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April 23, 2018 at 10:25 pm #2902
Anonymous
I have been working with various NCAAs for a couple of years now in Rosetta and noticed an issue with a residue a recently generated, which I have not previously experienced for structurally similar residues. I have attached the modified .mol file which I used as the input for the molfile_to_params_polymer.py script, as well as the output .params and .kin files. Curiously, the resultant params file is not fuctional as the internal coordinates for the CB atom references itself for the dihedral angle which is only allowed for the C atom. I have solved the problem manually by computing the dihedral for the CB-CA-N-C atom set and manually adjusting the params file, but I was wondering if there was some issue with my molfile input or some aspect of the script or script use.
Since I was unable to upload the multiple files, the contents are pasted below
Thank you,
Input.mol
Acd_Params_Gauss_In.log
OpenBabel10171709303D
Gaussian 09 # opt=(tight,modredundant) hf/6-31g(d) geom=connectivity
44 46 0 0 1 0 0 0 0 0999 V2000
4.4948 -0.4482 0.0284 N 0 0 0 0 0 0 0 0 0 0 0 0
5.1250 0.2766 0.2891 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1119 -0.0682 -0.1425 C 0 0 1 0 0 0 0 0 0 0 0 0
2.6828 -0.7027 -0.9053 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3157 -0.2457 1.1697 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1066 1.3909 -0.5868 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4097 -1.2870 1.4524 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8022 0.3459 1.9376 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8540 0.1352 1.0688 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8486 2.1884 -0.0687 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4025 1.3837 1.5236 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0773 -0.7179 0.5202 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1081 2.0709 1.9573 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9149 1.7561 1.4336 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4265 -0.3648 0.4078 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2091 -1.6917 0.1660 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2335 2.7176 1.7970 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8499 0.8787 0.8715 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2449 1.7147 -1.5634 N 0 0 0 0 0 0 0 0 0 0 0 0
1.5877 1.0306 -1.8598 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0482 3.0857 -1.9841 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0065 3.5686 -2.1027 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5310 3.0871 -2.9341 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4641 3.6477 -1.2630 H 0 0 0 0 0 0 0 0 0 0 0 0
4.9067 -1.7322 -0.0514 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3771 -1.9668 0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4904 -2.3252 1.2363 H 0 0 0 0 0 0 0 0 0 0 0 0
