!! $ #?& $ (>' "! 3:" & &!#&B!# 4!#&B!# & 4C 4!#&B!# &.4 &D -E!#

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

22 75A < $ "! " $ " $! " G 8& K 8 /H 752! '! & & ) V! &! $ 5 S ' &# " 5 S! V! V $ & $ 5 S, S " $ &# CM"D -/ 07 4! V $ & M" &# $ " 5 S $ & $ & >' G' V 5110 H $ &!! 5 S V ' & &". >" 6M C.>6D G' 511/H 8 &.>6 $ #! $ " $! # $%& &".>6 $ & '! & # & 5)) C & D 5)/) C &D &! $ ' 5)- V & $ $ $ " - $ "! & # 752! ' " " " &! # & $ ($! $ " &! # & & " ' " & # O)< & " $ $ 5 G(" 5110H $ $ 5 $ $ $ G 8& K 8 /H & (<36 G# 5100H &" & "#

23 3 &!!! $! $ (<36 & < % &! " &! & > & < &!! & & &! (" 5110 " $ $$ >' (<36 $ $ &# $ $ $ && (<36 7& ' $ $ ' % &! " # $!! ' # ' $ % ' " &. I $ 3:"6)3:" $ $ $)& $ $ " " # -5 & $ " # $ # $! / & $ # $! $ # " & & $ $ $ " $ $ 5 $ $ $ & 78&D #!?& ) $ & # $?& # - $ " $ / " $?& & / 79 & (>'! 3:" 3:"6B & (>'?&! C(>' D $ " $. # " " ' 3:" # $ & -- ' G A 511,H

24 077 + & (>' 3:" C D $ " $! & GO / H! $ = JJS " & G2 H < "! 5 SJ$ ' " " $ & O /B " " " " SJ$ 5 SJ$ $! "% " " ' $ &! $ $ $ 5 SJ$ $ " " ' " " &# $! $ 3:" & " % " " O / &! <$A 3 " " # "&! 3:" > 3:"! & $ >' G<$"# 511=H & - +! 3:" $ &. & :Q I3$0 +$01 3$, 4#// & & $ (>' &

25 8*&3/'!'&* &" & $ I83>' G d 5111H >' G<$"# 511=H > 6E (! (>' & &J! & " J&# $ ' $ &# # " &&!% & $ " $ 3:"B " #! " #$ $ " ' #$ $ I )* "#& ) )* " = S! "! ' &# $ 4 K '"# 5111 " 11 P )* $ " $ "% = S "#&! # & $$ ( # V " #$ $.& " / S "#& ) " = S! "! 82& ' 3:"6)3:" $ $ $ $ 5 Potentiel energi (kcal/mol) Energiminimering af AChE og ACh 6,0E+03 1,0E+03-4,0E+03-9,0E+03-1,4E Step 082. $ 3:"6)3:" $! $ &! $. &# # & &# # & 6 5 $ $ " & 5 6 3:"6)3:" $ #! 5 S # +./. & < # & =5/=5 " & -

26 085 3:"6)3:" $ & #! +./. $ 5 S ' # -5I " $ " " #. / $ $ Potentiel energi (kcal/mol) Energiminimering af solventet med AChE-ACh komplekset fikseret -2,3E+05-2,4E+05-2,5E+05-2,6E+05-2,7E+05-2,8E Step Potentiel energi (kcal/mol) Energiminimering af hele systemet 5,0E+06 4,0E+06 3,0E+06 2,0E+06 1,0E+06 0,0E+00-1,0E Step 08. $ "" " 3:"6)3:" $ " # & " " " & # & & " & "%! # ' & & % &!! &! $ '$M # $ ' " V $$ " $ 85&D (# $ / < - $?& & & #! 9 $ $ " $ - <

27 $ 6?& $ " &# $ "?& Potentiel energi (kcal/mol) ,783E+05-1,788E+05-1,793E+05-1,798E+05-1,803E+05 Step 087 $ $ C- $D?& # 6?&$! & #! $ ' >' ) )? ) CD $ & = $ "! C"# D &! " ' & #! 1,90 1,70 rmsd (Å) 1,50 1,30 1,10 0,90 0,70 0,50 0, Tid 088. "! C "#D &! "?& $ "! &! $ " &?& 5 5- S (?&$ - $ #!! $! - $?& " $ &!?& $ >' & = < $ =! " & $ $

