parameters.csv file for RNA modeling

[Samuel Flores]

You're not finished with the region around residue 145, chain A. You're trying to thread chain A residue 146 to chain B residue 192, when I believe it should be threaded to chain B residue 182. You are still assuming that the stem-loops in chain A and B are the same length in this region! It's pretty clear to me that the stem loop in chain A is shorter. Look closely at what you're doing using pencil and paper. Compare the secondary structure diagrams to correct your alignment. Make sure the threading makes sense in terms of the Watson-Crick base pairs that need to form in chain A.

As you'll see in my manuscript, doing the threading correctly requires lots of biological thought.

Sam

[Samuel Flores]

I think you're making great progress by the way.

Try not to refer to the crystal structure of chain A if you have it. Do read lots of papers, particularly about the biochemistry. Look for evidence of interactions that would justify modeling decisions, in places where there is not enough information or chain B structure to do threading.

Sam

[Deepak kumar]

Hi Sam,

Thanks you so much for your valuable suggestions. They are very useful for me.

I have tried to improve the threading/alignment. I am attaching the result based on this run below : Please have a look . I hope you agree with me on this threading . If not please let me know.

I have tried to fix the region 142 - 158 in this run. The other regions are 1- 32 and 103 - 137 and 188 - 219.

In the result, I see that the flexible regions dont make much movements although they are not fixed?

# Put chain A and B in last.1.pdb
firstStage 2
lastStage 2
reportingInterval .5
numReportingIntervals 200
removeRigidBodyMomentum False

#- "target" fragment
RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG

# "threaded" fragment
RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG

#constrainToGround A 1
#constrainToGround B 1
#constraint A 1 Weld A 229
#constraint B 1 Weld B 247
mobilizer Rigid B
#mobilizer Rigid A 33 102
#mobilizer Rigid A 139 229
#contact AllHeavyAtomSterics A 1 229
leontisWesthofInFileName parameters.csv
temperature 70.0
#Threading forces
threading A 30 50 B 1 21 300
threading A 51 80 B 104 133 300
threading A 81 104 B 150 173 300
#threading A 138 145 B 174 181 300
threading A 136 148 B 174 186 300
threading A 149 189 B 195 235 300
#threading A 146 189 B 192 235 300
threading A 218 229 B 236 247 300

#mobilizer Rigid A 32 102
#mobilizer Rigid A 140 229
#mobilizer Rigid A 138 229


mobilizer Rigid
mobilizer Default A 219 219
singleBondMobility A 218 O3* Free A 219 P
singleBondMobility A 219 O3* Free A 220 P

mobilizer Rigid
mobilizer Default A 189 189
singleBondMobility A 188 O3* Free A 189 P
singleBondMobility A 189 O3* Free A 190 P


mobilizer Rigid
mobilizer Default A 150 150
singleBondMobility A 149 O3* Free A 150 P
singleBondMobility A 150 O3* Free A 151 P

mobilizer Rigid
mobilizer Default A 80 80
singleBondMobility A 79 O3* Free A 80 P
singleBondMobility A 80 O3* Free A 81 P