6.7328 -2.7401 -0.4486 H 0 0 0 0 0 0 0 0 0 0 0 0
6.9789 -1.0743 0.0959 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1558 -2.6374 -0.3025 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.3915 -1.3098 -0.1932 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1377 0.4171 0.2455 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7913 -0.8419 -0.2429 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7862 -1.6644 -0.7834 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4906 -2.6284 -1.1515 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.4715 0.8419 0.1895 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.7389 1.8136 0.5665 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.0931 -1.2506 -0.8388 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.8525 -1.8867 -1.2543 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.4270 0.0143 -0.3455 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.4484 0.3489 -0.3835 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0571 -2.3855 -0.6163 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.1725 1.2382 0.7771 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.4483 2.1254 1.1308 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
3 4 1 6 0 0 0
3 1 1 0 0 0 0
3 5 1 0 0 0 0
5 7 1 0 0 0 0
5 8 1 0 0 0 0
6 3 1 0 0 0 0
6 10 2 0 0 0 0
9 5 1 0 0 0 0
9 11 2 0 0 0 0
11 13 1 0 0 0 0
12 9 1 0 0 0 0
14 11 1 0 0 0 0
14 17 1 0 0 0 0
15 12 2 0 0 0 0
15 18 1 0 0 0 0
16 12 1 0 0 0 0
18 14 2 0 0 0 0
19 6 1 0 0 0 0
20 19 1 0 0 0 0
21 19 1 0 0 0 0
21 24 1 0 0 0 0
22 21 1 0 0 0 0
23 21 1 0 0 0 0
25 1 1 0 0 0 0
25 26 1 0 0 0 0
26 27 1 0 0 0 0
28 26 1 0 0 0 0
29 26 1 0 0 0 0
30 25 2 0 0 0 0
31 15 1 0 0 0 0
32 43 1 0 0 0 0
33 31 1 0 0 0 0
33 32 2 0 0 0 0
34 33 1 0 0 0 0
35 34 1 0 0 0 0
36 32 1 0 0 0 0
36 37 1 0 0 0 0
38 34 2 0 0 0 0
38 40 1 0 0 0 0
39 38 1 0 0 0 0
40 36 2 0 0 0 0
41 40 1 0 0 0 0
42 31 2 0 0 0 0
43 18 1 0 0 0 0
43 44 1 0 0 0 0
M ROOT 1
M POLY_N_BB 1
M POLY_CA_BB 3
M POLY_C_BB 6
M POLY_O_BB 10
M POLY_IGNORE 20 21 22 23 24 26 27 28 29 30
M POLY_UPPER 19
M POLY_LOWER 25
M POLY_CHG 0
M POLY_PROPERTIES PROTEIN
M END
Output.kin
@text
View this file with KiNG or Mage from http://kinemage.biochem.duke.edu
@kinemage 1
@title {Acd.kin}
@onewidth
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{C} green 3.112 -0.068 -0.142
{C} green 3.107 1.391 -0.587
{O} red 3.849 2.188 -0.069
{N} sky 2.245 1.715 -1.563
{C} green 4.907 -1.732 -0.051
{H} gray 5.125 0.277 0.289
{H} gray 2.683 -0.703 -0.905
{C} green 2.316 -0.246 1.170
{H} gray 2.410 -1.287 1.452
{H} gray 2.802 0.346 1.938
{C} green 0.854 0.135 1.069
{C} green 0.403 1.384 1.524
{C} green -0.077 -0.718 0.520
{H} gray 1.108 2.071 1.957
{C} green -0.915 1.756 1.434
{C} green -1.427 -0.365 0.408
{H} gray 0.209 -1.692 0.166
{H} gray -1.234 2.718 1.797
{C} green -1.850 0.879 0.872
{C} green -2.392 -1.310 -0.193
{O} red -2.057 -2.385 -0.616
{N} sky -3.172 1.238 0.777
{C} green -3.791 -0.842 -0.243
