normal do_order issue with POPC (solution)

  • johnd
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2 years 5 months ago #7547 by johnd
Hi all,

I kept getting an index out of range error using the do-order-gmx5.py script, but only for POPC, and noticed several others were as well:

http://www.cgmartini.nl/index.php/component/kunena/9-tools/5520-order-parameters-calculation

http://www.cgmartini.nl/index.php/component/kunena/9-tools/4318-do-order-milti-py-for-popc

Tjserk mentioned a fix (second link), but from the context of 5 to 4 bead tail. The cause of the error which I think is what was tripping people up, however, is that the bead order is incorrect.

Current order (line 95):
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-D2B D2B-C3B C3B-C4B\n"

Fixed order:
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-D2A D2A-C3A C3A-C4A C1B-C2B C2B-C3B C3B-C4B\n"

Anyways, I figured I'd post it here so others can get to a solution faster until a fix is rolled out.

Cheers,

John

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8 months 3 weeks ago - 8 months 3 weeks ago #8337 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi john,
i am trying to calculate the order parameter of POPC lipid. i am getting the same error
Starting P2 calculationTaking care of snapshot frame_dump_0.gro
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in ?
vector[j] = first[j] - second[j]
IndexError: list index out of range
i have seen your post and also try to change the bead name but still i am getting the same error.
Here is my POPC bead
130POPC NC3 567 3.102 2.318 6.894 -0.1877 -0.2911 0.0367
130POPC PO4 568 3.015 2.746 6.999 0.1382 -0.1867 -0.1484
130POPC GL1 569 2.844 2.820 6.569 0.0013 0.0444 -0.0471
130POPC GL2 570 2.817 2.471 6.480 0.1707 0.1357 -0.1409
130POPC C1A 571 3.007 2.387 6.054 0.1505 0.0994 0.1694
130POPC C2A 572 2.839 2.146 5.771 0.0925 -0.0107 0.1411
130POPC C3A 573 2.805 2.153 5.359 0.0853 -0.0120 -0.0365
130POPC C4A 574 2.904 2.047 4.928 -0.0100 0.1171 0.1387
130POPC C1B 575 3.008 2.984 6.227 -0.2540 0.0974 -0.2841
130POPC C2B 576 3.007 2.914 5.756 -0.2559 -0.2164 -0.1563
130POPC D3B 577 3.014 2.526 5.523 -0.1330 0.2426 0.0318
130POPC C4B 578 3.043 2.516 5.045 0.1625 -0.1160 -0.1142
130POPC C5B 579 2.880 2.417 4.597 0.1166 0.2281 -0.0205

can you please guide me to solve this error.

i have a one more question, can we also done order parameter calculation by gromacs. For this what beads should be chosen.
thank you
Last edit: 8 months 3 weeks ago by cm.

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  • johnd
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8 months 3 weeks ago #8338 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Hi,

Based on your beads, it would appear that you are using an older version of the POPC topology

www.cgmartini.nl/index.php/force-field-p...ml?dir=PC&lipid=POPC

The currently used itp is the one that ends in _02.itp, and based on your output, you are using _01i.itp

So I think you would just need to end the line with the POPC definition to indicate the different bead setup. I haven't done it, and don't know if it will work, but you can try changing the chain 2 beads bond definition to C1-C2 C2-D3 D3-C4 C4-C5.

In regards to your other question - The Gromacs tool for this will not give meaningful results as far as I'm aware. See here: www.researchgate.net/post/Lipid_Order_Parameter_Calculation

Cheers,

John

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8 months 3 weeks ago #8341 by cm
Replied by cm on topic do_order issue with POPC (solution)
Hi,
Thank you so much for your reply and advice.I have followed your instruction, still i am getting the same error.

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8 months 1 week ago #8359 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi all,
does any one have any idea how i can solve this problem. I am still stuck in this problem.
thanking you

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8 months 1 week ago #8360 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Hi,

Can you upload a gro file, your topologies (top, itp), and the do-order script that you have to a google drive or something and post the link? I can try and take a look tomorrow.

John

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8 months 6 days ago #8361 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi,
sure here are my file

http://cgmartini.nl/index.php/tutorials-general-introduction/bilayers

system.top
#include "martini_v2.2.itp"
#include "Protein_A.itp"
#include "martini_v2.0_ions.itp"
#include "martini_v2.0_lipids.itp"

[ system ]
; name
Protein in INSANE! Membrane UpperLeaflet>POPC:POPG=7.0:3.0 LowerLeaflet>POPC:POPG=7.0:3.0

[ molecules ]
; name number
Protein_A 2
POPC 252
POPG 108
POPC 252
POPG 108
W 20797
NA+ 329
CL- 129

system.gro
(because of large size only uploading the popc part, if u send ur mail id then i can send the full file)
130POPC NC3 567 3.102 2.318 6.894 -0.1877 -0.2911 0.0367
130POPC PO4 568 3.015 2.746 6.999 0.1382 -0.1867 -0.1484
130POPC GL1 569 2.844 2.820 6.569 0.0013 0.0444 -0.0471
130POPC GL2 570 2.817 2.471 6.480 0.1707 0.1357 -0.1409
130POPC C1A 571 3.007 2.387 6.054 0.1505 0.0994 0.1694
130POPC C2A 572 2.839 2.146 5.771 0.0925 -0.0107 0.1411
130POPC C3A 573 2.805 2.153 5.359 0.0853 -0.0120 -0.0365
130POPC C4A 574 2.904 2.047 4.928 -0.0100 0.1171 0.1387
130POPC C1B 575 3.008 2.984 6.227 -0.2540 0.0974 -0.2841
130POPC C2B 576 3.007 2.914 5.756 -0.2559 -0.2164 -0.1563
130POPC D3B 577 3.014 2.526 5.523 -0.1330 0.2426 0.0318
130POPC C4B 578 3.043 2.516 5.045 0.1625 -0.1160 -0.1142
130POPC C5B 579 2.880 2.417 4.597 0.1166 0.2281 -0.0205
131POPC NC3 580 11.503 13.265 7.278 -0.0125 -0.2917 0.1341
131POPC PO4 581 11.626 13.017 6.883 0.1447 -0.0719 0.2214
131POPC GL1 582 11.969 12.934 6.658 0.1632 -0.0833 0.2834
131POPC GL2 583 11.986 12.724 6.410 0.2099 0.1329 -0.1217
131POPC C1A 584 12.412 12.610 6.403 0.1053 0.0665 -0.0988
131POPC C2A 585 12.540 12.586 6.011 0.2429 0.1078 0.1456
131POPC C3A 586 12.843 12.629 5.754 -0.0692 -0.1280 -0.0617
131POPC C4A 587 13.129 12.585 5.435 0.2716 0.3026 0.3400
131POPC C1B 588 12.424 13.072 6.509 -0.0888 -0.3082 -0.1695
131POPC C2B 589 12.648 13.039 6.186 -0.0568 -0.1984 0.2290
131POPC D3B 590 12.601 13.049 5.751 -0.2286 0.0725 0.1461
131POPC C4B 591 12.217 13.278 5.533 -0.1767 0.1662 -0.0620
131POPC C5B 592 11.914 13.450 5.239 0.0144 0.1272 0.2101

Protein.itp
; MARTINI (martini22) Coarse Grained topology file for "Protein_A"
; Created by py version 2.6
; Using the following options: -f 5B1F2.PDB -o system-vaccum.top -x prot-CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22 -cys auto
; Sequence:
; KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
; Secondary Structure:
; CCCC1111HH2222TTCTTCTTCC1111HHHH2222TTCTTCEEECTTSCEEETTTTEETTTSCCCSCSTTCCCTTCSCCCCCCSSST1111HHH2222TTTTCCCCS113322TTTSCCCCCCTTCCC