mobilizer Rigid
mobilizer Default A 142 158

baseInteraction A 30 Superimpose B 1 Superimpose Cis
baseInteraction A 31 Superimpose B 2 Superimpose Cis
baseInteraction A 32 Superimpose B 3 Superimpose Cis
baseInteraction A 33 Superimpose B 4 Superimpose Cis
baseInteraction A 34 Superimpose B 5 Superimpose Cis
baseInteraction A 35 Superimpose B 6 Superimpose Cis
baseInteraction A 36 Superimpose B 7 Superimpose Cis
baseInteraction A 37 Superimpose B 8 Superimpose Cis
baseInteraction A 38 Superimpose B 9 Superimpose Cis
baseInteraction A 39 Superimpose B 10 Superimpose Cis
baseInteraction A 40 Superimpose B 11 Superimpose Cis
baseInteraction A 41 Superimpose B 12 Superimpose Cis
baseInteraction A 42 Superimpose B 13 Superimpose Cis
baseInteraction A 43 Superimpose B 14 Superimpose Cis
baseInteraction A 44 Superimpose B 15 Superimpose Cis
baseInteraction A 45 Superimpose B 16 Superimpose Cis
baseInteraction A 46 Superimpose B 17 Superimpose Cis
baseInteraction A 47 Superimpose B 18 Superimpose Cis
baseInteraction A 48 Superimpose B 19 Superimpose Cis
baseInteraction A 49 Superimpose B 20 Superimpose Cis
baseInteraction A 50 Superimpose B 21 Superimpose Cis
baseInteraction A 51 Superimpose B 104 Superimpose Cis
baseInteraction A 52 Superimpose B 105 Superimpose Cis
baseInteraction A 53 Superimpose B 106 Superimpose Cis
baseInteraction A 54 Superimpose B 107 Superimpose Cis
baseInteraction A 55 Superimpose B 108 Superimpose Cis
baseInteraction A 56 Superimpose B 109 Superimpose Cis
baseInteraction A 57 Superimpose B 110 Superimpose Cis
baseInteraction A 58 Superimpose B 111 Superimpose Cis
baseInteraction A 59 Superimpose B 112 Superimpose Cis
baseInteraction A 60 Superimpose B 113 Superimpose Cis
baseInteraction A 61 Superimpose B 114 Superimpose Cis
baseInteraction A 62 Superimpose B 115 Superimpose Cis
baseInteraction A 63 Superimpose B 116 Superimpose Cis
baseInteraction A 64 Superimpose B 117 Superimpose Cis
baseInteraction A 65 Superimpose B 118 Superimpose Cis
baseInteraction A 66 Superimpose B 119 Superimpose Cis
baseInteraction A 67 Superimpose B 120 Superimpose Cis
baseInteraction A 68 Superimpose B 121 Superimpose Cis
baseInteraction A 69 Superimpose B 122 Superimpose Cis
baseInteraction A 70 Superimpose B 123 Superimpose Cis
baseInteraction A 71 Superimpose B 124 Superimpose Cis
baseInteraction A 72 Superimpose B 125 Superimpose Cis
baseInteraction A 73 Superimpose B 126 Superimpose Cis
baseInteraction A 74 Superimpose B 127 Superimpose Cis
baseInteraction A 75 Superimpose B 128 Superimpose Cis
baseInteraction A 76 Superimpose B 129 Superimpose Cis
baseInteraction A 77 Superimpose B 130 Superimpose Cis
baseInteraction A 78 Superimpose B 131 Superimpose Cis
baseInteraction A 79 Superimpose B 132 Superimpose Cis
baseInteraction A 80 Superimpose B 133 Superimpose Cis
baseInteraction A 81 Superimpose B 150 Superimpose Cis
baseInteraction A 82 Superimpose B 151 Superimpose Cis
baseInteraction A 83 Superimpose B 152 Superimpose Cis
baseInteraction A 84 Superimpose B 153 Superimpose Cis
baseInteraction A 85 Superimpose B 154 Superimpose Cis
baseInteraction A 86 Superimpose B 155 Superimpose Cis
baseInteraction A 87 Superimpose B 156 Superimpose Cis
baseInteraction A 88 Superimpose B 157 Superimpose Cis
baseInteraction A 89 Superimpose B 158 Superimpose Cis
baseInteraction A 90 Superimpose B 159 Superimpose Cis
baseInteraction A 91 Superimpose B 160 Superimpose Cis
baseInteraction A 92 Superimpose B 161 Superimpose Cis
baseInteraction A 93 Superimpose B 162 Superimpose Cis
baseInteraction A 94 Superimpose B 163 Superimpose Cis
baseInteraction A 95 Superimpose B 164 Superimpose Cis
baseInteraction A 96 Superimpose B 165 Superimpose Cis
baseInteraction A 97 Superimpose B 166 Superimpose Cis
baseInteraction A 98 Superimpose B 167 Superimpose Cis
baseInteraction A 99 Superimpose B 168 Superimpose Cis
