mm_count
Posted: Tue Oct 29, 2013 2:32 am
Hi users and developers,
I am trying to use EMMA to do the kinetic analysis of Trp-cage folding. When I use the command mm_count, it comes with this:
mm_count -i ../*.disctraj -o Count.dat -s pcca_sets.ascii -lagtime 5000 -sampling slidingwindow
Command line parameters valid.
All parameters fine.
Settings
========
Sampling mode is slidingwindow
Lagtime for sampling is 5000
Using 1 microstate trajectories for input:
Reading microstate trajectories.
Reading microstate trajectories finished.
Exception in thread "main" java.lang.IllegalArgumentException: Data file is not in block form.
at sherlock.emma.sets.StatesFromFile.<init>(StatesFromFile.java:41)
at sherlock.emma.sets.StatesFromFile.<init>(StatesFromFile.java:25)
at sherlock.emma.cmd.CountCmd.run(CountCmd.java:117)
at de.martin_senne.jcommandline.AbstractCmd.check(AbstractCmd.java:33)
at de.martin_senne.jcommandline.AbstractCmd.go(AbstractCmd.java:45)
at sherlock.emma.cmd.CountCmd.main(CountCmd.java:154)
It seems I use a wrong format of pcca_sets.ascii. My pcca_sets.ascii likes this:
0
7
1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 46 48 49 50 51 52 53 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
20 45 47 54 150 151 167
Is there something wrong?
Thanks very much for your help!
Xiakun
I am trying to use EMMA to do the kinetic analysis of Trp-cage folding. When I use the command mm_count, it comes with this:
mm_count -i ../*.disctraj -o Count.dat -s pcca_sets.ascii -lagtime 5000 -sampling slidingwindow
Command line parameters valid.
All parameters fine.
Settings
========
Sampling mode is slidingwindow
Lagtime for sampling is 5000
Using 1 microstate trajectories for input:
Reading microstate trajectories.
Reading microstate trajectories finished.
Exception in thread "main" java.lang.IllegalArgumentException: Data file is not in block form.
at sherlock.emma.sets.StatesFromFile.<init>(StatesFromFile.java:41)
at sherlock.emma.sets.StatesFromFile.<init>(StatesFromFile.java:25)
at sherlock.emma.cmd.CountCmd.run(CountCmd.java:117)
at de.martin_senne.jcommandline.AbstractCmd.check(AbstractCmd.java:33)
at de.martin_senne.jcommandline.AbstractCmd.go(AbstractCmd.java:45)
at sherlock.emma.cmd.CountCmd.main(CountCmd.java:154)
It seems I use a wrong format of pcca_sets.ascii. My pcca_sets.ascii likes this:
0
7
1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 46 48 49 50 51 52 53 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
20 45 47 54 150 151 167
Is there something wrong?
Thanks very much for your help!
Xiakun