{C} green -4.138 0.417 0.245
{C} green -4.786 -1.664 -0.783
{H} gray -4.491 -2.628 -1.151
{C} green -5.471 0.842 0.190
{H} gray -5.739 1.814 0.567
{C} green -6.093 -1.251 -0.839
{H} gray -3.448 2.125 1.131
{H} gray -6.853 -1.887 -1.254
{C} green -6.427 0.014 -0.345
{H} gray -7.448 0.349 -0.384
{H} gray 1.588 1.031 -1.860
{C} green 2.048 3.086 -1.984
{H} gray 3.006 3.569 -2.103
{H} gray 1.531 3.087 -2.934
{H} gray 1.464 3.648 -1.263
{C} green 6.377 -1.967 0.218
{H} gray 6.490 -2.325 1.236
{H} gray 6.733 -2.740 -0.449
{H} gray 6.979 -1.074 0.096
{O} red 4.156 -2.637 -0.302
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{ N1}P 4.495 -0.448 0.028
{ H1}L 5.125 0.277 0.289
{ C1}P 3.112 -0.068 -0.142
{ H2}L 2.683 -0.703 -0.905
{ C1}P 3.112 -0.068 -0.142
{ N1}L 4.495 -0.448 0.028
{ C1}P 3.112 -0.068 -0.142
{ C2}L 2.316 -0.246 1.170
{ C2}P 2.316 -0.246 1.170
{ H3}L 2.410 -1.287 1.452
{ C2}P 2.316 -0.246 1.170
{ H4}L 2.802 0.346 1.938
{ C3}P 3.107 1.391 -0.587
{ C1}L 3.112 -0.068 -0.142
{ C3}P 3.107 1.391 -0.587
{ O1}L 3.849 2.188 -0.069
{ C4}P 0.854 0.135 1.069
{ C2}L 2.316 -0.246 1.170
{ C4}P 0.854 0.135 1.069
{ C5}L 0.403 1.384 1.524
{ C5}P 0.403 1.384 1.524
{ H5}L 1.108 2.071 1.957
{ C6}P -0.077 -0.718 0.520
{ C4}L 0.854 0.135 1.069
{ C7}P -0.915 1.756 1.434
{ C5}L 0.403 1.384 1.524
{ C7}P -0.915 1.756 1.434
{ H7}L -1.234 2.718 1.797
{ C8}P -1.427 -0.365 0.408
{ C6}L -0.077 -0.718 0.520
{ C8}P -1.427 -0.365 0.408
{ C9}L -1.850 0.879 0.872
{ H6}P 0.209 -1.692 0.166
{ C6}L -0.077 -0.718 0.520
{ C9}P -1.850 0.879 0.872
{ C7}L -0.915 1.756 1.434
{ N2}P 2.245 1.715 -1.563
{ C3}L 3.107 1.391 -0.587
{ H8}P 1.588 1.031 -1.860
{ N2}L 2.245 1.715 -1.563
{ C10}P 2.048 3.086 -1.984
{ N2}L 2.245 1.715 -1.563
{ C10}P 2.048 3.086 -1.984
{ H11}L 1.464 3.648 -1.263
{ H9}P 3.006 3.569 -2.103
{ C10}L 2.048 3.086 -1.984
{ H10}P 1.531 3.087 -2.934
{ C10}L 2.048 3.086 -1.984
{ C11}P 4.907 -1.732 -0.051
{ N1}L 4.495 -0.448 0.028
{ C11}P 4.907 -1.732 -0.051
{ C12}L 6.377 -1.967 0.218
{ C12}P 6.377 -1.967 0.218
{ H12}L 6.490 -2.325 1.236
{ H13}P 6.733 -2.740 -0.449
{ C12}L 6.377 -1.967 0.218
{ H14}P 6.979 -1.074 0.096
{ C12}L 6.377 -1.967 0.218
{ O2}P 4.156 -2.637 -0.302
{ C11}L 4.907 -1.732 -0.051
{ C13}P -2.392 -1.310 -0.193
{ C8}L -1.427 -0.365 0.408
{ C14}P -4.138 0.417 0.245
{ N3}L -3.172 1.238 0.777
{ C15}P -3.791 -0.842 -0.243
{ C13}L -2.392 -1.310 -0.193
{ C15}P -3.791 -0.842 -0.243
{ C14}L -4.138 0.417 0.245
{ C16}P -4.786 -1.664 -0.783
{ C15}L -3.791 -0.842 -0.243
{ H15}P -4.491 -2.628 -1.151
{ C16}L -4.786 -1.664 -0.783
{ C17}P -5.471 0.842 0.190
{ C14}L -4.138 0.417 0.245
{ C17}P -5.471 0.842 0.190
{ H16}L -5.739 1.814 0.567
{ C18}P -6.093 -1.251 -0.839
{ C16}L -4.786 -1.664 -0.783
{ C18}P -6.093 -1.251 -0.839
{ C19}L -6.427 0.014 -0.345
{ H17}P -6.853 -1.887 -1.254
{ C18}L -6.093 -1.251 -0.839
{ C19}P -6.427 0.014 -0.345
{ C17}L -5.471 0.842 0.190
{ H18}P -7.448 0.349 -0.384
{ C19}L -6.427 0.014 -0.345
