parameters.csv file for RNA modeling

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Deepak kumar
Posts: 47
Joined: Thu Dec 12, 2013 9:13 am

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Wed Jan 01, 2014 8:02 am

with continuation to last message:

https://www.dropbox.com/s/bldf5oeffr13z ... edited.pdf

Please see the highlighted region in this pdf document for the secondary structure information on 1-32.

Thanks.
cheers!
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Samuel Flores
Posts: 189
Joined: Mon Apr 30, 2007 1:06 pm

Re: parameters.csv file for RNA modeling

Post by Samuel Flores » Wed Jan 01, 2014 10:19 am

base pairs between C-U :

http://www.ncbi.nlm.nih.gov/pubmed/10852704

and U-U:

http://www.ncbi.nlm.nih.gov/pubmed/8805576

do in fact exist. In an A-form helix, the WatsonCrick base pairs are always Cis. Just check your spelling and capitalization, it should be:

baseInteraction A X WatsonCrick A Y WatsonCrick Cis

.

Let me know how this goes.

Sam
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Deepak kumar
Posts: 47
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Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Wed Jan 01, 2014 2:02 pm

Thanks Sam.

I have modified the command file for the run focusing on region 1-32:

# Put chain A and B in last.1.pdb
firstStage 3
lastStage 3
reportingInterval .5
numReportingIntervals 120
removeRigidBodyMomentum False

# - "target" fragment
RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG

# - "threaded" fragment
RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG

mobilizer Rigid B
mobilizer Rigid A 33 229

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 136 148 B 174 186 300
#threading A 149 189 B 195 235 300
#threading A 218 229 B 236 247 300



#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
#nucleicAcidDuplex A 5 13 A 26 18

baseInteraction A 5 WatsonCrick A 26 WatsonCrick Cis
baseInteraction A 8 WatsonCrick A 23 WatsonCrick Cis
baseInteraction A 9 WatsonCrick A 22 WatsonCrick Cis
baseInteraction A 10 WatsonCrick A 21 WatsonCrick Cis
baseInteraction A 11 WatsonCrick A 20 WatsonCrick Cis
baseInteraction A 12 WatsonCrick A 19 WatsonCrick Cis
baseInteraction A 13 WatsonCrick A 18 WatsonCrick Cis
baseInteraction A 149 WatsonCrick A 153 WatsonCrick Cis

for the base interaction of u-u :
baseInteraction A 7 WatsonCrick A 24 WatsonCrick Cis

# as per the paper and the structure available from the paper the u-u interaction is very much like standard WC/WC --> C5-O5-P-O3-C3. So I have put it in the Wc/Wc interaction. Please let me know if you think I am right?

for the base interaction of u-c:

N4 of Cytidine interacts with O4 of Uridine

so I think it has to be :
baseInteraction A 6 Hoogsteen A 23 SugarEdge Cis

The files are :

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

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

Please let me know about your comments.

Thanks.
cheers!
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Deepak kumar
Posts: 47
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Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Wed Jan 01, 2014 2:41 pm

with continuation to last message:

I think I made a mistake in u-u and u-c interaction:

I think for u-u it should be :

baseInteraction A 7 SugarEdge A 24 SugarEdge Cis

and for u-c it should be :

baseInteraction A 6 SugarEdge A 23 SugarEdge Cis

Please let me know about your comments.

thanks!
cheers
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Samuel Flores
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Re: parameters.csv file for RNA modeling

Post by Samuel Flores » Wed Jan 01, 2014 3:00 pm

I think they should both be WatsonCrick / WatsonCrick / Cis

The Sugar edge doesn't include N4 or O4.

Sam
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Deepak kumar
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Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Wed Jan 01, 2014 3:41 pm

Hi Sam,

Here is the result based on this command file :

# Put chain A and B in last.1.pdb
firstStage 3
lastStage 3
reportingInterval .5
numReportingIntervals 200
removeRigidBodyMomentum False

# "target" fragment
RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG

# "threaded" fragment
RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG

mobilizer Rigid B
mobilizer Rigid A 33 229
leontisWesthofInFileName parameters.csv
temperature 70.0
#Threading forces


baseInteraction A 5 WatsonCrick A 26 WatsonCrick Cis
baseInteraction A 6 WatsonCrick A 25 WatsonCrick Cis
baseInteraction A 7 WatsonCrick A 24 WatsonCrick Cis
baseInteraction A 8 WatsonCrick A 23 WatsonCrick Cis
baseInteraction A 9 WatsonCrick A 22 WatsonCrick Cis
baseInteraction A 10 WatsonCrick A 21 WatsonCrick Cis
baseInteraction A 11 WatsonCrick A 20 WatsonCrick Cis
baseInteraction A 12 WatsonCrick A 19 WatsonCrick Cis
baseInteraction A 13 WatsonCrick A 18 WatsonCrick Cis
baseInteraction A 149 WatsonCrick A 153 WatsonCrick Cis