28 rmsd (Å) Residue &! " #?& ' # ' $ &!?& :) $ $ " ) Q)"E 3 " #!I-5)-/ 5,)5=/ )=5 /-- /=/)/== -5-5/ -5= = ' " V :"6 $ "& + (! " % & " +#55."// 3 $.&?& V +#55."// 0 ' "& $!! 3:" "?& 6 5 Afstand (Å) Step/100 08: V +#55."// $?&?& S " " GO / + 5H 6 5= $ & " Y- S < Y/ S $ $ /5- S

29 " B&! %&& " #! $?&, 08; ( # CD?& CD " " " &!?& (., %&& " # " " &! ' #."//! " &!?& V 3."// & " GO / < 511/H 8! - > $?& $ (>' "! 3:"B " " $ 5 SJ$ & & (>' & & " 3:" Kraft (pn) Tid (ps) 08<.!.!! 3:" J&# $ % >! & &#! 3:" &

30 9 & 3:"! $ $! +! $ =)0 $8 $ / $ "! $8 $ 0 $8 0 $ 5 $ #& 8!! 55 $ " $ $ = $8 55 $ " 5/ $ " 6 5- $! $ - $8 " " 5= $ +! & & & Y/ $ < - $8 " # $ 3:" $ $ &! & %&& 3:"B % 3:" 3:"6 82'4 F :8 (>' 3:" & & >' 3:"B! $ & )! " ) * 3:" +$,-."// "" Y- S Y S # $ $ 3:" 5 6 3:" " 4511! ) 3:" $ E# 4511 Y= S > &# E# $ 3:" 8< "! $ 4#551 Y/ S " "#& > &# & $ 3:" "#E# E# $ ( Y= S " // S G H 082F 3:" & 3:"6 3:" )* +$,-."// "#& 8< "! $ 4#551 6 ) $ 3:" 4511 )/ $! $! #! 3:" / $ 1 ' & 3:"

31 " &!! ( & +$,-."// #551 " 3:" %&& "" - $ - $ F%&& "" - - $ 3:" &!! & / $ 3:" " +$,-."// #551 / $ &#! # &# &! $ ' # "#$$! $ " +#55 " $ &! $ & ' &! # "#& 4#551 3:" & - S $$! " F%&& / $ 3:"B # &# &! $ +# 55 " '! " +$,-."// 4511

32 " # +$,-."// # "//5! 3:" "! )* # 55 5 $! " # &! $$ 6 0 $! 1 " # " & # " $$ &! " 85'4 :8 25F 6 0= $ &#."// %! 3:"B $ " $ " &# )*! 5/ ' &# &!! & "! 5 $ 1 :9 082 F%&& 0= $ 3:"! )*."// 3# $ % " CD 6! 3:"B $ )* 3:" +#//- ) 3:" 3$0 ' 3:" "! $ & 6 Y1= $ &! 3:" +#//- - S 3:" " & " )* +$,- =, S! " " 3:"B & ' 5- " %&& 1= $ " 3:" " & " 5 $ " 3:" $ $ 3:"B $ " & $ 1 Y5 $

33 <9 2F F%&& "" 1= 5 $ 3:" $ $ " "."//. " " 3:"B +#//- 3$0 8'4 25F 58F 3:" & " 5 55 $ $ 5- # " )* +#//-."// ) 3:" 3$0 = S '! $ 55 $ $ 1 < &# 3:" &!."//!! 3:" +$01B *)#! 5/ $ $ 1 > 5/ 5- $ 3:" $ +#//- S +$01 S 5 $" & Y5- $ $ 1 2F 0828 F%&& 5/ $ 3:" & " " " +#//- +$01

34 6 5- $! 3:" +#//- +#//-! *) # $ $ 3:" 5= '% +#//- 3:"! & " &! # ' $"! # 5-5= $ F%&& 5-= $ 3:"! )* +#//- 3:" " &! )* +$01 ' &!!! 3:" +$01B *) # - S 5= '! 3:" 40, 3$, & $ 3:"6! ' ) 3:" $ E# $ 40, 3$, "" 10 S 55 S! 3:" &! $ +$01 " " 3:" & 3:" :" " &!!! +#//- 0= S : F%&& 5= $ " 3:" "! " +$01 "