{ O3}P -2.057 -2.385 -0.616
{ C13}L -2.392 -1.310 -0.193
{ N3}P -3.172 1.238 0.777
{ C9}L -1.850 0.879 0.872
{ N3}P -3.172 1.238 0.777
{ H19}L -3.448 2.125 1.131
@vectorlist {rotatable bonds} color= white width= 4
{ C1}P 3.112 -0.068 -0.142
{ N1}L 4.495 -0.448 0.028
{ C1}P 3.112 -0.068 -0.142
{ C2}L 2.316 -0.246 1.170
{ C3}P 3.107 1.391 -0.587
{ C1}L 3.112 -0.068 -0.142
{ C4}P 0.854 0.135 1.069
{ C2}L 2.316 -0.246 1.170
{ N2}P 2.245 1.715 -1.563
{ C3}L 3.107 1.391 -0.587
{ C11}P 4.907 -1.732 -0.051
{ N1}L 4.495 -0.448 0.028
@labellist {atom indices} color= white off
{1} 4.495 -0.448 0.028
{2} 3.112 -0.068 -0.142
{3} 3.107 1.391 -0.587
{4} 3.849 2.188 -0.069
{5} 2.245 1.715 -1.563
{6} 4.907 -1.732 -0.051
{7} 5.125 0.277 0.289
{8} 2.683 -0.703 -0.905
{9} 2.316 -0.246 1.170
{10} 2.410 -1.287 1.452
{11} 2.802 0.346 1.938
{12} 0.854 0.135 1.069
{13} 0.403 1.384 1.524
{14} -0.077 -0.718 0.520
{15} 1.108 2.071 1.957
{16} -0.915 1.756 1.434
{17} -1.427 -0.365 0.408
{18} 0.209 -1.692 0.166
{19} -1.234 2.718 1.797
{20} -1.850 0.879 0.872
{21} -2.392 -1.310 -0.193
{22} -2.057 -2.385 -0.616
{23} -3.172 1.238 0.777
{24} -3.791 -0.842 -0.243
{25} -4.138 0.417 0.245
{26} -4.786 -1.664 -0.783
{27} -4.491 -2.628 -1.151
{28} -5.471 0.842 0.190
{29} -5.739 1.814 0.567
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{34} -7.448 0.349 -0.384
{35} 1.588 1.031 -1.860
{36} 2.048 3.086 -1.984
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{38} 1.531 3.087 -2.934
{39} 1.464 3.648 -1.263
{40} 6.377 -1.967 0.218
{41} 6.490 -2.325 1.236
{42} 6.733 -2.740 -0.449
{43} 6.979 -1.074 0.096
{44} 4.156 -2.637 -0.302
@labellist {original names} color= white off
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{C} 3.112 -0.068 -0.142
{C} 3.107 1.391 -0.587
{O} 3.849 2.188 -0.069
{N} 2.245 1.715 -1.563
{C} 4.907 -1.732 -0.051
{H} 5.125 0.277 0.289
{H} 2.683 -0.703 -0.905
{C} 2.316 -0.246 1.170
{H} 2.410 -1.287 1.452
{H} 2.802 0.346 1.938
{C} 0.854 0.135 1.069
{C} 0.403 1.384 1.524
{C} -0.077 -0.718 0.520
{H} 1.108 2.071 1.957
{C} -0.915 1.756 1.434
{C} -1.427 -0.365 0.408
{H} 0.209 -1.692 0.166
{H} -1.234 2.718 1.797
{C} -1.850 0.879 0.872
{C} -2.392 -1.310 -0.193
{O} -2.057 -2.385 -0.616
{N} -3.172 1.238 0.777
{C} -3.791 -0.842 -0.243
{C} -4.138 0.417 0.245
{C} -4.786 -1.664 -0.783
{H} -4.491 -2.628 -1.151
{C} -5.471 0.842 0.190
{H} -5.739 1.814 0.567
{C} -6.093 -1.251 -0.839
{H} -3.448 2.125 1.131
{H} -6.853 -1.887 -1.254
{C} -6.427 0.014 -0.345
{H} -7.448 0.349 -0.384
{H} 1.588 1.031 -1.860
{C} 2.048 3.086 -1.984
{H} 3.006 3.569 -2.103
{H} 1.531 3.087 -2.934
{H} 1.464 3.648 -1.263
{C} 6.377 -1.967 0.218
{H} 6.490 -2.325 1.236
{H} 6.733 -2.740 -0.449
{H} 6.979 -1.074 0.096
{O} 4.156 -2.637 -0.302
@labellist {atom names} color= white off
{ N1} 4.495 -0.448 0.028
{ C1} 3.112 -0.068 -0.142
{ C3} 3.107 1.391 -0.587
{ O1} 3.849 2.188 -0.069
{ N2} 2.245 1.715 -1.563
{ C11} 4.907 -1.732 -0.051
{ H1} 5.125 0.277 0.289