[ moleculetype ]
; Name Exclusions
Protein_A 1

[ atoms ]
1 Qd 1 LYS BB 1 1.0000 ; C
2 C3 1 LYS SC1 2 0.0000 ; C
3 Qd 1 LYS SC2 3 1.0000 ; C
4 P5 2 VAL BB 4 0.0000 ; C
5 AC2 2 VAL SC1 5 0.0000 ; C
6 P5 3 PHE BB 6 0.0000 ; C
7 SC5 3 PHE SC1 7 0.0000 ; C
8 SC5 3 PHE SC2 8 0.0000 ; C
9 SC5 3 PHE SC3 9 0.0000 ; C
10 P5 4 GLY BB 10 0.0000 ; C
11 Nd 5 ARG BB 11 0.0000 ; 1
12 N0 5 ARG SC1 12 0.0000 ; 1
13 Qd 5 ARG SC2 13 1.0000 ; 1
14 Nd 6 CYS BB 14 0.0000 ; 1
15 C5 6 CYS SC1 15 0.0000 ; 1
16 Nd 7 GLU BB 16 0.0000 ; 1
17 Qa 7 GLU SC1 17 -1.0000 ; 1
18 Nd 8 LEU BB 18 0.0000 ; 1
19 AC1 8 LEU SC1 19 0.0000 ; 1
20 C5 9 ALA BB 20 0.0000 ; H
21 C5 10 ALA BB 21 0.0000 ; H
22 N0 11 ALA BB 22 0.0000 ; 2
23 Na 12 MET BB 23 0.0000 ; 2
24 C5 12 MET SC1 24 0.0000 ; 2
25 Na 13 LYS BB 25 0.0000 ; 2
26 C3 13 LYS SC1 26 0.0000 ; 2
27 Qd 13 LYS SC2 27 1.0000 ; 2
28 Na 14 ARG BB 28 0.0000 ; 2
29 N0 14 ARG SC1 29 0.0000 ; 2
30 Qd 14 ARG SC2 30 1.0000 ; 2
31 Nda 15 HIS BB 31 0.0000 ; T
32 SC4 15 HIS SC1 32 0.0000 ; T
33 SP1 15 HIS SC2 33 0.0000 ; T
34 SP1 15 HIS SC3 34 0.0000 ; T
35 Nda 16 GLY BB 35 0.0000 ; T
36 P5 17 LEU BB 36 0.0000 ; C
37 AC1 17 LEU SC1 37 0.0000 ; C
38 Nda 18 ASP BB 38 0.0000 ; T
39 Qa 18 ASP SC1 39 -1.0000 ; T
40 Nda 19 ASN BB 40 0.0000 ; T
41 P5 19 ASN SC1 41 0.0000 ; T
42 P5 20 TYR BB 42 0.0000 ; C
43 SC4 20 TYR SC1 43 0.0000 ; C
44 SC4 20 TYR SC2 44 0.0000 ; C
45 SP1 20 TYR SC3 45 0.0000 ; C
46 Nda 21 ARG BB 46 0.0000 ; T
47 N0 21 ARG SC1 47 0.0000 ; T
48 Qd 21 ARG SC2 48 1.0000 ; T
49 Nda 22 GLY BB 49 0.0000 ; T
50 P5 23 TYR BB 50 0.0000 ; C
51 SC4 23 TYR SC1 51 0.0000 ; C
52 SC4 23 TYR SC2 52 0.0000 ; C
53 SP1 23 TYR SC3 53 0.0000 ; C
54 P5 24 SER BB 54 0.0000 ; C
55 P1 24 SER SC1 55 0.0000 ; C
56 Nd 25 LEU BB 56 0.0000 ; 1
57 AC1 25 LEU SC1 57 0.0000 ; 1
58 Nd 26 GLY BB 58 0.0000 ; 1
59 Nd 27 ASN BB 59 0.0000 ; 1
60 P5 27 ASN SC1 60 0.0000 ; 1
61 Nd 28 TRP BB 61 0.0000 ; 1
62 SC4 28 TRP SC1 62 0.0000 ; 1
63 SNd 28 TRP SC2 63 0.0000 ; 1
64 SC5 28 TRP SC3 64 0.0000 ; 1
65 SC5 28 TRP SC4 65 0.0000 ; 1
66 N0 29 VAL BB 66 0.0000 ; H
67 AC2 29 VAL SC1 67 0.0000 ; H
68 N0 30 CYS BB 68 0.0000 ; H
69 C5 30 CYS SC1 69 0.0000 ; H
70 C5 31 ALA BB 70 0.0000 ; H
71 C5 32 ALA BB 71 0.0000 ; H
72 Na 33 LYS BB 72 0.0000 ; 2
73 C3 33 LYS SC1 73 0.0000 ; 2
74 Qd 33 LYS SC2 74 1.0000 ; 2
75 Na 34 PHE BB 75 0.0000 ; 2
76 SC5 34 PHE SC1 76 0.0000 ; 2
77 SC5 34 PHE SC2 77 0.0000 ; 2
78 SC5 34 PHE SC3 78 0.0000 ; 2
79 Na 35 GLU BB 79 0.0000 ; 2
80 Qa 35 GLU SC1 80 -1.0000 ; 2
81 Na 36 SER BB 81 0.0000 ; 2
82 P1 36 SER SC1 82 0.0000 ; 2
83 Nda 37 ASN BB 83 0.0000 ; T
84 P5 37 ASN SC1 84 0.0000 ; T
85 Nda 38 PHE BB 85 0.0000 ; T
86 SC5 38 PHE SC1 86 0.0000 ; T
87 SC5 38 PHE SC2 87 0.0000 ; T
88 SC5 38 PHE SC3 88 0.0000 ; T
89 P5 39 ASN BB 89 0.0000 ; C
90 P5 39 ASN SC1 90 0.0000 ; C
91 Nda 40 THR BB 91 0.0000 ; T
92 P1 40 THR SC1 92 0.0000 ; T
93 Nda 41 GLN BB 93 0.0000 ; T
94 P4 41 GLN SC1 94 0.0000 ; T
95 P4 42 ALA BB 95 0.0000 ; C
96 Nda 43 THR BB 96 0.0000 ; E
97 P1 43 THR SC1 97 0.0000 ; E
98 Nda 44 ASN BB 98 0.0000 ; E
99 P5 44 ASN SC1 99 0.0000 ; E
100 Nda 45 ARG BB 100 0.0000 ; E
101 N0 45 ARG SC1 101 0.0000 ; E
102 Qd 45 ARG SC2 102 1.0000 ; E
103 P5 46 ASN BB 103 0.0000 ; C
104 P5 46 ASN SC1 104 0.0000 ; C
105 Nda 47 THR BB 105 0.0000 ; T
106 P1 47 THR SC1 106 0.0000 ; T
107 Nda 48 ASP BB 107 0.0000 ; T
108 Qa 48 ASP SC1 108 -1.0000 ; T
109 P5 49 GLY BB 109 0.0000 ; S
110 P5 50 SER BB 110 0.0000 ; C
111 P1 50 SER SC1 111 0.0000 ; C
112 Nda 51 THR BB 112 0.0000 ; E
113 P1 51 THR SC1 113 0.0000 ; E
114 Nda 52 ASP BB 114 0.0000 ; E
115 Qa 52 ASP SC1 115 -1.0000 ; E
116 Nda 53 TYR BB 116 0.0000 ; E
117 SC4 53 TYR SC1 117 0.0000 ; E
118 SC4 53 TYR SC2 118 0.0000 ; E
119 SP1 53 TYR SC3 119 0.0000 ; E
120 Nda 54 GLY BB 120 0.0000 ; T
121 Nda 55 ILE BB 121 0.0000 ; T
122 AC1 55 ILE SC1 122 0.0000 ; T
123 Nda 56 LEU BB 123 0.0000 ; T
124 AC1 56 LEU SC1 124 0.0000 ; T
125 Nda 57 GLN BB 125 0.0000 ; T
126 P4 57 GLN SC1 126 0.0000 ; T
127 Nda 58 ILE BB 127 0.0000 ; E
128 AC1 58 ILE SC1 128 0.0000 ; E
129 Nda 59 ASN BB 129 0.0000 ; E
130 P5 59 ASN SC1 130 0.0000 ; E
131 Nda 60 SER BB 131 0.0000 ; T
132 P1 60 SER SC1 132 0.0000 ; T
133 Nda 61 ARG BB 133 0.0000 ; T
134 N0 61 ARG SC1 134 0.0000 ; T
135 Qd 61 ARG SC2 135 1.0000 ; T
136 Nda 62 TRP BB 136 0.0000 ; T
137 SC4 62 TRP SC1 137 0.0000 ; T
138 SNd 62 TRP SC2 138 0.0000 ; T
139 SC5 62 TRP SC3 139 0.0000 ; T
140 SC5 62 TRP SC4 140 0.0000 ; T
141 P5 63 TRP BB 141 0.0000 ; S
142 SC4 63 TRP SC1 142 0.0000 ; S
143 SNd 63 TRP SC2 143 0.0000 ; S
144 SC5 63 TRP SC3 144 0.0000 ; S
145 SC5 63 TRP SC4 145 0.0000 ; S
146 P5 64 CYS BB 146 0.0000 ; C
147 C5 64 CYS SC1 147 0.0000 ; C
148 P5 65 ASN BB 148 0.0000 ; C
149 P5 65 ASN SC1 149 0.0000 ; C
150 P5 66 ASP BB 150 0.0000 ; C
151 Qa 66 ASP SC1 151 -1.0000 ; C
152 P5 67 GLY BB 152 0.0000 ; S
153 P5 68 ARG BB 153 0.0000 ; C
154 N0 68 ARG SC1 154 0.0000 ; C
155 Qd 68 ARG SC2 155 1.0000 ; C
156 P5 69 THR BB 156 0.0000 ; S
157 P1 69 THR SC1 157 0.0000 ; S
158 N0 70 PRO BB 158 0.0000 ; T
159 C3 70 PRO SC1 159 0.0000 ; T
160 Nda 71 GLY BB 160 0.0000 ; T
161 P5 72 SER BB 161 0.0000 ; C
162 P1 72 SER SC1 162 0.0000 ; C
163 P5 73 ARG BB 163 0.0000 ; C
164 N0 73 ARG SC1 164 0.0000 ; C
165 Qd 73 ARG SC2 165 1.0000 ; C
166 P5 74 ASN BB 166 0.0000 ; C
167 P5 74 ASN SC1 167 0.0000 ; C
168 Nda 75 LEU BB 168 0.0000 ; T
169 AC1 75 LEU SC1 169 0.0000 ; T
170 Nda 76 CYS BB 170 0.0000 ; T
171 C5 76 CYS SC1 171 0.0000 ; T
172 P5 77 ASN BB 172 0.0000 ; C
173 P5 77 ASN SC1 173 0.0000 ; C
174 P5 78 ILE BB 174 0.0000 ; S
175 AC1 78 ILE SC1 175 0.0000 ; S
176 P4 79 PRO BB 176 0.0000 ; C
177 C3 79 PRO SC1 177 0.0000 ; C
178 P5 80 CYS BB 178 0.0000 ; C
179 C5 80 CYS SC1 179 0.0000 ; C
180 P5 81 SER BB 180 0.0000 ; C
181 P1 81 SER SC1 181 0.0000 ; C
182 P4 82 ALA BB 182 0.0000 ; C
183 P5 83 LEU BB 183 0.0000 ; C
184 AC1 83 LEU SC1 184 0.0000 ; C
185 P5 84 LEU BB 185 0.0000 ; C
186 AC1 84 LEU SC1 186 0.0000 ; C
187 P5 85 SER BB 187 0.0000 ; S
188 P1 85 SER SC1 188 0.0000 ; S
189 P5 86 SER BB 189 0.0000 ; S
190 P1 86 SER SC1 190 0.0000 ; S
191 P5 87 ASP BB 191 0.0000 ; S
192 Qa 87 ASP SC1 192 -1.0000 ; S
193 Nda 88 ILE BB 193 0.0000 ; T
194 AC1 88 ILE SC1 194 0.0000 ; T
195 Nd 89 THR BB 195 0.0000 ; 1
196 P1 89 THR SC1 196 0.0000 ; 1
197 N0 90 ALA BB 197 0.0000 ; 1
198 Nd 91 SER BB 198 0.0000 ; 1
199 P1 91 SER SC1 199 0.0000 ; 1
200 Nd 92 VAL BB 200 0.0000 ; 1
201 AC2 92 VAL SC1 201 0.0000 ; 1
202 N0 93 ASN BB 202 0.0000 ; H
203 P5 93 ASN SC1 203 0.0000 ; H
204 N0 94 CYS BB 204 0.0000 ; H
205 C5 94 CYS SC1 205 0.0000 ; H
206 C5 95 ALA BB 206 0.0000 ; H
207 Na 96 LYS BB 207 0.0000 ; 2
208 C3 96 LYS SC1 208 0.0000 ; 2
209 Qd 96 LYS SC2 209 1.0000 ; 2
210 Na 97 LYS BB 210 0.0000 ; 2
211 C3 97 LYS SC1 211 0.0000 ; 2
212 Qd 97 LYS SC2 212 1.0000 ; 2
213 Na 98 ILE BB 213 0.0000 ; 2
214 AC1 98 ILE SC1 214 0.0000 ; 2
215 Na 99 VAL BB 215 0.0000 ; 2
216 AC2 99 VAL SC1 216 0.0000 ; 2
217 Nda 100 SER BB 217 0.0000 ; T
218 P1 100 SER SC1 218 0.0000 ; T
219 Nda 101 ASP BB 219 0.0000 ; T
220 Qa 101 ASP SC1 220 -1.0000 ; T
221 Nda 102 GLY BB 221 0.0000 ; T
222 Nda 103 ASN BB 222 0.0000 ; T
223 P5 103 ASN SC1 223 0.0000 ; T
224 P5 104 GLY BB 224 0.0000 ; C
225 P5 105 MET BB 225 0.0000 ; C
226 C5 105 MET SC1 226 0.0000 ; C
227 P5 106 ASN BB 227 0.0000 ; C
228 P5 106 ASN SC1 228 0.0000 ; C
229 P4 107 ALA BB 229 0.0000 ; C
230 P5 108 TRP BB 230 0.0000 ; S
231 SC4 108 TRP SC1 231 0.0000 ; S
232 SNd 108 TRP SC2 232 0.0000 ; S
233 SC5 108 TRP SC3 233 0.0000 ; S
234 SC5 108 TRP SC4 234 0.0000 ; S
235 Nd 109 VAL BB 235 0.0000 ; 1
236 AC2 109 VAL SC1 236 0.0000 ; 1
237 N0 110 ALA BB 237 0.0000 ; 1
238 Nda 111 TRP BB 238 0.0000 ; 3
239 SC4 111 TRP SC1 239 0.0000 ; 3
240 SNd 111 TRP SC2 240 0.0000 ; 3
241 SC5 111 TRP SC3 241 0.0000 ; 3
242 SC5 111 TRP SC4 242 0.0000 ; 3
243 Nda 112 ARG BB 243 0.0000 ; 3
244 N0 112 ARG SC1 244 0.0000 ; 3
245 Qd 112 ARG SC2 245 1.0000 ; 3
246 Na 113 ASN BB 246 0.0000 ; 2
247 P5 113 ASN SC1 247 0.0000 ; 2
248 Na 114 ARG BB 248 0.0000 ; 2
249 N0 114 ARG SC1 249 0.0000 ; 2
250 Qd 114 ARG SC2 250 1.0000 ; 2
251 Nda 115 CYS BB 251 0.0000 ; T
252 C5 115 CYS SC1 252 0.0000 ; T
253 Nda 116 LYS BB 253 0.0000 ; T
254 C3 116 LYS SC1 254 0.0000 ; T
255 Qd 116 LYS SC2 255 1.0000 ; T
256 Nda 117 GLY BB 256 0.0000 ; T
257 P5 118 THR BB 257 0.0000 ; S
258 P1 118 THR SC1 258 0.0000 ; S
259 P5 119 ASP BB 259 0.0000 ; C
260 Qa 119 ASP SC1 260 -1.0000 ; C
261 P5 120 VAL BB 261 0.0000 ; C
262 AC2 120 VAL SC1 262 0.0000 ; C
263 P5 121 GLN BB 263 0.0000 ; C
264 P4 121 GLN SC1 264 0.0000 ; C
265 P4 122 ALA BB 265 0.0000 ; C
266 P5 123 TRP BB 266 0.0000 ; C
267 SC4 123 TRP SC1 267 0.0000 ; C
268 SNd 123 TRP SC2 268 0.0000 ; C
269 SC5 123 TRP SC3 269 0.0000 ; C
270 SC5 123 TRP SC4 270 0.0000 ; C
271 P5 124 ILE BB 271 0.0000 ; C
272 AC1 124 ILE SC1 272 0.0000 ; C
273 Nda 125 ARG BB 273 0.0000 ; T
274 N0 125 ARG SC1 274 0.0000 ; T
275 Qd 125 ARG SC2 275 1.0000 ; T
276 Nda 126 GLY BB 276 0.0000 ; T
277 P5 127 CYS BB 277 0.0000 ; C
278 C5 127 CYS SC1 278 0.0000 ; C
279 P5 128 ARG BB 279 0.0000 ; C
280 N0 128 ARG SC1 280 0.0000 ; C
281 Qd 128 ARG SC2 281 1.0000 ; C
282 Qa 129 LEU BB 282 -1.0000 ; C
283 AC1 129 LEU SC1 283 0.0000 ; C