35 > 5= 5 $ " 3:"! $ 3:"6 )* +$01 < 3:" Y/ $ " 5, ' & 3:" +$01 / $ Y5 S 2 $ 1 & / $ $ 1 # 3:"B &! 5F 082; F%&& / $ " 3:" " 3:"6 + & 5 $ 3:"B $ % ' 82 '4 )/ $ /) $ )0 $ 0)5 $ 5)55 $ 55)5/ $ 5/)5- $ 5-)5= $ 5=)5 $ / $ 3:" " & +$,-."// #551 3# 3:" &! $ " 3:" 3 +$,-."// 3# " (! $."// % & +#//- 3$0 ' &# 3:" $ " 3:" "."// +#//- 3$0 3:"."// &!! $ &!! +$01 3:" " +#//- +$01 3:" +#//- &!! $!! +$01 3:" " &! +$01 $ 3:"6 3:" 3:"6

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

37 " &# $& ' &! $ :) & ' $ &! &# 3:"B & ( # # 3:"6 &?& & & "! 3:" & 0 $ V +#55."// " 3 5 / S Y/ $?&, $ & " " - S?& /5- S "?&!! 3:" & (>' " & # 3:"! ' &# $ >' " " & %& $ G /H + 5 / - S O / V = S " &!?& " $ " 3:" $ 3! " d! (>' & & 3:"B % 9 " " "!! +!" " " "% 3:" " % $ &!" " $ 5 SJ$! $ & O / "!" " SJ$ $ 5 SJ$ " <$A 3 & $ 3:"6 & $ "% " " '!" " $ "% 3:" & 3:"6 ' " $!" " 92-6 & # 3:"B % $! $ 1 ' &# & " 3:" & " & 3:"6B # " # 3:" $ % ' $ $ & J "! # & " & 3:" 3:"6 ' &# & # 3:" " ' $ # 3:"6! $ ( "## " # ( <-- & 4/0 " & " >' # 3:"B $ & # & "#& <-- (

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46 )+/!12 #Konfigurationsfil til energiminimering af AChE + ACh structure C:/NAMD/ /output/aa.psf coordinates C:/NAMD/ /output/aa.pdb paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 minimization on outputenergies 1000 outputtiming 1000 binaryoutput no outputname output/aa_mina restartname output/aa_mina restartfreq 100 binaryrestart no DCDfile output/aa_mina.dcd dcdfreq 100 numsteps 2000 cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater off #Konfigurationsfil til energiminimering af solvent hvor AChE + ACh er fikseret structure C:/NAMD/ /output/aa_min_vb.psf coordinates C:/NAMD/ /output/aa_min_vb.pdb paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 minimization on

47 outputenergies 1000 outputtiming 1000 binaryoutput no outputname output/aafix_minb_vb restartname output/aafix_minb_vb restartfreq 100 binaryrestart no DCDfile output/aafix_minb_vb.dcd dcdfreq 100 fixedatoms on fixedatomsfile output/aa_min_vb.ref fixedatomscol B numsteps 2000 cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater on #Konfigurationsfil til energiminimering af hele systemet structure C:/NAMD/ /output/aa_min_vb.psf coordinates C:/NAMD/ /output/aafix_minb_vb.coor paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 minimization on outputenergies 1000 outputtiming 1000 binaryoutput no outputname output/aa_minc_vb restartname output/aa_minc_vb restartfreq 100 binaryrestart no DCDfile output/aa_minc_vb.dcd dcdfreq 10 numsteps 2000 cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater on

48 )+/!15 #Konfigurationsfil til opvarmning af det energiminimerede systemet. structure C:/NAMD/ /output/aa_min_vb.psf coordinates C:/NAMD/ /output/aa_minc_vb.coor paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 timestep 2.0 fullelectfrequency 4 outputenergies 1000 outputtiming 1000 binaryoutput no outputname output/aa_min_vb_opv2 restartname output/aa_min_vb_opv2 restartfreq 100 binaryrestart yes DCDfile output/aa_min_vb_opv2.dcd dcdfreq 100 seed 2010 numsteps 2000 temperature 0 reassignfreq 1 reassignincr 0.15 reassignhold 300 cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater on