{ H2} 2.683 -0.703 -0.905
{ C2} 2.316 -0.246 1.170
{ H3} 2.410 -1.287 1.452
{ H4} 2.802 0.346 1.938
{ C4} 0.854 0.135 1.069
{ C5} 0.403 1.384 1.524
{ C6} -0.077 -0.718 0.520
{ H5} 1.108 2.071 1.957
{ C7} -0.915 1.756 1.434
{ C8} -1.427 -0.365 0.408
{ H6} 0.209 -1.692 0.166
{ H7} -1.234 2.718 1.797
{ C9} -1.850 0.879 0.872
{ C13} -2.392 -1.310 -0.193
{ O3} -2.057 -2.385 -0.616
{ N3} -3.172 1.238 0.777
{ C15} -3.791 -0.842 -0.243
{ C14} -4.138 0.417 0.245
{ C16} -4.786 -1.664 -0.783
{ H15} -4.491 -2.628 -1.151
{ C17} -5.471 0.842 0.190
{ H16} -5.739 1.814 0.567
{ C18} -6.093 -1.251 -0.839
{ H19} -3.448 2.125 1.131
{ H17} -6.853 -1.887 -1.254
{ C19} -6.427 0.014 -0.345
{ H18} -7.448 0.349 -0.384
{ H8} 1.588 1.031 -1.860
{ C10} 2.048 3.086 -1.984
{ H9} 3.006 3.569 -2.103
{ H10} 1.531 3.087 -2.934
{ H11} 1.464 3.648 -1.263
{ C12} 6.377 -1.967 0.218
{ H12} 6.490 -2.325 1.236
{ H13} 6.733 -2.740 -0.449
{ H14} 6.979 -1.074 0.096
{ O2} 4.156 -2.637 -0.302
@labellist {Rosetta types} color= white
{Nbb} 4.495 -0.448 0.028
{CAbb} 3.112 -0.068 -0.142
{CObb} 3.107 1.391 -0.587
{OCbb} 3.849 2.188 -0.069
{X} 2.245 1.715 -1.563
{X} 4.907 -1.732 -0.051
{HNbb} 5.125 0.277 0.289
{Hapo} 2.683 -0.703 -0.905
{CH2 } 2.316 -0.246 1.170
{Hapo} 2.410 -1.287 1.452
{Hapo} 2.802 0.346 1.938
{aroC} 0.854 0.135 1.069
{aroC} 0.403 1.384 1.524
{aroC} -0.077 -0.718 0.520
{Haro} 1.108 2.071 1.957
{aroC} -0.915 1.756 1.434
{aroC} -1.427 -0.365 0.408
{Haro} 0.209 -1.692 0.166
{Haro} -1.234 2.718 1.797
{aroC} -1.850 0.879 0.872
{COO } -2.392 -1.310 -0.193
{OOC } -2.057 -2.385 -0.616
{Ntrp} -3.172 1.238 0.777
{aroC} -3.791 -0.842 -0.243
{aroC} -4.138 0.417 0.245
{aroC} -4.786 -1.664 -0.783
{Haro} -4.491 -2.628 -1.151
{aroC} -5.471 0.842 0.190
{Haro} -5.739 1.814 0.567
{aroC} -6.093 -1.251 -0.839
{Hpol} -3.448 2.125 1.131
{Haro} -6.853 -1.887 -1.254
{aroC} -6.427 0.014 -0.345
{Haro} -7.448 0.349 -0.384
{Hpol} 1.588 1.031 -1.860
{CH3 } 2.048 3.086 -1.984
{Hapo} 3.006 3.569 -2.103
{Hapo} 1.531 3.087 -2.934
{Hapo} 1.464 3.648 -1.263
{CH3 } 6.377 -1.967 0.218
{Hapo} 6.490 -2.325 1.236
{Hapo} 6.733 -2.740 -0.449
{Hapo} 6.979 -1.074 0.096
{ONH2} 4.156 -2.637 -0.302
@labellist {MM types} color= white off
{NH1} 4.495 -0.448 0.028
{CT1} 3.112 -0.068 -0.142
{C} 3.107 1.391 -0.587
{O} 3.849 2.188 -0.069
{NH1} 2.245 1.715 -1.563
{C} 4.907 -1.732 -0.051
{H} 5.125 0.277 0.289
{HB} 2.683 -0.703 -0.905
{CT2} 2.316 -0.246 1.170
{HA} 2.410 -1.287 1.452
{HA} 2.802 0.346 1.938
{CE1} 0.854 0.135 1.069
{CE1} 0.403 1.384 1.524
{CE1} -0.077 -0.718 0.520
{HE1} 1.108 2.071 1.957
{CE1} -0.915 1.756 1.434
{CE1} -1.427 -0.365 0.408
{HE1} 0.209 -1.692 0.166
{HE1} -1.234 2.718 1.797
{CE1} -1.850 0.879 0.872
{C} -2.392 -1.310 -0.193
{O} -2.057 -2.385 -0.616
{NH1} -3.172 1.238 0.777
{CE1} -3.791 -0.842 -0.243
{CE1} -4.138 0.417 0.245
{CE1} -4.786 -1.664 -0.783
{HE1} -4.491 -2.628 -1.151
{CE1} -5.471 0.842 0.190
{HE1} -5.739 1.814 0.567
{CE1} -6.093 -1.251 -0.839
{H} -3.448 2.125 1.131