baseInteraction A 100 Superimpose B 169 Superimpose Cis
baseInteraction A 101 Superimpose B 170 Superimpose Cis
baseInteraction A 102 Superimpose B 171 Superimpose Cis
baseInteraction A 103 Superimpose B 172 Superimpose Cis
baseInteraction A 104 Superimpose B 173 Superimpose Cis
baseInteraction A 136 Superimpose B 174 Superimpose Cis
baseInteraction A 137 Superimpose B 175 Superimpose Cis
baseInteraction A 138 Superimpose B 176 Superimpose Cis
baseInteraction A 139 Superimpose B 177 Superimpose Cis
baseInteraction A 140 Superimpose B 178 Superimpose Cis
baseInteraction A 141 Superimpose B 179 Superimpose Cis
baseInteraction A 142 Superimpose B 180 Superimpose Cis
baseInteraction A 143 Superimpose B 181 Superimpose Cis
baseInteraction A 144 Superimpose B 182 Superimpose Cis
baseInteraction A 145 Superimpose B 183 Superimpose Cis
baseInteraction A 146 Superimpose B 184 Superimpose Cis
baseInteraction A 147 Superimpose B 185 Superimpose Cis
baseInteraction A 148 Superimpose B 186 Superimpose Cis
baseInteraction A 149 Superimpose B 195 Superimpose Cis
baseInteraction A 150 Superimpose B 196 Superimpose Cis
baseInteraction A 151 Superimpose B 197 Superimpose Cis
baseInteraction A 152 Superimpose B 198 Superimpose Cis
baseInteraction A 153 Superimpose B 199 Superimpose Cis
baseInteraction A 154 Superimpose B 200 Superimpose Cis
baseInteraction A 155 Superimpose B 201 Superimpose Cis
baseInteraction A 156 Superimpose B 202 Superimpose Cis
baseInteraction A 157 Superimpose B 203 Superimpose Cis
baseInteraction A 158 Superimpose B 204 Superimpose Cis
baseInteraction A 159 Superimpose B 205 Superimpose Cis
baseInteraction A 160 Superimpose B 206 Superimpose Cis
baseInteraction A 161 Superimpose B 207 Superimpose Cis
baseInteraction A 162 Superimpose B 208 Superimpose Cis
baseInteraction A 163 Superimpose B 209 Superimpose Cis
baseInteraction A 164 Superimpose B 210 Superimpose Cis
baseInteraction A 165 Superimpose B 211 Superimpose Cis
baseInteraction A 166 Superimpose B 212 Superimpose Cis
baseInteraction A 167 Superimpose B 213 Superimpose Cis
baseInteraction A 168 Superimpose B 214 Superimpose Cis
baseInteraction A 169 Superimpose B 215 Superimpose Cis
baseInteraction A 170 Superimpose B 216 Superimpose Cis
baseInteraction A 171 Superimpose B 217 Superimpose Cis
baseInteraction A 172 Superimpose B 218 Superimpose Cis
baseInteraction A 173 Superimpose B 219 Superimpose Cis
baseInteraction A 174 Superimpose B 220 Superimpose Cis
baseInteraction A 175 Superimpose B 221 Superimpose Cis
baseInteraction A 176 Superimpose B 222 Superimpose Cis
baseInteraction A 177 Superimpose B 223 Superimpose Cis
baseInteraction A 178 Superimpose B 224 Superimpose Cis
baseInteraction A 179 Superimpose B 225 Superimpose Cis
baseInteraction A 180 Superimpose B 226 Superimpose Cis
baseInteraction A 181 Superimpose B 227 Superimpose Cis
baseInteraction A 182 Superimpose B 228 Superimpose Cis
baseInteraction A 183 Superimpose B 229 Superimpose Cis
baseInteraction A 184 Superimpose B 230 Superimpose Cis
baseInteraction A 185 Superimpose B 231 Superimpose Cis
baseInteraction A 186 Superimpose B 232 Superimpose Cis
baseInteraction A 187 Superimpose B 233 Superimpose Cis
baseInteraction A 188 Superimpose B 234 Superimpose Cis
baseInteraction A 189 Superimpose B 235 Superimpose Cis
baseInteraction A 219 Superimpose B 237 Superimpose Cis
baseInteraction A 220 Superimpose B 238 Superimpose Cis
baseInteraction A 221 Superimpose B 239 Superimpose Cis
baseInteraction A 222 Superimpose B 240 Superimpose Cis
baseInteraction A 223 Superimpose B 241 Superimpose Cis
baseInteraction A 224 Superimpose B 242 Superimpose Cis
baseInteraction A 225 Superimpose B 243 Superimpose Cis
baseInteraction A 226 Superimpose B 244 Superimpose Cis
baseInteraction A 227 Superimpose B 245 Superimpose Cis
baseInteraction A 228 Superimpose B 246 Superimpose Cis
baseInteraction A 229 Superimpose B 247 Superimpose Cis

