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seq2itp.pl seems not to work
- cescoxonta
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13 years 5 months ago #437
by cescoxonta
seq2itp.pl seems not to work was created by cescoxonta
Hello to everybody. It seems I have a problem with seq2itp tool. If I try to run it I have the following error:
Error: The number of residues in the sequence file (1356) does not match the number of residues in the structure file (128).
However, to me, the structure file seems ok. I can not attach the full ssd file, which is too long, however, I will copy here the beginning and the part around resid 128.
...
Error: The number of residues in the sequence file (1356) does not match the number of residues in the structure file (128).
However, to me, the structure file seems ok. I can not attach the full ssd file, which is too long, however, I will copy here the beginning and the part around resid 128.
==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=16-NOV-2010 .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
1356 6 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
62913.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
976 72.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
41 3.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
1 0.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
1 0.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
43 3.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
136 10.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
720 53.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
26 1.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
0 0 0 4 0 2 4 3 2 1 4 0 1 0 0 0 5 1 0 0 0 1 0 1 0 1 1 1 0 12 RESIDUES PER ALPHA HELIX .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
0 9 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
2 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
1 1 M 0 0 69 0, 0.0 3,-0.1 0, 0.0 1172,-0.0 0.000 360.0 360.0 360.0 -66.5 67.9 62.8 64.5
2 2 D + 0 0 145 1,-0.3 4,-0.4 1134,-0.0 3,-0.1 0.027 360.0 106.9 80.5 -13.6 68.0 61.9 60.6
3 3 W + 0 0 16 1,-0.1 2,-1.9 2,-0.1 -1,-0.3 -0.084 58.7 35.5 -85.1 176.1 71.6 63.4 59.9
4 4 G S > S+ 0 0 1 1,-0.2 4,-2.7 -3,-0.1 5,-0.2 -0.229 96.8 83.2 75.3 -49.4 75.1 61.8 59.3
5 5 T H > S+ 0 0 37 -2,-1.9 4,-1.2 1,-0.2 -1,-0.2 0.903 100.6 32.3 -45.5 -59.6 73.6 58.8 57.2
6 6 L H > S+ 0 0 131 -4,-0.4 4,-2.5 2,-0.2 5,-0.3 0.880 114.8 57.7 -69.5 -49.9 73.4 60.7 54.0
7 7 Q H > S+ 0 0 29 1,-0.2 4,-1.5 2,-0.2 -2,-0.2 0.883 108.3 51.1 -50.2 -31.0 76.5 63.0 54.6
8 8 T H < S+ 0 0 12 -4,-2.7 -1,-0.2 2,-0.2 -2,-0.2 0.915 109.2 49.0 -65.4 -49.9 78.6 59.6 54.9
9 9 I H >< S+ 0 0 94 -4,-1.2 3,-2.1 -5,-0.2 -2,-0.2 0.938 107.8 52.1 -60.1 -53.4 77.2 58.3 51.6
10 10 L H 3< S+ 0 0 98 -4,-2.5 3,-0.3 1,-0.3 -1,-0.2 0.886 111.9 50.2 -51.1 -46.2 78.0 61.5 49.8