{HE1} -6.853 -1.887 -1.254
{CE1} -6.427 0.014 -0.345
{HE1} -7.448 0.349 -0.384
{H} 1.588 1.031 -1.860
{CT3} 2.048 3.086 -1.984
{HA} 3.006 3.569 -2.103
{HA} 1.531 3.087 -2.934
{HA} 1.464 3.648 -1.263
{CT3} 6.377 -1.967 0.218
{HA} 6.490 -2.325 1.236
{HA} 6.733 -2.740 -0.449
{HA} 6.979 -1.074 0.096
{O} 4.156 -2.637 -0.302
@labellist {PDB names} color= white off
{ N } 4.495 -0.448 0.028
{ CA } 3.112 -0.068 -0.142
{ C } 3.107 1.391 -0.587
{ O } 3.849 2.188 -0.069
{UPPER} 2.245 1.715 -1.563
{LOWER} 4.907 -1.732 -0.051
{ H } 5.125 0.277 0.289
{ HA } 2.683 -0.703 -0.905
{ CB } 2.316 -0.246 1.170
{1HB } 2.410 -1.287 1.452
{2HB } 2.802 0.346 1.938
{ CG } 0.854 0.135 1.069
{ CD1} 0.403 1.384 1.524
{ CD2} -0.077 -0.718 0.520
{1HD1} 1.108 2.071 1.957
{ CE1} -0.915 1.756 1.434
{ CE2} -1.427 -0.365 0.408
{1HD2} 0.209 -1.692 0.166
{1HE1} -1.234 2.718 1.797
{ CZ1} -1.850 0.879 0.872
{ CZ2} -2.392 -1.310 -0.193
{ OT1} -2.057 -2.385 -0.616
{ NT2} -3.172 1.238 0.777
{ CT3} -3.791 -0.842 -0.243
{ CI1} -4.138 0.417 0.245
{ CI2} -4.786 -1.664 -0.783
{1HI2} -4.491 -2.628 -1.151
{ CK1} -5.471 0.842 0.190
{1HK1} -5.739 1.814 0.567
{ CK2} -6.093 -1.251 -0.839
{1HT2} -3.448 2.125 1.131
{1HK2} -6.853 -1.887 -1.254
{ CL } -6.427 0.014 -0.345
{1HL } -7.448 0.349 -0.384
{ H } 1.588 1.031 -1.860
{ C } 2.048 3.086 -1.984
{ H } 3.006 3.569 -2.103
{ H } 1.531 3.087 -2.934
{ H } 1.464 3.648 -1.263
{ C } 6.377 -1.967 0.218
{ H } 6.490 -2.325 1.236
{ H } 6.733 -2.740 -0.449
{ H } 6.979 -1.074 0.096
{ O } 4.156 -2.637 -0.302
@labellist {partial charges} color= white off
{-0.59} 4.495 -0.448 0.028
{-0.07} 3.112 -0.068 -0.142
{0.64} 3.107 1.391 -0.587
{-0.53} 3.849 2.188 -0.069
{-0.59} 2.245 1.715 -1.563
{0.64} 4.907 -1.732 -0.051
{0.45} 5.125 0.277 0.289
{0.12} 2.683 -0.703 -0.905
{-0.16} 2.316 -0.246 1.170
{0.12} 2.410 -1.287 1.452
{0.12} 2.802 0.346 1.938
{-0.09} 0.854 0.135 1.069
{-0.09} 0.403 1.384 1.524
{-0.09} -0.077 -0.718 0.520
{0.14} 1.108 2.071 1.957
{-0.09} -0.915 1.756 1.434
{-0.09} -1.427 -0.365 0.408
{0.14} 0.209 -1.692 0.166
{0.14} -1.234 2.718 1.797
{-0.09} -1.850 0.879 0.872
{0.64} -2.392 -1.310 -0.193
{-0.74} -2.057 -2.385 -0.616
{-0.59} -3.172 1.238 0.777
{-0.09} -3.791 -0.842 -0.243
{-0.09} -4.138 0.417 0.245
{-0.09} -4.786 -1.664 -0.783
{0.14} -4.491 -2.628 -1.151
{-0.09} -5.471 0.842 0.190
{0.14} -5.739 1.814 0.567
{-0.09} -6.093 -1.251 -0.839
{0.45} -3.448 2.125 1.131
{0.14} -6.853 -1.887 -1.254
{-0.09} -6.427 0.014 -0.345
{0.14} -7.448 0.349 -0.384
{0.45} 1.588 1.031 -1.860
{-0.25} 2.048 3.086 -1.984
{0.12} 3.006 3.569 -2.103
{0.12} 1.531 3.087 -2.934
{0.12} 1.464 3.648 -1.263
{-0.25} 6.377 -1.967 0.218
{0.12} 6.490 -2.325 1.236
{0.12} 6.733 -2.740 -0.449
{0.12} 6.979 -1.074 0.096
{-0.53} 4.156 -2.637 -0.302
@group {frag 1} master= {fragments}
@balllist {root atom} color= purple radius= 0.2 master={root atoms}
{ N1 frag 1} 4.495 -0.448 0.028
@ringlist {nbr atom} color= purple radius= 8.431 master={nbr atoms} off