last.1.pdb:
https://www.dropbox.com/s/drt9q3f4njei3a2/last.1.pdb

last.2.pdb:
https://www.dropbox.com/s/e2zqqq0ecrelzxu/last.2.pdb

trajectory.2.pdb:
https://www.dropbox.com/s/ncuwqbgsecww8 ... tory.2.pdb

Thanks.
cheers!

[Samuel Flores]

Is there not an A-U, Watson-Crick base pairing interaction between residues 149 and 153 on chain A? Other than that, it looks great!

it doesn't surprise me that your motion is restricted to residues 142-158. The other flexibility zones are just to repair the bad geometries, which you did in earlier runs. I would get rid of those flexibility zones now.

I would suggest doing something about residues 1-32 as a next step. That's the only part that has no structure at all. Then we can start doing domain motions to adjust the three regions you mentioned. How did you get the 3D structure of regions 103 - 137 and 188 - 219? Did you use an additional template?

This is a group I Intron, correct?

[Samuel Flores]

Are you a PhD student at the Indian Institute of Science? When do you graduate?

[Deepak kumar]

Thanks much again Sam.

Yes, you are right about the WC between 149 and 153 . I will use MMb "baseinteraction" to solve this problem.

Regarding the regions 103-137 and 188-219 , I have not used additional template. These regions as we see are the insertions in chain A when aligned to chain B. I used a program called ModeRNA to generate the initial model (as i mentioned to you before). The initial structure of these 2 regions (103-137 , 188-219) that we see are from the program ModeRNA. The region 1-32 is the isolated one having no region of chain B aligned to it.

Now, I am concentrating on the region 1-32 . For the same, this is the command file I have prepared. Can you please have a look and let me know about your comments.

# Put chain A and B in last.1.pdb

firstStage 2

lastStage 2

reportingInterval .5

numReportingIntervals 200

removeRigidBodyMomentum False



# "target" fragment

RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG



# "threaded" fragment

RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG



#constrainToGround A 1

#constrainToGround B 1

#constraint A 1 Weld A 229

#constraint B 1 Weld B 247

mobilizer Rigid B

#mobilizer Rigid A 33 102

#mobilizer Rigid A 139 229

#contact AllHeavyAtomSterics A 1 229

leontisWesthofInFileName parameters.csv

temperature 70.0

#Threading forces

threading A 30 50 B 1 21 300

threading A 51 80 B 104 133 300

threading A 81 104 B 150 173 300

#threading A 138 145 B 174 181 300

threading A 136 148 B 174 186 300

threading A 149 189 B 195 235 300

#threading A 146 189 B 192 235 300

threading A 218 229 B 236 247 300



#mobilizer Rigid A 32 102

#mobilizer Rigid A 140 229

#mobilizer Rigid A 138 229





mobilizer Rigid

mobilizer Default A 219 219

singleBondMobility A 218 O3* Free A 219 P

singleBondMobility A 219 O3* Free A 220 P



mobilizer Rigid

mobilizer Default A 189 189

singleBondMobility A 188 O3* Free A 189 P

singleBondMobility A 189 O3* Free A 190 P





mobilizer Rigid

mobilizer Default A 150 150

singleBondMobility A 149 O3* Free A 150 P

singleBondMobility A 150 O3* Free A 151 P



mobilizer Rigid

mobilizer Default A 80 80

singleBondMobility A 79 O3* Free A 80 P

singleBondMobility A 80 O3* Free A 81 P



mobilizer Rigid

mobilizer Default A 142 158



mobilizer Rigid

mobilizer Default A 1 32

baseInteraction A 149 WatsonCrick A 153 WatsonCrick Cis #for the WC/WC interaction between 149 and 153
baseInteraction A 30 Superimpose B 1 Superimpose Cis