49 )+/!1 #Konfigurationsfil til equilibrering af systemet structure C:/NAMD/ /output/aa_min_vb.psf coordinates C:/NAMD/ /output/aa_min_vb_opv2.coor paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 timestep 2.0 fullelectfrequency 4 outputenergies 500 outputtiming 1000 binaryoutput no outputname output/aa_opv_eq restartname output/aa_opv_eq restartfreq 100 binaryrestart yes DCDfile output/aa_opv_eq.dcd dcdfreq 100 seed 3010 numsteps temperature 300 rescalefreq 1 rescaletemp 300 cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater on

50 )+/!17 #Skript til beregning af en selektions massecenter proc center_of_mass {selection} { if {[$selection num] <= 0} { error "center_of_mass: needs a selection with atoms" } set com [veczero] set mass 0 foreach coord [$selection get {x y z}] m [$selection get mass] { set mass [expr $mass +$m] set com [vecadd $com [vecscale $m $coord]] } if {$mass == 0} { error "center_of_mass: total mass is zero" } return [vecscale [expr 1.0/$mass] $com] }

51 )+/!18 #Konfigurationsfil til SMD simuleringen structure C:/NAMD/ /output/aa_min_vb.psf coordinates C:/NAMD/ /output/aa_opv_eq.pdb bincoordinates C:/NAMD/ /output/aa_opv_eq1.coor.bak paratypecharmm on parameters C:/toppar/par_all27_prot_lipid.inp temperature 300 exclude scaled scaling 1.0 dielectric 1.0 switching on switchdist 8.5 cutoff 10.0 pairlistdist 11.5 margin 0.0 stepspercycle 20 rigidbonds all rigidtolerance rigiditerations 100 PME on PMETolerance PMEGridSizeX 55 PMEGridSizeY 55 PMEGridSizeZ 55 timestep 2.0 fullelectfrequency 4 outputenergies 100 outputtiming 10 binaryoutput no outputname output/smd restartname output/smd_res restartfreq 1000 binaryrestart yes DCDfile output/smd.dcd dcdfreq 100 fixedatoms on fixedatomsfile C:/NAMD/ /output/aa_opv_eq.ref fixedatomscol B SMD on SMDfile C:/NAMD/ /output/aa_opv_eq.ref SMDk 6 SMDvel SMDDir SMDOutputFreq 100 seed 6010 numsteps cellbasisvector cellbasisvector cellbasisvector cellorigin wrapwater on

52 )+/!19 #Skript til beregning af rmsd for hovedkædeatomerne som funktion af tiden set outfile [open rmsd.dat w]; set nf [molinfo top get numframes] set frame0 [atomselect top "protein and backbone and noh" frame 0] set sel [atomselect top "protein and backbone and noh"] set all [atomselect top all] for {set i 1 } {$i < $nf } { incr i } { $sel frame $i $all frame $i $all move [measure fit $sel $frame0] puts $outfile "[measure rmsd $sel $frame0]" } close $outfile #Skript til beregning af rmsd pr. residue proc rmsd_residue_over_time {{mol top} res} { set reference [atomselect $mol "protein" frame 0] set compare [atomselect $mol "protein"] set all [atomselect top all] set num_steps [molinfo $mol get numframes] foreach r $res { set rmsd($r) 0 } for {set frame 0} {$frame < $num_steps} {incr frame} { puts "Calculating rmsd for frame $frame..." $compare frame $frame set trans_mat [measure fit $compare $reference] $all move $trans_mat foreach r $res { set ref [atomselect $mol "segname PRO and resid $r and noh" frame 0] set comp [atomselect $mol "segname PRO and resid $r and noh" frame $frame] set rmsd($r) [expr $rmsd($r) + [measure rmsd $comp $ref]] $comp delete $ref delete } } set ave 0 foreach r $res { set rmsd($r) [expr $rmsd($r)/$num_steps] puts "RMSD of residue $r is $rmsd($r)" set res_b [atomselect $mol "resid $r"] $res_b set beta $rmsd($r) $res_b delete set ave [expr $ave + $rmsd($r)] } set ave [expr $ave/[llength $res]] puts " Average rmsd per residue: $ave" } rmsd_residue_over_time top $sel_resid