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

last.3.pdb:
https://www.dropbox.com/s/u6gaynr1qfem24u/last.3.pdb

As we see that the region 1-32 seems to do good with the conformation but i noticed that the threading already present in last.2.pdb is disturbed in last.3.pdb even though i used :

mobilizer Rigid A 33 229

Please have alook and let me know about your comments and suggestions.

Thanks.
cheers!
Deepak
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User avatar
Samuel Flores
Posts: 189
Joined: Mon Apr 30, 2007 1:06 pm

Re: parameters.csv file for RNA modeling

Post by Samuel Flores » Thu Jan 02, 2014 2:54 am

the "mobilizer" command applies to the internal degrees of freedom in residues 33-229. It does not prevent rigid body motions of the whole body.

I guess this is my fault, since I suggested removing the "threading" commands which were holding model and template together. If you redo this with the threading commands left in, you will not have this problem. Alternatively, you could constrain the molecules to each other, e.g.:

constraint A 33 Weld B FirstResidue

Or to ground:

constraint A 33 Weld Ground
constraint B FirstResidue Weld Ground

Sam
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Deepak kumar
Posts: 47
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Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Thu Jan 02, 2014 8:08 am

Thanks Sam.

Here attached is the result of the run based on this command file :

# Put chian A and B in last.1.pdb
firstStage 3
lastStage 3
reportingInterval .5
numReportingIntervals 200
removeRigidBodyMomentum False

# "target" fragment
RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG

# "threaded" fragment
RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG

mobilizer Rigid B
mobilizer Rigid A 33 229

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 136 148 B 174 186 300
threading A 149 189 B 195 235 300
threading A 218 229 B 236 247 300

baseInteraction A 5 WatsonCrick A 26 WatsonCrick Cis
baseInteraction A 6 WatsonCrick A 25 WatsonCrick Cis
baseInteraction A 7 WatsonCrick A 24 WatsonCrick Cis
baseInteraction A 8 WatsonCrick A 23 WatsonCrick Cis
baseInteraction A 9 WatsonCrick A 22 WatsonCrick Cis
baseInteraction A 10 WatsonCrick A 21 WatsonCrick Cis
baseInteraction A 11 WatsonCrick A 20 WatsonCrick Cis
baseInteraction A 12 WatsonCrick A 19 WatsonCrick Cis
baseInteraction A 13 WatsonCrick A 18 WatsonCrick Cis
baseInteraction A 149 WatsonCrick A 153 WatsonCrick Cis
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


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

last.3.pdb:
https://www.dropbox.com/s/u6gaynr1qfem24u/last.3.pdb

trajectory.3.pdb:
https://www.dropbox.com/s/ngxw2tdldrhgb ... tory.3.pdb

As we see that the region 1-32 has taken a conformation but the position of the helix (region 1-32) is not justified as it generates clashes.

Please have a look at the files and give your suggestions on improving the result for region 1-32

Thanks.
cheers!
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User avatar
Samuel Flores
Posts: 189
Joined: Mon Apr 30, 2007 1:06 pm

Re: parameters.csv file for RNA modeling

Post by Samuel Flores » Thu Jan 02, 2014 9:26 am

I think you've done an excellent job on this. Your modeling project is now at an advanced stage. You have the secondary folded, and of course the core of the intron is now close to its final tertiary structure.

It is not only 1-32, but also the two other regions we mentioned earlier, which currently have steric clashes. The clashes themselves shouldn't concern you right now, the more immediate task is fixing the underlying issue, which is that since you don't have a template for these regions, the orientation is random and therefore incorrect almost by definition. To fix this requires not technical but rather biological skill. You have to figure out in which direction you think these helices are pointing. This should be based on tertiary contacts which might be known from biochemistry, coevolution, or crystallographic structures of additional homologs. You should pick just one of these three regions to work on next, probably the one that you understand best, i.e. is best studied in the literature. Once you have found some information that could guide your modeling, propose how MMB can turn that into 3D structure. Play with it a bit and let me know how it goes.