baseInteraction A 31 Superimpose B 2 Superimpose Cis

baseInteraction A 32 Superimpose B 3 Superimpose Cis

baseInteraction A 33 Superimpose B 4 Superimpose Cis

baseInteraction A 34 Superimpose B 5 Superimpose Cis

baseInteraction A 35 Superimpose B 6 Superimpose Cis

baseInteraction A 36 Superimpose B 7 Superimpose Cis

baseInteraction A 37 Superimpose B 8 Superimpose Cis

baseInteraction A 38 Superimpose B 9 Superimpose Cis

baseInteraction A 39 Superimpose B 10 Superimpose Cis

baseInteraction A 40 Superimpose B 11 Superimpose Cis

baseInteraction A 41 Superimpose B 12 Superimpose Cis

baseInteraction A 42 Superimpose B 13 Superimpose Cis

baseInteraction A 43 Superimpose B 14 Superimpose Cis

baseInteraction A 44 Superimpose B 15 Superimpose Cis

baseInteraction A 45 Superimpose B 16 Superimpose Cis

baseInteraction A 46 Superimpose B 17 Superimpose Cis

baseInteraction A 47 Superimpose B 18 Superimpose Cis

baseInteraction A 48 Superimpose B 19 Superimpose Cis

baseInteraction A 49 Superimpose B 20 Superimpose Cis

baseInteraction A 50 Superimpose B 21 Superimpose Cis

baseInteraction A 51 Superimpose B 104 Superimpose Cis

baseInteraction A 52 Superimpose B 105 Superimpose Cis

baseInteraction A 53 Superimpose B 106 Superimpose Cis

baseInteraction A 54 Superimpose B 107 Superimpose Cis

baseInteraction A 55 Superimpose B 108 Superimpose Cis

baseInteraction A 56 Superimpose B 109 Superimpose Cis

baseInteraction A 57 Superimpose B 110 Superimpose Cis

baseInteraction A 58 Superimpose B 111 Superimpose Cis

baseInteraction A 59 Superimpose B 112 Superimpose Cis

baseInteraction A 60 Superimpose B 113 Superimpose Cis

baseInteraction A 61 Superimpose B 114 Superimpose Cis

baseInteraction A 62 Superimpose B 115 Superimpose Cis

baseInteraction A 63 Superimpose B 116 Superimpose Cis

baseInteraction A 64 Superimpose B 117 Superimpose Cis

baseInteraction A 65 Superimpose B 118 Superimpose Cis

baseInteraction A 66 Superimpose B 119 Superimpose Cis

baseInteraction A 67 Superimpose B 120 Superimpose Cis

baseInteraction A 68 Superimpose B 121 Superimpose Cis

baseInteraction A 69 Superimpose B 122 Superimpose Cis

baseInteraction A 70 Superimpose B 123 Superimpose Cis

baseInteraction A 71 Superimpose B 124 Superimpose Cis

baseInteraction A 72 Superimpose B 125 Superimpose Cis

baseInteraction A 73 Superimpose B 126 Superimpose Cis

baseInteraction A 74 Superimpose B 127 Superimpose Cis

baseInteraction A 75 Superimpose B 128 Superimpose Cis

baseInteraction A 76 Superimpose B 129 Superimpose Cis

baseInteraction A 77 Superimpose B 130 Superimpose Cis

baseInteraction A 78 Superimpose B 131 Superimpose Cis

baseInteraction A 79 Superimpose B 132 Superimpose Cis

baseInteraction A 80 Superimpose B 133 Superimpose Cis

baseInteraction A 81 Superimpose B 150 Superimpose Cis

baseInteraction A 82 Superimpose B 151 Superimpose Cis

baseInteraction A 83 Superimpose B 152 Superimpose Cis

baseInteraction A 84 Superimpose B 153 Superimpose Cis

baseInteraction A 85 Superimpose B 154 Superimpose Cis

baseInteraction A 86 Superimpose B 155 Superimpose Cis

baseInteraction A 87 Superimpose B 156 Superimpose Cis

baseInteraction A 88 Superimpose B 157 Superimpose Cis

baseInteraction A 89 Superimpose B 158 Superimpose Cis

baseInteraction A 90 Superimpose B 159 Superimpose Cis

baseInteraction A 91 Superimpose B 160 Superimpose Cis

baseInteraction A 92 Superimpose B 161 Superimpose Cis

baseInteraction A 93 Superimpose B 162 Superimpose Cis