{ C4 frag 1} 0.854 0.135 1.069
{ C4 frag 1} r=0.3 0.854 0.135 1.069
@arrowlist {atom tree} color= purple master= {atom trees}
{ N1}P 4.495 -0.448 0.028
{ C1}L 3.112 -0.068 -0.142
{ C1}P 3.112 -0.068 -0.142
{ C3}L 3.107 1.391 -0.587
{ C3}P 3.107 1.391 -0.587
{ O1}L 3.849 2.188 -0.069
{ C3}P 3.107 1.391 -0.587
{ N2}L 2.245 1.715 -1.563
{ N1}P 4.495 -0.448 0.028
{ C11}L 4.907 -1.732 -0.051
{ N1}P 4.495 -0.448 0.028
{ H1}L 5.125 0.277 0.289
{ C1}P 3.112 -0.068 -0.142
{ H2}L 2.683 -0.703 -0.905
{ C1}P 3.112 -0.068 -0.142
{ C2}L 2.316 -0.246 1.170
{ C2}P 2.316 -0.246 1.170
{ H3}L 2.410 -1.287 1.452
{ C2}P 2.316 -0.246 1.170
{ H4}L 2.802 0.346 1.938
{ C2}P 2.316 -0.246 1.170
{ C4}L 0.854 0.135 1.069
{ C4}P 0.854 0.135 1.069
{ C5}L 0.403 1.384 1.524
{ C8}P -1.427 -0.365 0.408
{ C6}L -0.077 -0.718 0.520
{ C5}P 0.403 1.384 1.524
{ H5}L 1.108 2.071 1.957
{ C5}P 0.403 1.384 1.524
{ C7}L -0.915 1.756 1.434
{ C9}P -1.850 0.879 0.872
{ C8}L -1.427 -0.365 0.408
{ C6}P -0.077 -0.718 0.520
{ H6}L 0.209 -1.692 0.166
{ C7}P -0.915 1.756 1.434
{ H7}L -1.234 2.718 1.797
{ C7}P -0.915 1.756 1.434
{ C9}L -1.850 0.879 0.872
{ C8}P -1.427 -0.365 0.408
{ C13}L -2.392 -1.310 -0.193
{ C13}P -2.392 -1.310 -0.193
{ O3}L -2.057 -2.385 -0.616
{ C14}P -4.138 0.417 0.245
{ N3}L -3.172 1.238 0.777
{ C13}P -2.392 -1.310 -0.193
{ C15}L -3.791 -0.842 -0.243
{ C15}P -3.791 -0.842 -0.243
{ C14}L -4.138 0.417 0.245
{ C18}P -6.093 -1.251 -0.839
{ C16}L -4.786 -1.664 -0.783
{ C16}P -4.786 -1.664 -0.783
{ H15}L -4.491 -2.628 -1.151
{ C14}P -4.138 0.417 0.245
{ C17}L -5.471 0.842 0.190
{ C17}P -5.471 0.842 0.190
{ H16}L -5.739 1.814 0.567
{ C19}P -6.427 0.014 -0.345
{ C18}L -6.093 -1.251 -0.839
{ N3}P -3.172 1.238 0.777
{ H19}L -3.448 2.125 1.131
{ C18}P -6.093 -1.251 -0.839
{ H17}L -6.853 -1.887 -1.254
{ C17}P -5.471 0.842 0.190
{ C19}L -6.427 0.014 -0.345
{ C19}P -6.427 0.014 -0.345
{ H18}L -7.448 0.349 -0.384
{ N2}P 2.245 1.715 -1.563
{ H8}L 1.588 1.031 -1.860
{ N2}P 2.245 1.715 -1.563
{ C10}L 2.048 3.086 -1.984
{ C10}P 2.048 3.086 -1.984
{ H9}L 3.006 3.569 -2.103
{ C10}P 2.048 3.086 -1.984
{ H10}L 1.531 3.087 -2.934
{ C10}P 2.048 3.086 -1.984
{ H11}L 1.464 3.648 -1.263
{ C11}P 4.907 -1.732 -0.051
{ C12}L 6.377 -1.967 0.218
{ C12}P 6.377 -1.967 0.218
{ H12}L 6.490 -2.325 1.236
{ C12}P 6.377 -1.967 0.218
{ H13}L 6.733 -2.740 -0.449
{ C12}P 6.377 -1.967 0.218
{ H14}L 6.979 -1.074 0.096
{ C11}P 4.907 -1.732 -0.051
{ O2}L 4.156 -2.637 -0.302
@arrowlist {connections} color= purple master= {connections}
Output.params
NAME ACD
IO_STRING ACD X
TYPE POLYMER
AA UNK
ATOM N Nbb NH1 -0.59
ATOM CA CAbb CT1 -0.07
ATOM C CObb C 0.64
ATOM O OCbb O -0.53
ATOM H HNbb H 0.45
ATOM HA Hapo HB 0.12
ATOM CB CH2 CT2 -0.16
ATOM 1HB Hapo HA 0.12
ATOM 2HB Hapo HA 0.12
ATOM CG aroC CE1 -0.09
ATOM CD1 aroC CE1 -0.09
ATOM CD2 aroC CE1 -0.09
ATOM 1HD1 Haro HE1 0.14
ATOM CE1 aroC CE1 -0.09
ATOM CE2 aroC CE1 -0.09
ATOM 1HD2 Haro HE1 0.14
ATOM 1HE1 Haro HE1 0.14
ATOM CZ1 aroC CE1 -0.09