...
100 100 X H X S+ 0 0 132 -4,-2.7 4,-1.8 1,-0.2 -3,-0.2 0.912 114.5 49.3 -59.6 -37.1 83.5 71.7 38.8
101 101 E H X S+ 0 0 43 -4,-1.4 4,-1.3 2,-0.2 -1,-0.2 0.946 113.4 44.0 -56.9 -60.5 85.4 75.0 39.0
102 102 K H X S+ 0 0 67 -4,-2.1 4,-2.7 2,-0.2 3,-0.3 0.925 111.9 52.2 -62.0 -37.2 88.7 73.7 37.3
103 103 K H X S+ 0 0 131 -4,-2.9 4,-1.3 -5,-0.2 -1,-0.2 0.915 106.9 56.1 -65.6 -36.4 86.8 71.9 34.6
104 104 R H < S+ 0 0 220 -4,-1.8 -2,-0.2 -5,-0.4 -1,-0.2 0.819 114.2 38.8 -56.2 -35.0 85.0 75.4 34.1
105 105 K H >< S+ 0 0 113 -4,-1.3 3,-2.1 -3,-0.3 4,-0.4 0.882 107.6 65.9 -73.4 -45.1 88.4 77.1 33.5
106 106 F H >< S+ 0 0 26 -4,-2.7 3,-1.4 1,-0.3 -2,-0.1 0.877 90.3 61.0 -53.8 -43.6 89.9 74.2 31.4
107 107 I T 3< S+ 0 0 133 -4,-1.3 -1,-0.3 1,-0.3 -2,-0.1 0.625 124.4 19.4 -59.8 -15.0 87.7 74.3 28.4
108 108 K T < S+ 0 0 165 -3,-2.1 -1,-0.3 -4,-0.1 2,-0.3 0.149 111.5 157.6-141.4 16.2 88.8 77.9 27.7
109 109 G < - 0 0 7 -3,-1.4 7,-0.2 -4,-0.4 8,-0.2 -0.985 43.2 -93.7-171.3 163.8 92.2 78.2 29.6
110 110 E + 0 0 143 -2,-0.3 6,-0.1 2,-0.3 5,-0.0 -0.977 62.5 87.6-150.4 -11.1 95.0 79.0 30.7
111 111 I S S+ 0 0 120 -2,-0.1 2,-0.2 2,-0.1 4,-0.1 0.731 101.2 15.8 -49.9 -33.2 98.7 77.9 30.2
112 112 K S S- 0 0 113 2,-0.3 -2,-0.3 3,-0.0 5,-0.0 -0.580 93.4 -83.5-127.3-171.8 99.4 80.3 27.3
113 113 S S S+ 0 0 136 -2,-0.2 2,-0.3 -4,-0.1 -2,-0.1 0.533 108.2 37.8 -74.7 -15.5 98.0 83.3 25.3
114 114 E S S- 0 0 161 2,-0.0 -2,-0.3 0, 0.0 2,-0.1 -0.974 100.4 -54.5-140.4 162.3 95.5 81.2 23.2
115 115 F S S- 0 0 74 -2,-0.3 -5,-0.2 -4,-0.1 2,-0.1 -0.286 82.9 -10.6 57.3-147.8 93.2 78.1 23.7
116 116 K - 0 0 130 -7,-0.2 2,-0.3 -9,-0.1 -6,-0.1 -0.603 61.8-170.6 67.7 93.3 93.7 73.9 25.1
117 117 D > - 0 0 23 -8,-0.2 4,-1.7 -2,-0.1 5,-0.2 -0.880 39.9-115.1-136.9 158.2 97.3 72.4 25.7
118 118 I H > S+ 0 0 188 -2,-0.3 4,-1.7 2,-0.2 5,-0.1 0.742 118.5 55.9 -69.1 -27.5 99.3 69.2 26.5
119 119 E H > S+ 0 0 62 2,-0.2 4,-3.4 3,-0.2 -1,-0.2 0.844 108.8 46.5 -62.6 -47.7 100.4 70.8 29.9
120 120 E H > S+ 0 0 23 2,-0.2 4,-2.3 1,-0.2 -2,-0.2 0.854 114.1 47.7 -71.8 -21.1 96.7 71.3 30.6
121 121 I H X S+ 0 0 103 -4,-1.7 4,-1.3 2,-0.2 -2,-0.2 0.790 111.9 49.7 -89.2 -23.8 96.1 67.6 29.4
122 122 K H X>S+ 0 0 90 -4,-1.7 4,-1.9 2,-0.2 5,-1.1 0.952 111.0 51.6 -69.0 -51.8 99.1 66.4 31.7
123 123 T H <>S+ 0 0 39 -4,-3.4 5,-2.4 3,-0.2 6,-0.4 0.964 108.5 49.9 -49.1 -64.2 97.4 68.4 34.4
124 124 Q H <5S+ 0 0 70 -4,-2.3 -1,-0.2 3,-0.2 -2,-0.2 0.818 114.3 44.0 -39.1 -47.4 94.0 66.6 33.8
125 125 K H <5S- 0 0 68 -4,-1.3 -1,-0.2 -3,-0.3 -2,-0.2 0.966 141.0 -11.9 -66.9 -52.3 95.5 63.0 33.9
126 126 V T >X5S+ 0 0 54 -4,-1.9 3,-0.6 -5,-0.1 4,-0.6 0.722 122.4 62.2-126.6 -43.8 97.8 63.5 37.0
127 127 R H >><S+ 0 0 147 -5,-1.1 4,-0.7 1,-0.2 3,-0.6 0.858 104.1 53.4 -72.3 -27.8 98.4 67.1 38.4
128 128 I H 34<S+ 0 0 18 -5,-2.4 -1,-0.2 1,-0.3 4,-0.2 0.680 116.6 39.6 -75.4 -25.0 94.7 67.7 39.2