[ bonds ]
; Backbone bonds
1 4 1 0.35000 1250 ; LYS(C)-VAL(C)
4 6 1 0.35000 1250 ; VAL(C)-PHE(C)
6 10 1 0.35000 1250 ; PHE(C)-GLY(C)
31 35 1 0.35000 1250 ; HIS(T)-GLY(T)
35 36 1 0.35000 1250 ; GLY(T)-LEU(C)
36 38 1 0.35000 1250 ; LEU(C)-ASP(T)
38 40 1 0.35000 1250 ; ASP(T)-ASN(T)
40 42 1 0.35000 1250 ; ASN(T)-TYR(C)
42 46 1 0.35000 1250 ; TYR(C)-ARG(T)
46 49 1 0.35000 1250 ; ARG(T)-GLY(T)
49 50 1 0.35000 1250 ; GLY(T)-TYR(C)
50 54 1 0.35000 1250 ; TYR(C)-SER(C)
83 85 1 0.35000 1250 ; ASN(T)-PHE(T)
85 89 1 0.35000 1250 ; PHE(T)-ASN(C)
89 91 1 0.35000 1250 ; ASN(C)-THR(T)
91 93 1 0.35000 1250 ; THR(T)-GLN(T)
93 95 1 0.35000 1250 ; GLN(T)-ALA(C)
95 96 1 0.35000 1250 ; ALA(C)-THR(E)
96 98 1 0.35000 1250 ; THR(E)-ASN(E)
98 100 1 0.35000 1250 ; ASN(E)-ARG(E)
100 103 1 0.35000 1250 ; ARG(E)-ASN(C)
103 105 1 0.35000 1250 ; ASN(C)-THR(T)
105 107 1 0.35000 1250 ; THR(T)-ASP(T)
107 109 1 0.35000 1250 ; ASP(T)-GLY(S)
109 110 1 0.35000 1250 ; GLY(S)-SER(C)
110 112 1 0.35000 1250 ; SER(C)-THR(E)
112 114 1 0.35000 1250 ; THR(E)-ASP(E)
114 116 1 0.35000 1250 ; ASP(E)-TYR(E)
116 120 1 0.35000 1250 ; TYR(E)-GLY(T)
120 121 1 0.35000 1250 ; GLY(T)-ILE(T)
121 123 1 0.35000 1250 ; ILE(T)-LEU(T)
123 125 1 0.35000 1250 ; LEU(T)-GLN(T)
125 127 1 0.35000 1250 ; GLN(T)-ILE(E)
127 129 1 0.35000 1250 ; ILE(E)-ASN(E)
129 131 1 0.35000 1250 ; ASN(E)-SER(T)
131 133 1 0.35000 1250 ; SER(T)-ARG(T)
133 136 1 0.35000 1250 ; ARG(T)-TRP(T)
136 141 1 0.35000 1250 ; TRP(T)-TRP(S)
141 146 1 0.35000 1250 ; TRP(S)-CYS(C)
146 148 1 0.35000 1250 ; CYS(C)-ASN(C)
148 150 1 0.35000 1250 ; ASN(C)-ASP(C)
150 152 1 0.35000 1250 ; ASP(C)-GLY(S)
152 153 1 0.35000 1250 ; GLY(S)-ARG(C)
153 156 1 0.35000 1250 ; ARG(C)-THR(S)
156 158 1 0.35000 1250 ; THR(S)-PRO(T)
158 160 1 0.35000 1250 ; PRO(T)-GLY(T)
160 161 1 0.35000 1250 ; GLY(T)-SER(C)
161 163 1 0.35000 1250 ; SER(C)-ARG(C)
163 166 1 0.35000 1250 ; ARG(C)-ASN(C)
166 168 1 0.35000 1250 ; ASN(C)-LEU(T)
168 170 1 0.35000 1250 ; LEU(T)-CYS(T)
170 172 1 0.35000 1250 ; CYS(T)-ASN(C)
172 174 1 0.35000 1250 ; ASN(C)-ILE(S)
174 176 1 0.35000 1250 ; ILE(S)-PRO(C)
176 178 1 0.35000 1250 ; PRO(C)-CYS(C)
178 180 1 0.35000 1250 ; CYS(C)-SER(C)
180 182 1 0.35000 1250 ; SER(C)-ALA(C)
182 183 1 0.35000 1250 ; ALA(C)-LEU(C)
183 185 1 0.35000 1250 ; LEU(C)-LEU(C)
185 187 1 0.35000 1250 ; LEU(C)-SER(S)
187 189 1 0.35000 1250 ; SER(S)-SER(S)
189 191 1 0.35000 1250 ; SER(S)-ASP(S)
191 193 1 0.35000 1250 ; ASP(S)-ILE(T)
217 219 1 0.35000 1250 ; SER(T)-ASP(T)
219 221 1 0.35000 1250 ; ASP(T)-GLY(T)
221 222 1 0.35000 1250 ; GLY(T)-ASN(T)
222 224 1 0.35000 1250 ; ASN(T)-GLY(C)
224 225 1 0.35000 1250 ; GLY(C)-MET(C)
225 227 1 0.35000 1250 ; MET(C)-ASN(C)
227 229 1 0.35000 1250 ; ASN(C)-ALA(C)
229 230 1 0.35000 1250 ; ALA(C)-TRP(S)
251 253 1 0.35000 1250 ; CYS(T)-LYS(T)
253 256 1 0.35000 1250 ; LYS(T)-GLY(T)
256 257 1 0.35000 1250 ; GLY(T)-THR(S)
257 259 1 0.35000 1250 ; THR(S)-ASP(C)
259 261 1 0.35000 1250 ; ASP(C)-VAL(C)
261 263 1 0.35000 1250 ; VAL(C)-GLN(C)
263 265 1 0.35000 1250 ; GLN(C)-ALA(C)
265 266 1 0.35000 1250 ; ALA(C)-TRP(C)
266 271 1 0.35000 1250 ; TRP(C)-ILE(C)
271 273 1 0.35000 1250 ; ILE(C)-ARG(T)
273 276 1 0.35000 1250 ; ARG(T)-GLY(T)
276 277 1 0.35000 1250 ; GLY(T)-CYS(C)
277 279 1 0.35000 1250 ; CYS(C)-ARG(C)
279 282 1 0.35000 1250 ; ARG(C)-LEU(C)
; Sidechain bonds
1 2 1 0.33000 5000 ; LYS
2 3 1 0.28000 5000 ; LYS
6 7 1 0.31000 7500 ; PHE
11 12 1 0.33000 5000 ; ARG
12 13 1 0.34000 5000 ; ARG
14 15 1 0.31000 7500 ; CYS
16 17 1 0.40000 5000 ; GLU
18 19 1 0.33000 7500 ; LEU
23 24 1 0.40000 2500 ; MET
25 26 1 0.33000 5000 ; LYS
26 27 1 0.28000 5000 ; LYS
28 29 1 0.33000 5000 ; ARG
29 30 1 0.34000 5000 ; ARG
31 32 1 0.32000 7500 ; HIS
36 37 1 0.33000 7500 ; LEU
38 39 1 0.32000 7500 ; ASP
40 41 1 0.32000 5000 ; ASN
42 43 1 0.32000 5000 ; TYR
46 47 1 0.33000 5000 ; ARG
47 48 1 0.34000 5000 ; ARG
50 51 1 0.32000 5000 ; TYR
54 55 1 0.25000 7500 ; SER
56 57 1 0.33000 7500 ; LEU
59 60 1 0.32000 5000 ; ASN
61 62 1 0.30000 5000 ; TRP
68 69 1 0.31000 7500 ; CYS
72 73 1 0.33000 5000 ; LYS
73 74 1 0.28000 5000 ; LYS
75 76 1 0.31000 7500 ; PHE
79 80 1 0.40000 5000 ; GLU
81 82 1 0.25000 7500 ; SER
83 84 1 0.32000 5000 ; ASN
85 86 1 0.31000 7500 ; PHE
89 90 1 0.32000 5000 ; ASN
93 94 1 0.40000 5000 ; GLN
98 99 1 0.32000 5000 ; ASN
100 101 1 0.33000 5000 ; ARG
101 102 1 0.34000 5000 ; ARG
103 104 1 0.32000 5000 ; ASN
107 108 1 0.32000 7500 ; ASP
110 111 1 0.25000 7500 ; SER
114 115 1 0.32000 7500 ; ASP
116 117 1 0.32000 5000 ; TYR
123 124 1 0.33000 7500 ; LEU
125 126 1 0.40000 5000 ; GLN
129 130 1 0.32000 5000 ; ASN
131 132 1 0.25000 7500 ; SER
133 134 1 0.33000 5000 ; ARG
134 135 1 0.34000 5000 ; ARG
136 137 1 0.30000 5000 ; TRP
141 142 1 0.30000 5000 ; TRP
146 147 1 0.31000 7500 ; CYS
148 149 1 0.32000 5000 ; ASN
150 151 1 0.32000 7500 ; ASP
153 154 1 0.33000 5000 ; ARG
154 155 1 0.34000 5000 ; ARG
158 159 1 0.30000 7500 ; PRO
161 162 1 0.25000 7500 ; SER
163 164 1 0.33000 5000 ; ARG
164 165 1 0.34000 5000 ; ARG
166 167 1 0.32000 5000 ; ASN
168 169 1 0.33000 7500 ; LEU
170 171 1 0.31000 7500 ; CYS
172 173 1 0.32000 5000 ; ASN
176 177 1 0.30000 7500 ; PRO
178 179 1 0.31000 7500 ; CYS
180 181 1 0.25000 7500 ; SER
183 184 1 0.33000 7500 ; LEU
185 186 1 0.33000 7500 ; LEU
187 188 1 0.25000 7500 ; SER
189 190 1 0.25000 7500 ; SER
191 192 1 0.32000 7500 ; ASP
198 199 1 0.25000 7500 ; SER
202 203 1 0.32000 5000 ; ASN
204 205 1 0.31000 7500 ; CYS
207 208 1 0.33000 5000 ; LYS
208 209 1 0.28000 5000 ; LYS
210 211 1 0.33000 5000 ; LYS
211 212 1 0.28000 5000 ; LYS
217 218 1 0.25000 7500 ; SER
219 220 1 0.32000 7500 ; ASP
222 223 1 0.32000 5000 ; ASN
225 226 1 0.40000 2500 ; MET
227 228 1 0.32000 5000 ; ASN
230 231 1 0.30000 5000 ; TRP
238 239 1 0.30000 5000 ; TRP
243 244 1 0.33000 5000 ; ARG
244 245 1 0.34000 5000 ; ARG
246 247 1 0.32000 5000 ; ASN
248 249 1 0.33000 5000 ; ARG
249 250 1 0.34000 5000 ; ARG
251 252 1 0.31000 7500 ; CYS
253 254 1 0.33000 5000 ; LYS
254 255 1 0.28000 5000 ; LYS
259 260 1 0.32000 7500 ; ASP
263 264 1 0.40000 5000 ; GLN
266 267 1 0.30000 5000 ; TRP
273 274 1 0.33000 5000 ; ARG
274 275 1 0.34000 5000 ; ARG
277 278 1 0.31000 7500 ; CYS
279 280 1 0.33000 5000 ; ARG
280 281 1 0.34000 5000 ; ARG
282 283 1 0.33000 7500 ; LEU