baseInteraction A 94 Superimpose B 163 Superimpose Cis

baseInteraction A 95 Superimpose B 164 Superimpose Cis

baseInteraction A 96 Superimpose B 165 Superimpose Cis

baseInteraction A 97 Superimpose B 166 Superimpose Cis

baseInteraction A 98 Superimpose B 167 Superimpose Cis

baseInteraction A 99 Superimpose B 168 Superimpose Cis

baseInteraction A 100 Superimpose B 169 Superimpose Cis

baseInteraction A 101 Superimpose B 170 Superimpose Cis

baseInteraction A 102 Superimpose B 171 Superimpose Cis

baseInteraction A 103 Superimpose B 172 Superimpose Cis

baseInteraction A 104 Superimpose B 173 Superimpose Cis

baseInteraction A 136 Superimpose B 174 Superimpose Cis

baseInteraction A 137 Superimpose B 175 Superimpose Cis

baseInteraction A 138 Superimpose B 176 Superimpose Cis

baseInteraction A 139 Superimpose B 177 Superimpose Cis

baseInteraction A 140 Superimpose B 178 Superimpose Cis

baseInteraction A 141 Superimpose B 179 Superimpose Cis

baseInteraction A 142 Superimpose B 180 Superimpose Cis

baseInteraction A 143 Superimpose B 181 Superimpose Cis

baseInteraction A 144 Superimpose B 182 Superimpose Cis

baseInteraction A 145 Superimpose B 183 Superimpose Cis

baseInteraction A 146 Superimpose B 184 Superimpose Cis

baseInteraction A 147 Superimpose B 185 Superimpose Cis

baseInteraction A 148 Superimpose B 186 Superimpose Cis

baseInteraction A 149 Superimpose B 195 Superimpose Cis

baseInteraction A 150 Superimpose B 196 Superimpose Cis

baseInteraction A 151 Superimpose B 197 Superimpose Cis

baseInteraction A 152 Superimpose B 198 Superimpose Cis

baseInteraction A 153 Superimpose B 199 Superimpose Cis

baseInteraction A 154 Superimpose B 200 Superimpose Cis

baseInteraction A 155 Superimpose B 201 Superimpose Cis

baseInteraction A 156 Superimpose B 202 Superimpose Cis

baseInteraction A 157 Superimpose B 203 Superimpose Cis

baseInteraction A 158 Superimpose B 204 Superimpose Cis

baseInteraction A 159 Superimpose B 205 Superimpose Cis

baseInteraction A 160 Superimpose B 206 Superimpose Cis

baseInteraction A 161 Superimpose B 207 Superimpose Cis

baseInteraction A 162 Superimpose B 208 Superimpose Cis

baseInteraction A 163 Superimpose B 209 Superimpose Cis

baseInteraction A 164 Superimpose B 210 Superimpose Cis

baseInteraction A 165 Superimpose B 211 Superimpose Cis

baseInteraction A 166 Superimpose B 212 Superimpose Cis

baseInteraction A 167 Superimpose B 213 Superimpose Cis

baseInteraction A 168 Superimpose B 214 Superimpose Cis

baseInteraction A 169 Superimpose B 215 Superimpose Cis

baseInteraction A 170 Superimpose B 216 Superimpose Cis

baseInteraction A 171 Superimpose B 217 Superimpose Cis

baseInteraction A 172 Superimpose B 218 Superimpose Cis

baseInteraction A 173 Superimpose B 219 Superimpose Cis

baseInteraction A 174 Superimpose B 220 Superimpose Cis

baseInteraction A 175 Superimpose B 221 Superimpose Cis

baseInteraction A 176 Superimpose B 222 Superimpose Cis

baseInteraction A 177 Superimpose B 223 Superimpose Cis

baseInteraction A 178 Superimpose B 224 Superimpose Cis

baseInteraction A 179 Superimpose B 225 Superimpose Cis

baseInteraction A 180 Superimpose B 226 Superimpose Cis

baseInteraction A 181 Superimpose B 227 Superimpose Cis

baseInteraction A 182 Superimpose B 228 Superimpose Cis

baseInteraction A 183 Superimpose B 229 Superimpose Cis

baseInteraction A 184 Superimpose B 230 Superimpose Cis

baseInteraction A 185 Superimpose B 231 Superimpose Cis