129 129 E H <> S+ 0 0 7 -3,-0.6 4,-2.6 -6,-0.4 -1,-0.3 0.445 99.4 82.2 -85.2 -18.6 94.7 64.4 41.3
130 130 G H <X S+ 0 0 5 -3,-0.6 4,-1.4 -4,-0.6 -2,-0.1 0.973 102.1 25.5 -73.6 -56.0 98.3 65.0 42.8
131 131 S H X S+ 0 0 57 -4,-0.7 4,-2.9 2,-0.2 5,-0.3 0.797 118.2 65.3 -71.5 -26.3 97.7 67.3 45.8
132 132 L H > S+ 0 0 16 -5,-0.2 4,-2.6 2,-0.2 5,-0.3 0.957 101.2 48.5 -60.0 -51.6 94.1 65.9 45.9
133 133 W H X S+ 0 0 20 -4,-2.6 4,-3.3 3,-0.2 5,-0.4 0.950 114.1 47.4 -43.2 -58.1 95.6 62.5 46.9
134 134 W H X S+ 0 0 142 -4,-1.4 4,-2.4 2,-0.2 5,-0.2 0.967 117.3 38.5 -60.8 -53.6 97.8 64.2 49.6
135 135 T H X S+ 0 0 90 -4,-2.9 4,-2.3 2,-0.2 -1,-0.2 0.926 120.4 48.7 -67.0 -38.3 95.0 66.4 51.2
136 136 Y H X S+ 0 0 1 -4,-2.6 4,-2.3 -5,-0.3 -2,-0.2 0.953 112.9 44.5 -62.1 -48.5 92.4 63.6 50.9
137 137 T H X S+ 0 0 5 -4,-3.3 4,-2.7 -5,-0.3 -2,-0.2 0.936 112.5 52.7 -63.8 -39.1 94.7 60.7 52.3
138 138 S H X S+ 0 0 32 -4,-2.4 4,-3.0 -5,-0.4 5,-0.3 0.957 108.9 51.1 -58.6 -52.2 95.7 63.2 55.1
139 139 S H X S+ 0 0 33 -4,-2.3 4,-1.6 -5,-0.2 -2,-0.2 0.941 110.5 49.5 -39.3 -47.1 91.7 63.5 55.6
140 140 I H X S+ 0 0 18 -4,-2.3 4,-0.9 1,-0.2 -2,-0.2 0.881 111.8 47.4 -71.0 -43.6 91.6 59.6 55.7
141 141 F H >X S+ 0 0 88 -4,-2.7 4,-0.9 2,-0.2 3,-0.7 0.929 110.6 51.3 -61.8 -50.9 94.4 59.5 58.4
142 142 F H 3X S+ 0 0 101 -4,-3.0 4,-2.1 1,-0.2 3,-0.3 0.825 100.3 65.3 -50.8 -35.6 92.7 62.3 60.5
143 143 R H 3X S+ 0 0 19 -4,-1.6 4,-1.9 -5,-0.3 -1,-0.2 0.894 93.9 57.7 -61.5 -40.4 89.5 60.2 60.3
144 144 V H <X S+ 0 0 24 -4,-0.9 4,-1.8 -3,-0.7 -1,-0.2 0.820 109.4 47.5 -48.1 -46.6 91.3 57.4 62.4
145 145 I H X S+ 0 0 111 -4,-0.9 4,-2.8 -3,-0.3 -2,-0.2 0.980 108.2 52.4 -64.4 -50.9 91.8 60.1 65.2
146 146 F H X S+ 0 0 61 -4,-2.1 4,-0.6 1,-0.2 -2,-0.2 0.809 114.8 44.8 -56.0 -36.9 88.1 61.4 65.0
147 147 E H X S+ 0 0 0 -4,-1.9 4,-0.7 -5,-0.2 3,-0.4 0.973 118.7 40.0 -58.7 -71.7 87.0 57.8 65.6
148 148 A H X S+ 0 0 29 -4,-1.8 4,-1.5 2,-0.2 3,-0.4 0.817 99.0 79.2 -48.7 -34.6 89.5 56.9 68.4
149 149 A H X S+ 0 0 31 -4,-2.8 4,-1.3 1,-0.3 3,-0.3 0.872 95.5 43.4 -54.2 -46.2 89.2 60.3 70.2
150 150 F H X S+ 0 0 12 -4,-0.6 4,-0.9 -3,-0.4 3,-0.3 0.906 105.6 61.0 -70.4 -39.2 86.0 59.5 71.9
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- xavier
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13 years 4 months ago #439
by xavier
Replied by xavier on topic seq2itp.pl seems not to work
Your problem might be in the sequence file and not the structure one ... did you check it?
XAvier.
XAvier.
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- cescoxonta
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13 years 4 months ago #446
by cescoxonta
Replied by cescoxonta on topic seq2itp.pl seems not to work
solved, it required only the sequence of secondary structure and not the whole file
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