[ constraints ]
10 11 1 0.33000 ; GLY(C)-ARG(1)
11 14 1 0.31000 ; ARG(1)-CYS(1)
14 16 1 0.31000 ; CYS(1)-GLU(1)
16 18 1 0.31000 ; GLU(1)-LEU(1)
18 20 1 0.31000 ; LEU(1)-ALA(H)
20 21 1 0.31000 ; ALA(H)-ALA(H)
21 22 1 0.31000 ; ALA(H)-ALA(2)
22 23 1 0.31000 ; ALA(2)-MET(2)
23 25 1 0.31000 ; MET(2)-LYS(2)
25 28 1 0.31000 ; LYS(2)-ARG(2)
28 31 1 0.33000 ; ARG(2)-HIS(T)
54 56 1 0.33000 ; SER(C)-LEU(1)
56 58 1 0.31000 ; LEU(1)-GLY(1)
58 59 1 0.31000 ; GLY(1)-ASN(1)
59 61 1 0.31000 ; ASN(1)-TRP(1)
61 66 1 0.31000 ; TRP(1)-VAL(H)
66 68 1 0.31000 ; VAL(H)-CYS(H)
68 70 1 0.31000 ; CYS(H)-ALA(H)
70 71 1 0.31000 ; ALA(H)-ALA(H)
71 72 1 0.31000 ; ALA(H)-LYS(2)
72 75 1 0.31000 ; LYS(2)-PHE(2)
75 79 1 0.31000 ; PHE(2)-GLU(2)
79 81 1 0.31000 ; GLU(2)-SER(2)
81 83 1 0.33000 ; SER(2)-ASN(T)
193 195 1 0.33000 ; ILE(T)-THR(1)
195 197 1 0.31000 ; THR(1)-ALA(1)
197 198 1 0.31000 ; ALA(1)-SER(1)
198 200 1 0.31000 ; SER(1)-VAL(1)
200 202 1 0.31000 ; VAL(1)-ASN(H)
202 204 1 0.31000 ; ASN(H)-CYS(H)
204 206 1 0.31000 ; CYS(H)-ALA(H)
206 207 1 0.31000 ; ALA(H)-LYS(2)
207 210 1 0.31000 ; LYS(2)-LYS(2)
210 213 1 0.31000 ; LYS(2)-ILE(2)
213 215 1 0.31000 ; ILE(2)-VAL(2)
215 217 1 0.33000 ; VAL(2)-SER(T)
230 235 1 0.33000 ; TRP(S)-VAL(1)
235 237 1 0.31000 ; VAL(1)-ALA(1)
237 238 1 0.31000 ; ALA(1)-TRP(3)
238 243 1 0.31000 ; TRP(3)-ARG(3)
243 246 1 0.31000 ; ARG(3)-ASN(2)
246 248 1 0.31000 ; ASN(2)-ARG(2)
248 251 1 0.33000 ; ARG(2)-CYS(T)
4 5 1 0.26500 ; VAL
7 8 1 0.27000 ; PHE
7 9 1 0.27000 ; PHE
8 9 1 0.27000 ; PHE
32 33 1 0.27000 ; HIS
32 34 1 0.27000 ; HIS
33 34 1 0.27000 ; HIS
43 44 1 0.27000 ; TYR
43 45 1 0.27000 ; TYR
44 45 1 0.27000 ; TYR
51 52 1 0.27000 ; TYR
51 53 1 0.27000 ; TYR
52 53 1 0.27000 ; TYR
62 63 1 0.27000 ; TRP
62 64 1 0.27000 ; TRP
63 64 1 0.27000 ; TRP
63 65 1 0.27000 ; TRP
64 65 1 0.27000 ; TRP
66 67 1 0.26500 ; VAL
76 77 1 0.27000 ; PHE
76 78 1 0.27000 ; PHE
77 78 1 0.27000 ; PHE
86 87 1 0.27000 ; PHE
86 88 1 0.27000 ; PHE
87 88 1 0.27000 ; PHE
91 92 1 0.26000 ; THR
96 97 1 0.26000 ; THR
105 106 1 0.26000 ; THR
112 113 1 0.26000 ; THR
117 118 1 0.27000 ; TYR
117 119 1 0.27000 ; TYR
118 119 1 0.27000 ; TYR
121 122 1 0.31000 ; ILE
127 128 1 0.31000 ; ILE
137 138 1 0.27000 ; TRP
137 139 1 0.27000 ; TRP
138 139 1 0.27000 ; TRP
138 140 1 0.27000 ; TRP
139 140 1 0.27000 ; TRP
142 143 1 0.27000 ; TRP
142 144 1 0.27000 ; TRP
143 144 1 0.27000 ; TRP
143 145 1 0.27000 ; TRP
144 145 1 0.27000 ; TRP
156 157 1 0.26000 ; THR
174 175 1 0.31000 ; ILE
193 194 1 0.31000 ; ILE
195 196 1 0.26000 ; THR
200 201 1 0.26500 ; VAL
213 214 1 0.31000 ; ILE
215 216 1 0.26500 ; VAL
231 232 1 0.27000 ; TRP
231 233 1 0.27000 ; TRP
232 233 1 0.27000 ; TRP
232 234 1 0.27000 ; TRP
233 234 1 0.27000 ; TRP
235 236 1 0.26500 ; VAL
239 240 1 0.27000 ; TRP
239 241 1 0.27000 ; TRP
240 241 1 0.27000 ; TRP
240 242 1 0.27000 ; TRP
241 242 1 0.27000 ; TRP
257 258 1 0.26000 ; THR
261 262 1 0.26500 ; VAL
267 268 1 0.27000 ; TRP
267 269 1 0.27000 ; TRP
268 269 1 0.27000 ; TRP
268 270 1 0.27000 ; TRP
269 270 1 0.27000 ; TRP
271 272 1 0.31000 ; ILE
15 278 1 0.24000 ; Cys-bonds/special link
69 252 1 0.24000 ; Cys-bonds/special link
147 179 1 0.24000 ; Cys-bonds/special link
171 205 1 0.24000 ; Cys-bonds/special link