baseInteraction A 186 Superimpose B 232 Superimpose Cis

baseInteraction A 187 Superimpose B 233 Superimpose Cis

baseInteraction A 188 Superimpose B 234 Superimpose Cis

baseInteraction A 189 Superimpose B 235 Superimpose Cis

baseInteraction A 218 Superimpose B 236 Superimpose Cis

baseInteraction A 219 Superimpose B 237 Superimpose Cis

baseInteraction A 220 Superimpose B 238 Superimpose Cis

baseInteraction A 221 Superimpose B 239 Superimpose Cis

baseInteraction A 222 Superimpose B 240 Superimpose Cis

baseInteraction A 223 Superimpose B 241 Superimpose Cis

baseInteraction A 224 Superimpose B 242 Superimpose Cis

baseInteraction A 225 Superimpose B 243 Superimpose Cis

baseInteraction A 226 Superimpose B 244 Superimpose Cis

baseInteraction A 227 Superimpose B 245 Superimpose Cis

baseInteraction A 228 Superimpose B 246 Superimpose Cis

baseInteraction A 229 Superimpose B 247 Superimpose Cis

Yes, this is group 1 intron.

If you could please give your email ID where I can contact you? I can explain my status to you better. My email is "deepak.k.choubey@gmail.com" and if am right this is your email "samuel.flores@icm.uu.se"? (found it in "http://xray.bmc.uu.se/~flores/HOME.html")

Thanks.
cheers!
Deepak

[Deepak kumar]

and continuing the last message:

This is the result based on the command file in the last message:

last.1.pdb
https://www.dropbox.com/s/drt9q3f4njei3a2/last.1.pdb

last.2.pdb:
https://www.dropbox.com/s/e2zqqq0ecrelzxu/last.2.pdb

trajectory.2.pdb:
https://www.dropbox.com/s/ncuwqbgsecww8 ... tory.2.pdb

I guess i am missing some parameters to be added to the command file because the region 1-32 I am trying to remodel does not seem to be working well.

Could you please have alook at the command file in last message and give your suggestions on what could be wrong in the run?

Thanks.
cheers!
Deepak

PS : A very Happy new year !!

[Samuel Flores]

Hi Deepak,

You haven't done anything with residues 1-32. All you did was add flexibility, but no base pairing or other forces. MMB is not a de novo modeling code! You should gather all the available information on secondary and tertiary contacts in this region. The secondary structure should be easy, just to MFOLD if nothing else is available. But surely the secondary structure is published.

I repeat my earlier suggestion .. get rid of the commands corresponding to regions that are already converged. I find this generates cognitive overhead.

Sam

[Deepak kumar]

Thanks Sam.

I somehow skipped the part of providing information about the interactions for region 1-32, was thinking have already mentioned them in the command file. I am doing it and will let you know when the run is finished.

cheers!
Deepak

[Deepak kumar]

Hi Sam,

I have the secondary structure information for chain A model region 1-32.

This highlighted region in this pdf is the region 1-32:
https://www.dropbox.com/s/nd26y42zk755g ... %2C2-1.pfl

I would like to ask that :

for the standard WC/Wc interaction as seen in the secondary structure notation I can use

baseinteraction A X watsoncrick A Y watconcrick cis/trans

but how to know if it's a cis/trans conformation?

and for the pairs like u-c, c-u , u-u, c-c.. how to present these interactions in MMB ?

Basically, how the available secondary structure information can be presented in MMB so as to obtain a suitable structural conformation?

I hope, I am clear with my query. It would be nice if you could please give your comments on this?

Thanks.
cheers!
Deepak