Sam
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Deepak kumar
Posts: 47
Joined: Thu Dec 12, 2013 9:13 am

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Thu Jan 02, 2014 3:32 pm

Hi Sam,

Thanks for that suggestion . I am on to it.

I looked in to the other 2 regions 103-137 and 188-219 . From the secondary structure information :

https://www.dropbox.com/s/bldf5oeffr13z ... edited.pdf

The region p7.1 and p7.2 (103-137)
The region p9 and p9.1 (188-219)

I added the secondary structure information in to the command file (the bold lines for these 2 regions above) :

From the interaction information obtained from the SS , i noticed that there is an interaction :
interaction 136 with 37

this interaction (present in secondary structure but not present in the modeled chain A) could explain the tilt in the region 103-137.

Here are the results of the run:

last.3.pdb:
https://www.dropbox.com/s/u6gaynr1qfem24u/last.3.pdb

last.4.pdb:
https://www.dropbox.com/s/2n7irf7rcb8i4p8/last.4.pdb

trajectory.4.pdb:
https://www.dropbox.com/s/o76nwlwil3chw ... tory.4.pdb

In the result we see that the something wrong happened for the regions 103-137 and 188-219 even though base interactions have been mentioned in the command file. Is it because the run has not finished yet and I should run it for more number of reporting intervals?

command file :

# Put in last.1.pdb
firstStage 4
lastStage 4
reportingInterval .5
numReportingIntervals 5000
removeRigidBodyMomentum False

# -- "target" fragment
RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG

# "threaded" fragment
RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG

mobilizer Rigid B
mobilizer Rigid A 1 102
mobilizer Rigid A 138 187
mobilizer Rigid A 220 229
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 136 148 B 174 186 300
threading A 149 189 B 195 235 300
threading A 218 229 B 236 247 300


#baseInteraction A 5 WatsonCrick A 26 WatsonCrick Cis
#baseInteraction A 6 WatsonCrick A 25 WatsonCrick Cis
#baseInteraction A 7 WatsonCrick A 24 WatsonCrick Cis
#baseInteraction A 8 WatsonCrick A 23 WatsonCrick Cis
#baseInteraction A 9 WatsonCrick A 22 WatsonCrick Cis
#baseInteraction A 10 WatsonCrick A 21 WatsonCrick Cis
#baseInteraction A 11 WatsonCrick A 20 WatsonCrick Cis
#baseInteraction A 12 WatsonCrick A 19 WatsonCrick Cis
#baseInteraction A 13 WatsonCrick A 18 WatsonCrick Cis
#baseInteraction A 149 WatsonCrick A 153 WatsonCrick Cis
baseInteraction A 103 WatsonCrick A 165 WatsonCrick Cis
baseInteraction A 104 WatsonCrick A 115 WatsonCrick Cis
baseInteraction A 105 WatsonCrick A 114 WatsonCrick Cis
baseInteraction A 106 WatsonCrick A 113 WatsonCrick Cis
baseInteraction A 107 WatsonCrick A 112 WatsonCrick Cis
baseInteraction A 37 WatsonCrick A 136 WatsonCrick Cis
baseInteraction A 117 WatsonCrick A 134 WatsonCrick Cis
baseInteraction A 118 WatsonCrick A 133 WatsonCrick Cis
baseInteraction A 119 WatsonCrick A 132 WatsonCrick Cis
baseInteraction A 120 WatsonCrick A 131 WatsonCrick Cis
baseInteraction A 121 WatsonCrick A 130 WatsonCrick Cis
baseInteraction A 122 WatsonCrick A 129 WatsonCrick Cis
baseInteraction A 123 WatsonCrick A 128 WatsonCrick Cis
baseInteraction A 188 WatsonCrick A 179 WatsonCrick Cis
baseInteraction A 189 WatsonCrick A 178 WatsonCrick Cis
baseInteraction A 190 WatsonCrick A 177 WatsonCrick Cis
baseInteraction A 191 WatsonCrick A 176 WatsonCrick Cis
baseInteraction A 195 WatsonCrick A 217 WatsonCrick Cis
baseInteraction A 196 WatsonCrick A 216 WatsonCrick Cis
baseInteraction A 197 WatsonCrick A 215 WatsonCrick Cis
baseInteraction A 198 WatsonCrick A 214 WatsonCrick Cis
baseInteraction A 199 WatsonCrick A 213 WatsonCrick Cis
baseInteraction A 200 WatsonCrick A 212 WatsonCrick Cis
baseInteraction A 201 WatsonCrick A 211 WatsonCrick Cis
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


please let me know about your suggestions?

Thanks.
cheers!
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