[ angles ]
; Backbone angles
1 4 6 2 127 20 ; LYS(C)-VAL(C)-PHE(C)
4 6 10 2 127 20 ; VAL(C)-PHE(C)-GLY(C)
6 10 11 2 127 20 ; PHE(C)-GLY(C)-ARG(1)
10 11 14 2 127 20 ; GLY(C)-ARG(1)-CYS(1)
11 14 16 2 96 700 ; ARG(1)-CYS(1)-GLU(1)
14 16 18 2 96 700 ; CYS(1)-GLU(1)-LEU(1)
16 18 20 2 96 700 ; GLU(1)-LEU(1)-ALA(H)
18 20 21 2 96 700 ; LEU(1)-ALA(H)-ALA(H)
20 21 22 2 96 700 ; ALA(H)-ALA(H)-ALA(2)
21 22 23 2 96 700 ; ALA(H)-ALA(2)-MET(2)
22 23 25 2 96 700 ; ALA(2)-MET(2)-LYS(2)
23 25 28 2 96 700 ; MET(2)-LYS(2)-ARG(2)
25 28 31 2 100 20 ; LYS(2)-ARG(2)-HIS(T)
28 31 35 2 100 20 ; ARG(2)-HIS(T)-GLY(T)
31 35 36 2 100 20 ; HIS(T)-GLY(T)-LEU(C)
35 36 38 2 100 20 ; GLY(T)-LEU(C)-ASP(T)
36 38 40 2 100 20 ; LEU(C)-ASP(T)-ASN(T)
38 40 42 2 100 20 ; ASP(T)-ASN(T)-TYR(C)
40 42 46 2 100 20 ; ASN(T)-TYR(C)-ARG(T)
42 46 49 2 100 20 ; TYR(C)-ARG(T)-GLY(T)
46 49 50 2 100 20 ; ARG(T)-GLY(T)-TYR(C)
49 50 54 2 100 20 ; GLY(T)-TYR(C)-SER(C)
50 54 56 2 127 20 ; TYR(C)-SER(C)-LEU(1)
54 56 58 2 127 20 ; SER(C)-LEU(1)-GLY(1)
56 58 59 2 96 700 ; LEU(1)-GLY(1)-ASN(1)
58 59 61 2 96 700 ; GLY(1)-ASN(1)-TRP(1)
59 61 66 2 96 700 ; ASN(1)-TRP(1)-VAL(H)
61 66 68 2 96 700 ; TRP(1)-VAL(H)-CYS(H)
66 68 70 2 96 700 ; VAL(H)-CYS(H)-ALA(H)
68 70 71 2 96 700 ; CYS(H)-ALA(H)-ALA(H)
70 71 72 2 96 700 ; ALA(H)-ALA(H)-LYS(2)
71 72 75 2 96 700 ; ALA(H)-LYS(2)-PHE(2)
72 75 79 2 96 700 ; LYS(2)-PHE(2)-GLU(2)
75 79 81 2 96 700 ; PHE(2)-GLU(2)-SER(2)
79 81 83 2 100 20 ; GLU(2)-SER(2)-ASN(T)
81 83 85 2 100 20 ; SER(2)-ASN(T)-PHE(T)
83 85 89 2 100 20 ; ASN(T)-PHE(T)-ASN(C)
85 89 91 2 100 20 ; PHE(T)-ASN(C)-THR(T)
89 91 93 2 100 20 ; ASN(C)-THR(T)-GLN(T)
91 93 95 2 100 20 ; THR(T)-GLN(T)-ALA(C)
93 95 96 2 100 20 ; GLN(T)-ALA(C)-THR(E)
95 96 98 2 127 20 ; ALA(C)-THR(E)-ASN(E)
96 98 100 2 134 25 ; THR(E)-ASN(E)-ARG(E)
98 100 103 2 127 20 ; ASN(E)-ARG(E)-ASN(C)
100 103 105 2 100 20 ; ARG(E)-ASN(C)-THR(T)
103 105 107 2 100 20 ; ASN(C)-THR(T)-ASP(T)
105 107 109 2 100 20 ; THR(T)-ASP(T)-GLY(S)
107 109 110 2 100 20 ; ASP(T)-GLY(S)-SER(C)
109 110 112 2 127 20 ; GLY(S)-SER(C)-THR(E)
110 112 114 2 127 20 ; SER(C)-THR(E)-ASP(E)
112 114 116 2 134 25 ; THR(E)-ASP(E)-TYR(E)
114 116 120 2 100 20 ; ASP(E)-TYR(E)-GLY(T)
116 120 121 2 100 20 ; TYR(E)-GLY(T)-ILE(T)
120 121 123 2 100 20 ; GLY(T)-ILE(T)-LEU(T)
121 123 125 2 100 20 ; ILE(T)-LEU(T)-GLN(T)
123 125 127 2 100 20 ; LEU(T)-GLN(T)-ILE(E)
125 127 129 2 100 20 ; GLN(T)-ILE(E)-ASN(E)
127 129 131 2 100 20 ; ILE(E)-ASN(E)-SER(T)
129 131 133 2 100 20 ; ASN(E)-SER(T)-ARG(T)
131 133 136 2 100 20 ; SER(T)-ARG(T)-TRP(T)
133 136 141 2 100 20 ; ARG(T)-TRP(T)-TRP(S)
136 141 146 2 100 20 ; TRP(T)-TRP(S)-CYS(C)
141 146 148 2 127 20 ; TRP(S)-CYS(C)-ASN(C)
146 148 150 2 127 20 ; CYS(C)-ASN(C)-ASP(C)
148 150 152 2 127 20 ; ASN(C)-ASP(C)-GLY(S)
150 152 153 2 127 20 ; ASP(C)-GLY(S)-ARG(C)
152 153 156 2 127 20 ; GLY(S)-ARG(C)-THR(S)
153 156 158 2 127 20 ; ARG(C)-THR(S)-PRO(T)
156 158 160 2 100 20 ; THR(S)-PRO(T)-GLY(T)
158 160 161 2 100 20 ; PRO(T)-GLY(T)-SER(C)
160 161 163 2 100 20 ; GLY(T)-SER(C)-ARG(C)
161 163 166 2 127 20 ; SER(C)-ARG(C)-ASN(C)
163 166 168 2 100 20 ; ARG(C)-ASN(C)-LEU(T)
166 168 170 2 100 20 ; ASN(C)-LEU(T)-CYS(T)
168 170 172 2 100 20 ; LEU(T)-CYS(T)-ASN(C)
170 172 174 2 100 20 ; CYS(T)-ASN(C)-ILE(S)
172 174 176 2 127 20 ; ASN(C)-ILE(S)-PRO(C)
174 176 178 2 127 20 ; ILE(S)-PRO(C)-CYS(C)
176 178 180 2 127 20 ; PRO(C)-CYS(C)-SER(C)
178 180 182 2 127 20 ; CYS(C)-SER(C)-ALA(C)
180 182 183 2 127 20 ; SER(C)-ALA(C)-LEU(C)
182 183 185 2 127 20 ; ALA(C)-LEU(C)-LEU(C)
183 185 187 2 127 20 ; LEU(C)-LEU(C)-SER(S)
185 187 189 2 127 20 ; LEU(C)-SER(S)-SER(S)
187 189 191 2 130 20 ; SER(S)-SER(S)-ASP(S)
189 191 193 2 100 20 ; SER(S)-ASP(S)-ILE(T)
191 193 195 2 100 20 ; ASP(S)-ILE(T)-THR(1)
193 195 197 2 100 20 ; ILE(T)-THR(1)-ALA(1)
195 197 198 2 96 700 ; THR(1)-ALA(1)-SER(1)
197 198 200 2 96 700 ; ALA(1)-SER(1)-VAL(1)
198 200 202 2 96 700 ; SER(1)-VAL(1)-ASN(H)
200 202 204 2 96 700 ; VAL(1)-ASN(H)-CYS(H)
202 204 206 2 96 700 ; ASN(H)-CYS(H)-ALA(H)
204 206 207 2 96 700 ; CYS(H)-ALA(H)-LYS(2)
206 207 210 2 96 700 ; ALA(H)-LYS(2)-LYS(2)
207 210 213 2 96 700 ; LYS(2)-LYS(2)-ILE(2)
210 213 215 2 96 700 ; LYS(2)-ILE(2)-VAL(2)
213 215 217 2 100 20 ; ILE(2)-VAL(2)-SER(T)
215 217 219 2 100 20 ; VAL(2)-SER(T)-ASP(T)
217 219 221 2 100 20 ; SER(T)-ASP(T)-GLY(T)
219 221 222 2 100 20 ; ASP(T)-GLY(T)-ASN(T)
221 222 224 2 100 20 ; GLY(T)-ASN(T)-GLY(C)
222 224 225 2 100 20 ; ASN(T)-GLY(C)-MET(C)
224 225 227 2 127 20 ; GLY(C)-MET(C)-ASN(C)
225 227 229 2 127 20 ; MET(C)-ASN(C)-ALA(C)
227 229 230 2 127 20 ; ASN(C)-ALA(C)-TRP(S)
229 230 235 2 127 20 ; ALA(C)-TRP(S)-VAL(1)
230 235 237 2 130 20 ; TRP(S)-VAL(1)-ALA(1)
235 237 238 2 96 700 ; VAL(1)-ALA(1)-TRP(3)
237 238 243 2 96 700 ; ALA(1)-TRP(3)-ARG(3)
238 243 246 2 96 700 ; TRP(3)-ARG(3)-ASN(2)
243 246 248 2 96 700 ; ARG(3)-ASN(2)-ARG(2)
246 248 251 2 100 20 ; ASN(2)-ARG(2)-CYS(T)
248 251 253 2 100 20 ; ARG(2)-CYS(T)-LYS(T)
251 253 256 2 100 20 ; CYS(T)-LYS(T)-GLY(T)
253 256 257 2 100 20 ; LYS(T)-GLY(T)-THR(S)
256 257 259 2 100 20 ; GLY(T)-THR(S)-ASP(C)
257 259 261 2 127 20 ; THR(S)-ASP(C)-VAL(C)
259 261 263 2 127 20 ; ASP(C)-VAL(C)-GLN(C)
261 263 265 2 127 20 ; VAL(C)-GLN(C)-ALA(C)
263 265 266 2 127 20 ; GLN(C)-ALA(C)-TRP(C)
265 266 271 2 127 20 ; ALA(C)-TRP(C)-ILE(C)
266 271 273 2 100 20 ; TRP(C)-ILE(C)-ARG(T)
271 273 276 2 100 20 ; ILE(C)-ARG(T)-GLY(T)
273 276 277 2 100 20 ; ARG(T)-GLY(T)-CYS(C)
276 277 279 2 100 20 ; GLY(T)-CYS(C)-ARG(C)
277 279 282 2 127 20 ; CYS(C)-ARG(C)-LEU(C)
; Backbone-sidechain angles
2 1 4 2 100 25 ; LYS(C)-VAL(C) SBB
1 4 5 2 100 25 ; LYS(C)-VAL(C) SBB
4 6 7 2 100 25 ; VAL(C)-PHE(C) SBB
10 11 12 2 100 25 ; GLY(C)-ARG(1) SBB
11 14 15 2 100 25 ; ARG(1)-CYS(1) SBB
14 16 17 2 100 25 ; CYS(1)-GLU(1) SBB
16 18 19 2 100 25 ; GLU(1)-LEU(1) SBB
22 23 24 2 100 25 ; ALA(2)-MET(2) SBB
23 25 26 2 100 25 ; MET(2)-LYS(2) SBB
25 28 29 2 100 25 ; LYS(2)-ARG(2) SBB
28 31 32 2 100 25 ; ARG(2)-HIS(T) SBB
35 36 37 2 100 25 ; GLY(T)-LEU(C) SBB
36 38 39 2 100 25 ; LEU(C)-ASP(T) SBB
38 40 41 2 100 25 ; ASP(T)-ASN(T) SBB
40 42 43 2 100 25 ; ASN(T)-TYR(C) SBB
42 46 47 2 100 25 ; TYR(C)-ARG(T) SBB
49 50 51 2 100 25 ; GLY(T)-TYR(C) SBB
50 54 55 2 100 25 ; TYR(C)-SER(C) SBB
54 56 57 2 100 25 ; SER(C)-LEU(1) SBB
58 59 60 2 100 25 ; GLY(1)-ASN(1) SBB
59 61 62 2 100 25 ; ASN(1)-TRP(1) SBB
61 66 67 2 100 25 ; TRP(1)-VAL(H) SBB
66 68 69 2 100 25 ; VAL(H)-CYS(H) SBB
71 72 73 2 100 25 ; ALA(H)-LYS(2) SBB
72 75 76 2 100 25 ; LYS(2)-PHE(2) SBB
75 79 80 2 100 25 ; PHE(2)-GLU(2) SBB
79 81 82 2 100 25 ; GLU(2)-SER(2) SBB
81 83 84 2 100 25 ; SER(2)-ASN(T) SBB
83 85 86 2 100 25 ; ASN(T)-PHE(T) SBB
85 89 90 2 100 25 ; PHE(T)-ASN(C) SBB
89 91 92 2 100 25 ; ASN(C)-THR(T) SBB
91 93 94 2 100 25 ; THR(T)-GLN(T) SBB
95 96 97 2 100 25 ; ALA(C)-THR(E) SBB
96 98 99 2 100 25 ; THR(E)-ASN(E) SBB
98 100 101 2 100 25 ; ASN(E)-ARG(E) SBB
100 103 104 2 100 25 ; ARG(E)-ASN(C) SBB
103 105 106 2 100 25 ; ASN(C)-THR(T) SBB
105 107 108 2 100 25 ; THR(T)-ASP(T) SBB
109 110 111 2 100 25 ; GLY(S)-SER(C) SBB
110 112 113 2 100 25 ; SER(C)-THR(E) SBB
112 114 115 2 100 25 ; THR(E)-ASP(E) SBB
114 116 117 2 100 25 ; ASP(E)-TYR(E) SBB
120 121 122 2 100 25 ; GLY(T)-ILE(T) SBB
121 123 124 2 100 25 ; ILE(T)-LEU(T) SBB
123 125 126 2 100 25 ; LEU(T)-GLN(T) SBB
125 127 128 2 100 25 ; GLN(T)-ILE(E) SBB
127 129 130 2 100 25 ; ILE(E)-ASN(E) SBB
129 131 132 2 100 25 ; ASN(E)-SER(T) SBB
131 133 134 2 100 25 ; SER(T)-ARG(T) SBB
133 136 137 2 100 25 ; ARG(T)-TRP(T) SBB
136 141 142 2 100 25 ; TRP(T)-TRP(S) SBB
141 146 147 2 100 25 ; TRP(S)-CYS(C) SBB
146 148 149 2 100 25 ; CYS(C)-ASN(C) SBB
148 150 151 2 100 25 ; ASN(C)-ASP(C) SBB
152 153 154 2 100 25 ; GLY(S)-ARG(C) SBB
153 156 157 2 100 25 ; ARG(C)-THR(S) SBB
156 158 159 2 100 25 ; THR(S)-PRO(T) SBB
160 161 162 2 100 25 ; GLY(T)-SER(C) SBB
161 163 164 2 100 25 ; SER(C)-ARG(C) SBB
163 166 167 2 100 25 ; ARG(C)-ASN(C) SBB
166 168 169 2 100 25 ; ASN(C)-LEU(T) SBB
168 170 171 2 100 25 ; LEU(T)-CYS(T) SBB
170 172 173 2 100 25 ; CYS(T)-ASN(C) SBB
172 174 175 2 100 25 ; ASN(C)-ILE(S) SBB
174 176 177 2 100 25 ; ILE(S)-PRO(C) SBB
176 178 179 2 100 25 ; PRO(C)-CYS(C) SBB
178 180 181 2 100 25 ; CYS(C)-SER(C) SBB
182 183 184 2 100 25 ; ALA(C)-LEU(C) SBB
183 185 186 2 100 25 ; LEU(C)-LEU(C) SBB
185 187 188 2 100 25 ; LEU(C)-SER(S) SBB
187 189 190 2 100 25 ; SER(S)-SER(S) SBB
189 191 192 2 100 25 ; SER(S)-ASP(S) SBB
191 193 194 2 100 25 ; ASP(S)-ILE(T) SBB
193 195 196 2 100 25 ; ILE(T)-THR(1) SBB
197 198 199 2 100 25 ; ALA(1)-SER(1) SBB
198 200 201 2 100 25 ; SER(1)-VAL(1) SBB
200 202 203 2 100 25 ; VAL(1)-ASN(H) SBB
202 204 205 2 100 25 ; ASN(H)-CYS(H) SBB
206 207 208 2 100 25 ; ALA(H)-LYS(2) SBB
207 210 211 2 100 25 ; LYS(2)-LYS(2) SBB
210 213 214 2 100 25 ; LYS(2)-ILE(2) SBB
213 215 216 2 100 25 ; ILE(2)-VAL(2) SBB
215 217 218 2 100 25 ; VAL(2)-SER(T) SBB
217 219 220 2 100 25 ; SER(T)-ASP(T) SBB
221 222 223 2 100 25 ; GLY(T)-ASN(T) SBB
224 225 226 2 100 25 ; GLY(C)-MET(C) SBB
225 227 228 2 100 25 ; MET(C)-ASN(C) SBB
229 230 231 2 100 25 ; ALA(C)-TRP(S) SBB
230 235 236 2 100 25 ; TRP(S)-VAL(1) SBB
237 238 239 2 100 25 ; ALA(1)-TRP(3) SBB
238 243 244 2 100 25 ; TRP(3)-ARG(3) SBB
243 246 247 2 100 25 ; ARG(3)-ASN(2) SBB
246 248 249 2 100 25 ; ASN(2)-ARG(2) SBB
248 251 252 2 100 25 ; ARG(2)-CYS(T) SBB
251 253 254 2 100 25 ; CYS(T)-LYS(T) SBB
256 257 258 2 100 25 ; GLY(T)-THR(S) SBB
257 259 260 2 100 25 ; THR(S)-ASP(C) SBB
259 261 262 2 100 25 ; ASP(C)-VAL(C) SBB
261 263 264 2 100 25 ; VAL(C)-GLN(C) SBB
265 266 267 2 100 25 ; ALA(C)-TRP(C) SBB
266 271 272 2 100 25 ; TRP(C)-ILE(C) SBB
271 273 274 2 100 25 ; ILE(C)-ARG(T) SBB
276 277 278 2 100 25 ; GLY(T)-CYS(C) SBB
277 279 280 2 100 25 ; CYS(C)-ARG(C) SBB
279 282 283 2 100 25 ; ARG(C)-LEU(C) SBB
; Sidechain angles
1 2 3 2 180 25 ; LYS
6 7 8 2 150 50 ; PHE
6 7 9 2 150 50 ; PHE
11 12 13 2 180 25 ; ARG
25 26 27 2 180 25 ; LYS
28 29 30 2 180 25 ; ARG
31 32 33 2 150 50 ; HIS
31 32 34 2 150 50 ; HIS
42 43 44 2 150 50 ; TYR
42 43 45 2 150 50 ; TYR
46 47 48 2 180 25 ; ARG
50 51 52 2 150 50 ; TYR
50 51 53 2 150 50 ; TYR
61 62 63 2 210 50 ; TRP
61 62 64 2 90 50 ; TRP
72 73 74 2 180 25 ; LYS
75 76 77 2 150 50 ; PHE
75 76 78 2 150 50 ; PHE
85 86 87 2 150 50 ; PHE
85 86 88 2 150 50 ; PHE
100 101 102 2 180 25 ; ARG
116 117 118 2 150 50 ; TYR
116 117 119 2 150 50 ; TYR
133 134 135 2 180 25 ; ARG
136 137 138 2 210 50 ; TRP
136 137 139 2 90 50 ; TRP
141 142 143 2 210 50 ; TRP
141 142 144 2 90 50 ; TRP
153 154 155 2 180 25 ; ARG
163 164 165 2 180 25 ; ARG
207 208 209 2 180 25 ; LYS
210 211 212 2 180 25 ; LYS
230 231 232 2 210 50 ; TRP
230 231 233 2 90 50 ; TRP
238 239 240 2 210 50 ; TRP
238 239 241 2 90 50 ; TRP
243 244 245 2 180 25 ; ARG
248 249 250 2 180 25 ; ARG
253 254 255 2 180 25 ; LYS
266 267 268 2 210 50 ; TRP
266 267 269 2 90 50 ; TRP
273 274 275 2 180 25 ; ARG
279 280 281 2 180 25 ; ARG