ATOM CZ2 COO C 0.64
ATOM OT1 OOC O -0.74
ATOM NT2 Ntrp NH1 -0.59
ATOM CT3 aroC CE1 -0.09
ATOM CI1 aroC CE1 -0.09
ATOM CI2 aroC CE1 -0.09
ATOM 1HI2 Haro HE1 0.14
ATOM CK1 aroC CE1 -0.09
ATOM 1HK1 Haro HE1 0.14
ATOM CK2 aroC CE1 -0.09
ATOM 1HT2 Hpol H 0.45
ATOM 1HK2 Haro HE1 0.14
ATOM CL aroC CE1 -0.09
ATOM 1HL Haro HE1 0.14
BOND N H
BOND CA HA
BOND CA N
BOND CA CB
BOND CB 1HB
BOND CB 2HB
BOND C CA
BOND C O
BOND CG CB
BOND CG CD1
BOND CD1 1HD1
BOND CD2 CG
BOND CE1 CD1
BOND CE1 1HE1
BOND CE2 CD2
BOND CE2 CZ1
BOND CD2 1HD2
BOND CZ1 CE1
BOND CZ2 CE2
BOND CI1 NT2
BOND CT3 CZ2
BOND CT3 CI1
BOND CI2 CT3
BOND CI2 1HI2
BOND CK1 CI1
BOND CK1 1HK1
BOND CK2 CI2
BOND CK2 CL
BOND CK2 1HK2
BOND CL CK1
BOND CL 1HL
BOND OT1 CZ2
BOND NT2 CZ1
BOND NT2 1HT2
LOWER_CONNECT N
UPPER_CONNECT C
CHI 1 N CA CB CG
CHI 2 N CA C O
CHI 3 CA CB CG CD1
NBR_ATOM CB
NBR_RADIUS 12.280143
FIRST_SIDECHAIN_ATOM CB
PROPERTIES PROTEIN
ICOOR_INTERNAL N 0.000000 0.000000 0.000000 N CA C
ICOOR_INTERNAL CA 0.000000 0.000000 1.444306 N CA C
ICOOR_INTERNAL C 0.000000 73.172829 1.525255 CA N C
ICOOR_INTERNAL CB 0.000000 68.734888 1.545092 CA N CB
ICOOR_INTERNAL CG 179.935787 65.666987 1.513880 CB CA N
ICOOR_INTERNAL CD1 -99.380381 59.144427 1.403370 CG CB CA
ICOOR_INTERNAL CE1 179.484026 58.052182 1.371978 CD1 CG CB
ICOOR_INTERNAL CZ1 -0.151501 60.164286 1.400004 CE1 CD1 CG
ICOOR_INTERNAL CE2 -0.094042 60.653316 1.393046 CZ1 CE1 CD1
ICOOR_INTERNAL CD2 0.426984 60.553015 1.399162 CE2 CZ1 CE1
ICOOR_INTERNAL 1HD2 179.033144 62.676412 1.075067 CD2 CE2 CZ1
ICOOR_INTERNAL CZ2 179.719030 59.500099 1.478327 CE2 CZ1 CD2
ICOOR_INTERNAL CT3 -0.600223 64.539444 1.476767 CZ2 CE2 CZ1
ICOOR_INTERNAL CI1 0.448978 59.345551 1.394134 CT3 CZ2 CE2
ICOOR_INTERNAL NT2 0.156462 59.960396 1.374196 CI1 CT3 CZ2
ICOOR_INTERNAL 1HT2 -179.099166 61.574211 0.994129 NT2 CI1 CT3
ICOOR_INTERNAL CK1 179.867849 60.238285 1.400933 CI1 CT3 NT2
ICOOR_INTERNAL CL 0.031373 60.296936 1.372635 CK1 CI1 CT3
ICOOR_INTERNAL CK2 -0.034103 58.885882 1.398144 CL CK1 CI1
ICOOR_INTERNAL CI2 0.010790 60.914690 1.371965 CK2 CL CK1
ICOOR_INTERNAL 1HI2 179.977017 58.711095 1.073393 CI2 CK2 CL
ICOOR_INTERNAL 1HK2 179.976703 59.777415 1.074221 CK2 CL CI2
ICOOR_INTERNAL 1HL 179.988908 60.837188 1.075481 CL CK1 CK2
ICOOR_INTERNAL 1HK1 179.965301 60.236548 1.076026 CK1 CI1 CL
ICOOR_INTERNAL OT1 179.797617 57.792635 1.203315 CZ2 CE2 CT3
ICOOR_INTERNAL 1HE1 179.728239 59.691703 1.076126 CE1 CD1 CZ1
ICOOR_INTERNAL 1HD1 179.926703 60.807894 1.076202 CD1 CG CE1
ICOOR_INTERNAL 1HB 121.925663 73.297809 1.083079 CB CA CG
ICOOR_INTERNAL 2HB 115.269286 72.092426 1.084594 CB CA 1HB
ICOOR_INTERNAL O -42.181593 59.654133 1.206233 C CA N
ICOOR_INTERNAL UPPER 137.852883 63.576031 1.342058 C CA N
ICOOR_INTERNAL HA 119.196971 71.992890 1.081009 CA N C
ICOOR_INTERNAL LOWER -155.920448 57.651795 1.350809 N CA C
ICOOR_INTERNAL H -174.775908 63.532455 0.995214 N CA LOWER
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