[ dihedrals ]
; Backbone dihedrals
11 14 16 18 1 -120 400 1 ; ARG(1)-CYS(1)-GLU(1)-LEU(1)
14 16 18 20 1 -120 400 1 ; CYS(1)-GLU(1)-LEU(1)-ALA(H)
16 18 20 21 1 -120 400 1 ; GLU(1)-LEU(1)-ALA(H)-ALA(H)
18 20 21 22 1 -120 400 1 ; LEU(1)-ALA(H)-ALA(H)-ALA(2)
20 21 22 23 1 -120 400 1 ; ALA(H)-ALA(H)-ALA(2)-MET(2)
21 22 23 25 1 -120 400 1 ; ALA(H)-ALA(2)-MET(2)-LYS(2)
22 23 25 28 1 -120 400 1 ; ALA(2)-MET(2)-LYS(2)-ARG(2)
56 58 59 61 1 -120 400 1 ; LEU(1)-GLY(1)-ASN(1)-TRP(1)
58 59 61 66 1 -120 400 1 ; GLY(1)-ASN(1)-TRP(1)-VAL(H)
59 61 66 68 1 -120 400 1 ; ASN(1)-TRP(1)-VAL(H)-CYS(H)
61 66 68 70 1 -120 400 1 ; TRP(1)-VAL(H)-CYS(H)-ALA(H)
66 68 70 71 1 -120 400 1 ; VAL(H)-CYS(H)-ALA(H)-ALA(H)
68 70 71 72 1 -120 400 1 ; CYS(H)-ALA(H)-ALA(H)-LYS(2)
70 71 72 75 1 -120 400 1 ; ALA(H)-ALA(H)-LYS(2)-PHE(2)
71 72 75 79 1 -120 400 1 ; ALA(H)-LYS(2)-PHE(2)-GLU(2)
72 75 79 81 1 -120 400 1 ; LYS(2)-PHE(2)-GLU(2)-SER(2)
195 197 198 200 1 -120 400 1 ; THR(1)-ALA(1)-SER(1)-VAL(1)
197 198 200 202 1 -120 400 1 ; ALA(1)-SER(1)-VAL(1)-ASN(H)
198 200 202 204 1 -120 400 1 ; SER(1)-VAL(1)-ASN(H)-CYS(H)
200 202 204 206 1 -120 400 1 ; VAL(1)-ASN(H)-CYS(H)-ALA(H)
202 204 206 207 1 -120 400 1 ; ASN(H)-CYS(H)-ALA(H)-LYS(2)
204 206 207 210 1 -120 400 1 ; CYS(H)-ALA(H)-LYS(2)-LYS(2)
206 207 210 213 1 -120 400 1 ; ALA(H)-LYS(2)-LYS(2)-ILE(2)
207 210 213 215 1 -120 400 1 ; LYS(2)-LYS(2)-ILE(2)-VAL(2)
235 237 238 243 1 -120 400 1 ; VAL(1)-ALA(1)-TRP(3)-ARG(3)
237 238 243 246 1 -120 400 1 ; ALA(1)-TRP(3)-ARG(3)-ASN(2)
238 243 246 248 1 -120 400 1 ; TRP(3)-ARG(3)-ASN(2)-ARG(2)
; Sidechain improper dihedrals
6 8 9 7 2 0 50 ; PHE
31 33 34 32 2 0 50 ; HIS
42 44 45 43 2 0 50 ; TYR
50 52 53 51 2 0 50 ; TYR
61 63 64 62 2 0 50 ; TRP
62 63 65 64 2 0 200 ; TRP
75 77 78 76 2 0 50 ; PHE
85 87 88 86 2 0 50 ; PHE
116 118 119 117 2 0 50 ; TYR
136 138 139 137 2 0 50 ; TRP
137 138 140 139 2 0 200 ; TRP
141 143 144 142 2 0 50 ; TRP
142 143 145 144 2 0 200 ; TRP
230 232 233 231 2 0 50 ; TRP
231 232 234 233 2 0 200 ; TRP
238 240 241 239 2 0 50 ; TRP
239 240 242 241 2 0 200 ; TRP
266 268 269 267 2 0 50 ; TRP
267 268 270 269 2 0 200 ; TRP

#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
4 1 POSRES_FC POSRES_FC POSRES_FC
6 1 POSRES_FC POSRES_FC POSRES_FC
10 1 POSRES_FC POSRES_FC POSRES_FC
11 1 POSRES_FC POSRES_FC POSRES_FC
14 1 POSRES_FC POSRES_FC POSRES_FC
16 1 POSRES_FC POSRES_FC POSRES_FC
18 1 POSRES_FC POSRES_FC POSRES_FC
20 1 POSRES_FC POSRES_FC POSRES_FC
21 1 POSRES_FC POSRES_FC POSRES_FC
22 1 POSRES_FC POSRES_FC POSRES_FC
23 1 POSRES_FC POSRES_FC POSRES_FC
25 1 POSRES_FC POSRES_FC POSRES_FC
28 1 POSRES_FC POSRES_FC POSRES_FC
31 1 POSRES_FC POSRES_FC POSRES_FC
35 1 POSRES_FC POSRES_FC POSRES_FC
36 1 POSRES_FC POSRES_FC POSRES_FC
38 1 POSRES_FC POSRES_FC POSRES_FC
40 1 POSRES_FC POSRES_FC POSRES_FC
42 1 POSRES_FC POSRES_FC POSRES_FC
46 1 POSRES_FC POSRES_FC POSRES_FC
49 1 POSRES_FC POSRES_FC POSRES_FC
50 1 POSRES_FC POSRES_FC POSRES_FC
54 1 POSRES_FC POSRES_FC POSRES_FC
56 1 POSRES_FC POSRES_FC POSRES_FC
58 1 POSRES_FC POSRES_FC POSRES_FC
59 1 POSRES_FC POSRES_FC POSRES_FC
61 1 POSRES_FC POSRES_FC POSRES_FC
66 1 POSRES_FC POSRES_FC POSRES_FC
68 1 POSRES_FC POSRES_FC POSRES_FC
70 1 POSRES_FC POSRES_FC POSRES_FC
71 1 POSRES_FC POSRES_FC POSRES_FC
72 1 POSRES_FC POSRES_FC POSRES_FC
75 1 POSRES_FC POSRES_FC POSRES_FC
79 1 POSRES_FC POSRES_FC POSRES_FC
81 1 POSRES_FC POSRES_FC POSRES_FC
83 1 POSRES_FC POSRES_FC POSRES_FC
85 1 POSRES_FC POSRES_FC POSRES_FC
89 1 POSRES_FC POSRES_FC POSRES_FC
91 1 POSRES_FC POSRES_FC POSRES_FC
93 1 POSRES_FC POSRES_FC POSRES_FC
95 1 POSRES_FC POSRES_FC POSRES_FC
96 1 POSRES_FC POSRES_FC POSRES_FC
98 1 POSRES_FC POSRES_FC POSRES_FC
100 1 POSRES_FC POSRES_FC POSRES_FC
103 1 POSRES_FC POSRES_FC POSRES_FC
105 1 POSRES_FC POSRES_FC POSRES_FC
107 1 POSRES_FC POSRES_FC POSRES_FC
109 1 POSRES_FC POSRES_FC POSRES_FC
110 1 POSRES_FC POSRES_FC POSRES_FC
112 1 POSRES_FC POSRES_FC POSRES_FC
114 1 POSRES_FC POSRES_FC POSRES_FC
116 1 POSRES_FC POSRES_FC POSRES_FC
120 1 POSRES_FC POSRES_FC POSRES_FC
121 1 POSRES_FC POSRES_FC POSRES_FC
123 1 POSRES_FC POSRES_FC POSRES_FC
125 1 POSRES_FC POSRES_FC POSRES_FC
127 1 POSRES_FC POSRES_FC POSRES_FC
129 1 POSRES_FC POSRES_FC POSRES_FC
131 1 POSRES_FC POSRES_FC POSRES_FC
133 1 POSRES_FC POSRES_FC POSRES_FC
136 1 POSRES_FC POSRES_FC POSRES_FC
141 1 POSRES_FC POSRES_FC POSRES_FC
146 1 POSRES_FC POSRES_FC POSRES_FC
148 1 POSRES_FC POSRES_FC POSRES_FC
150 1 POSRES_FC POSRES_FC POSRES_FC
152 1 POSRES_FC POSRES_FC POSRES_FC
153 1 POSRES_FC POSRES_FC POSRES_FC
156 1 POSRES_FC POSRES_FC POSRES_FC
158 1 POSRES_FC POSRES_FC POSRES_FC
160 1 POSRES_FC POSRES_FC POSRES_FC
161 1 POSRES_FC POSRES_FC POSRES_FC
163 1 POSRES_FC POSRES_FC POSRES_FC
166 1 POSRES_FC POSRES_FC POSRES_FC
168 1 POSRES_FC POSRES_FC POSRES_FC
170 1 POSRES_FC POSRES_FC POSRES_FC
172 1 POSRES_FC POSRES_FC POSRES_FC
174 1 POSRES_FC POSRES_FC POSRES_FC
176 1 POSRES_FC POSRES_FC POSRES_FC
178 1 POSRES_FC POSRES_FC POSRES_FC
180 1 POSRES_FC POSRES_FC POSRES_FC
182 1 POSRES_FC POSRES_FC POSRES_FC
183 1 POSRES_FC POSRES_FC POSRES_FC
185 1 POSRES_FC POSRES_FC POSRES_FC
187 1 POSRES_FC POSRES_FC POSRES_FC
189 1 POSRES_FC POSRES_FC POSRES_FC
191 1 POSRES_FC POSRES_FC POSRES_FC
193 1 POSRES_FC POSRES_FC POSRES_FC
195 1 POSRES_FC POSRES_FC POSRES_FC
197 1 POSRES_FC POSRES_FC POSRES_FC
198 1 POSRES_FC POSRES_FC POSRES_FC
200 1 POSRES_FC POSRES_FC POSRES_FC
202 1 POSRES_FC POSRES_FC POSRES_FC
204 1 POSRES_FC POSRES_FC POSRES_FC
206 1 POSRES_FC POSRES_FC POSRES_FC
207 1 POSRES_FC POSRES_FC POSRES_FC
210 1 POSRES_FC POSRES_FC POSRES_FC
213 1 POSRES_FC POSRES_FC POSRES_FC
215 1 POSRES_FC POSRES_FC POSRES_FC
217 1 POSRES_FC POSRES_FC POSRES_FC
219 1 POSRES_FC POSRES_FC POSRES_FC
221 1 POSRES_FC POSRES_FC POSRES_FC
222 1 POSRES_FC POSRES_FC POSRES_FC
224 1 POSRES_FC POSRES_FC POSRES_FC
225 1 POSRES_FC POSRES_FC POSRES_FC
227 1 POSRES_FC POSRES_FC POSRES_FC
229 1 POSRES_FC POSRES_FC POSRES_FC
230 1 POSRES_FC POSRES_FC POSRES_FC
235 1 POSRES_FC POSRES_FC POSRES_FC
237 1 POSRES_FC POSRES_FC POSRES_FC
238 1 POSRES_FC POSRES_FC POSRES_FC
243 1 POSRES_FC POSRES_FC POSRES_FC
246 1 POSRES_FC POSRES_FC POSRES_FC
248 1 POSRES_FC POSRES_FC POSRES_FC
251 1 POSRES_FC POSRES_FC POSRES_FC
253 1 POSRES_FC POSRES_FC POSRES_FC
256 1 POSRES_FC POSRES_FC POSRES_FC
257 1 POSRES_FC POSRES_FC POSRES_FC
259 1 POSRES_FC POSRES_FC POSRES_FC
261 1 POSRES_FC POSRES_FC POSRES_FC
263 1 POSRES_FC POSRES_FC POSRES_FC
265 1 POSRES_FC POSRES_FC POSRES_FC
266 1 POSRES_FC POSRES_FC POSRES_FC
271 1 POSRES_FC POSRES_FC POSRES_FC
273 1 POSRES_FC POSRES_FC POSRES_FC
276 1 POSRES_FC POSRES_FC POSRES_FC
277 1 POSRES_FC POSRES_FC POSRES_FC
279 1 POSRES_FC POSRES_FC POSRES_FC
282 1 POSRES_FC POSRES_FC POSRES_FC
#endif

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8 months 6 days ago #8362 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Ok, a couple of things.
1) You have the old 5-bead lipid tails for POPC, as detemerined earlier
2) I assume the POPG is the same 5-bead thing
3) The script for order often needs a bit of manual adjusting.

Open up the script, and grep "phosphatidylcholine_bond_names". This is the section where the lipids being analyzed are defined. Notice two things.
1) It's for the 4-bead tails
2) There are no POPG definitions

In the area with the HEADGROUP_bond_names, insert this line below it:
phosphatidylglycerol_bond_names = " GL0-PO4 PO4-GL1 GL1-GL2 "

Below that there are a bunch of "if/elif lipid_type =="

Change the one for POPC from 4 to 5 bead tails (for your own sake, check the itp files to make sure these are correct):
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-D2B D2B-C3B C3B-C4B\n"
to:
elif lipid_type == "POPC": bond_names = phosphatidylcholine_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-C2B C2B-D3B D3B-C4B C4B-C5B\n"

Below the last elif for POPE, insert a new definition for POPG:
elif lipid_type == "POPG": bond_names = phosphatidylglycerol_bond_names + "GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-C2B C2B-D3B D3B-C4B C4B-C5B\n"

This should theoretically work.

John

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8 months 3 days ago #8368 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi,
thank you so much for your continuous help and reply.
previously i have changed the bead name , which you have told. but still it is not working.
when both popc and popg are mentioned in the script then the following error is coming
"./do-order-gmx5.py traj.xtc topol.tpr 0 15000n20 0 0 1 3276 POPC 2808 POPG"
or "./do-order-gmx5.py traj.xtc topol.tpr 0 15000n20 0 0 1 3276 POPC"
error is
IndentationError: unident does not match any outer indentation level


even when popg bead name is off and using this command
/do-order-gmx5.py traj.xtc topol.tpr 0 15000n20 0 0 1 3276 POPC"
getting the same error
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in ?
vector[j] = first[j] - second[j]
IndexError: list index out of range

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8 months 3 days ago #8370 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Did you make sure that the new lines have the same indentation as the other lines there? i.e., there are two spaces before the start of the original lines, and do the new ones have that?

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7 months 4 weeks ago #8374 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi,
thanks for your reply.
./do-order-gmx5.py traj.xtc topol.tpr 0 15000n20 0 0 1 2808 POPG"
or "./do-order-gmx5.py traj.xtc topol.tpr 0 15000n20 0 0 1 3276 POPC"

getting the same error
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in ?
vector[j] = first[j] - second[j]
IndexError: list index out of range
i am not getting why this error still is coming , even i haved changed the bead name.

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7 months 4 weeks ago #8375 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Hi,

This means that there is a mismatch between what is in your file, and and what you are requesting it to analyze.

Your above topol has 108 POPG and 252 POPC
The documentation in the script says:
Usage: %s <traj file> <tpr file> <initial time> <final time> <skip frames> <bilayer normal - xyz> <#lipids> <lipid type>

I believe that instead of #lipids, you are giving the lipid index, and now your script is expecting 3276 POPC molecules. Also, I don't know if that's a typo, but there shouldn't be an "n" in your command (15000n20)
Try this and see if it works
./do-order-gmx5.py traj.xtc topol.tpr 0 15000 20 0 0 1 252 POPC

Also try this. I was looking through my files and found something that might be useful. Try to extract and make an xtc file with just the lipids you want to analyze. So if you want the order parameters for your top leaflet, and POPC, then you should make an xtc file with just that, and then make a modified top, and grompp to make a tpr for just that as well to feed into the script (just use a minimization mdp file). That's what I have lying around, and that worked for me when I did it. The script isn't terribly intelligent, so if you just say "252 POPC" it has no was of knowing which of your 504 POPC total to analyze.

Hopefully that helps.

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7 months 4 weeks ago - 7 months 4 weeks ago #8376 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi,
yessss...now it is working. Actually i was giving the index number of lipid.

you have mentioned
"So if you want the order parameters for your top leaflet, and POPC"
i want to calculate the order parameter of upper leaflet of popc and popg.
also the lipid which are within 10 angstrom of protein. so to do this should i make individual files, which contain only that group.
thank you so much for your continuous reply and help.
Last edit: 7 months 4 weeks ago by cm.

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7 months 4 weeks ago #8377 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Glad it finally worked out. Sorry for not mentioning some of this sooner. I really only used the script once, for a supplemental piece of information so I totally forgot some of the nuances.

I'm not sure if you will realistically be able to do within 10 ang of the protein. Bilayers are so dynamic that what is there one frame may be quite a bit different a few frames later. Either way, best of luck

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7 months 4 weeks ago - 7 months 4 weeks ago #8379 by cm
Replied by cm on topic do_order issue with POPC (solution)
hi,
i am able to do the order parameter calculation of upper leaf let of both popc and popg. but when i am selecting the residues which are within 10 angstrom of protein, same list error
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in ?
vector[j] = first[j] - second[j]
IndexError: list index out of range
is coming.
i think it may be due to the not presence of continuous residue number.
thanking you
Last edit: 7 months 4 weeks ago by cm.

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7 months 4 weeks ago #8380 by johnd
Replied by johnd on topic do_order issue with POPC (solution)
Yes, I already commented on this above.

I don't think you will be able to calculate this particular value because both the number of residues within 10 ang, and the residue indices, will be dynamic with this type of measurement. I cannot help any further with the measurement.

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