parameters.csv file for RNA modeling

Easily model the structure and dynamics of macromolecules
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User avatar
Deepak kumar
Posts: 47
Joined: Thu Dec 12, 2013 9:13 am

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Sat Dec 21, 2013 7:19 pm

Hi Sam,

I ran the process with new MMB package and here is the result. I removed the problem causing residues from the model chain A of the pdb file "last.1.pdb ".

but there is some problem . When looking at the trajectory.2.pdb or last.2.pdb file I see some of the residues floating away from the structure. These residues are the ones I deleted from the chain A of pdb file last.1.pdb.

The files are here :

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

The command file is :

# Put chain A and B in last.1.pdb
firstStage 2
lastStage 2
reportingInterval .5
numReportingIntervals 160
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 40.0
#Threading forces
threading A 32 48 B 3 19 300
threading A 53 78 B 106 131 300
threading A 83 102 B 152 171 300
threading A 139 160 B 176 197 300
threading A 165 187 B 211 233 300
threading A 220 229 B 238 247 300

mobilizer Rigid A 33 102
mobilizer Rigid A 139 229

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 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 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 139 Superimpose B 176 Superimpose Cis
baseInteraction A 140 Superimpose B 177 Superimpose Cis
baseInteraction A 141 Superimpose B 178 Superimpose Cis
baseInteraction A 142 Superimpose B 179 Superimpose Cis
baseInteraction A 143 Superimpose B 180 Superimpose Cis
baseInteraction A 144 Superimpose B 181 Superimpose Cis
baseInteraction A 145 Superimpose B 182 Superimpose Cis
baseInteraction A 146 Superimpose B 183 Superimpose Cis
baseInteraction A 147 Superimpose B 184 Superimpose Cis
baseInteraction A 148 Superimpose B 185 Superimpose Cis
baseInteraction A 149 Superimpose B 186 Superimpose Cis
baseInteraction A 150 Superimpose B 187 Superimpose Cis
baseInteraction A 151 Superimpose B 188 Superimpose Cis
baseInteraction A 152 Superimpose B 189 Superimpose Cis
baseInteraction A 153 Superimpose B 190 Superimpose Cis
baseInteraction A 154 Superimpose B 191 Superimpose Cis
baseInteraction A 155 Superimpose B 192 Superimpose Cis
baseInteraction A 156 Superimpose B 193 Superimpose Cis
baseInteraction A 157 Superimpose B 194 Superimpose Cis
baseInteraction A 158 Superimpose B 195 Superimpose Cis
baseInteraction A 159 Superimpose B 196 Superimpose Cis
baseInteraction A 160 Superimpose B 197 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 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 have a look.

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 » Sun Dec 22, 2013 7:28 am

This is not unexpected. When MMB guesses atom coordinates in this way, it does it assuming an extended conformation of the biopolymer, whereas your molecule is quite compactly folded. This is why at time zero you see the "problem" residues making a straight line -- this is the way the extended chain would have gone. Anyway, it's easy enough to fix. Just set the bonds connecting 03* to P on each end of each problem residue to bond mobility "Free". Then the Amber99 force field will take care of equilibrating the bond length to something more reasonable. You also need to make sure the rest of that residue is flexible ("Default" bond mobility is fine) for best results. Here is your input file, where I've added the commands you need to fix the geometry for residue 145:

firstStage 2
lastStage 2
reportingInterval .5
numReportingIntervals 160
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

#### here is what you need to do to fix the bond geometry around residue 145:
mobilizer Rigid
mobilizer Default A 145 145
singleBondMobility A 144 O3* Free A 145 P
singleBondMobility A 145 O3* Free A 146 P
####

Just add similar commands for the other problem residues. You should be able to do all of them in one shot.

At one point I did figure out how to get the atom guessing feature to connect the ends properly, and I can probably do that again, but I'm afraid I can't get on that right now.

Anyway, let me know how this goes and we'll discuss the next step.

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

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Sun Dec 22, 2013 12:08 pm

Thanks Sam.

Here are the results of the run based on this command file :

# Put chain A and B in last.1.pdb
firstStage 2
lastStage 2
reportingInterval .5
numReportingIntervals 160
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 40.0
#Threading forces
threading A 32 48 B 3 19 300
threading A 53 78 B 106 131 300
threading A 83 102 B 152 171 300
threading A 139 160 B 176 197 300
threading A 165 187 B 211 233 300
threading A 220 229 B 238 247 300

mobilizer Rigid A 33 102 #to morph the region 1-32 only
mobilizer Rigid A 139 229 # to morph the region 103-138 only

mobilizer Rigid
mobilizer Default A 145 145
singleBondMobility A 144 O3* Free A 145 P
singleBondMobility A 145 O3* Free A 146 P

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 147 147
singleBondMobility A 146 O3* Free A 147 P
singleBondMobility A 147 O3* Free A 148 P

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

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 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 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 139 Superimpose B 176 Superimpose Cis
baseInteraction A 140 Superimpose B 177 Superimpose Cis
baseInteraction A 141 Superimpose B 178 Superimpose Cis
baseInteraction A 142 Superimpose B 179 Superimpose Cis
baseInteraction A 143 Superimpose B 180 Superimpose Cis
baseInteraction A 144 Superimpose B 181 Superimpose Cis
baseInteraction A 145 Superimpose B 182 Superimpose Cis
baseInteraction A 146 Superimpose B 183 Superimpose Cis
baseInteraction A 147 Superimpose B 184 Superimpose Cis
baseInteraction A 148 Superimpose B 185 Superimpose Cis
baseInteraction A 149 Superimpose B 186 Superimpose Cis
baseInteraction A 150 Superimpose B 187 Superimpose Cis
baseInteraction A 151 Superimpose B 188 Superimpose Cis
baseInteraction A 152 Superimpose B 189 Superimpose Cis
baseInteraction A 153 Superimpose B 190 Superimpose Cis
baseInteraction A 154 Superimpose B 191 Superimpose Cis
baseInteraction A 155 Superimpose B 192 Superimpose Cis
baseInteraction A 156 Superimpose B 193 Superimpose Cis
baseInteraction A 157 Superimpose B 194 Superimpose Cis
baseInteraction A 158 Superimpose B 195 Superimpose Cis
baseInteraction A 159 Superimpose B 196 Superimpose Cis
baseInteraction A 160 Superimpose B 197 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 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

When we see the last.2.pdb and trajectory.2.pdb, there dont seem to be much changes in the morphing/conformation compared to last.1.pdb.
Is it because the threading is not finished yet? or some other reason? because there are not much changes in the trajectories too.

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!
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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 » Sat Dec 28, 2013 3:13 am

Hi Deepak,

Did I answer your last question? I believe I did, but now I don't see my response on the forum. How did things turn out?

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

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Sat Dec 28, 2013 5:06 am

Hi Sam.
You did not reply to the last mesg.

In the last mesg the files are attached along with the command file .
I ran the process with the modifications suggested by you.
Please have a look at the last messag.

Cheers!
Deepak
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User avatar
Deepak kumar
Posts: 47
Joined: Thu Dec 12, 2013 9:13 am

Re: parameters.csv file for RNA modeling

Post by Deepak kumar » Sat Dec 28, 2013 5:11 pm

Hi Sam,

The files attached to the last message have expired so I am attaching the results based on this command file :

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

firstStage 2

lastStage 6

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 32 48 B 3 19 300

threading A 53 78 B 106 131 300

threading A 83 102 B 152 171 300

threading A 139 160 B 176 197 300

threading A 165 187 B 211 233 300

threading A 220 229 B 238 247 300



mobilizer Rigid A 33 102

mobilizer Rigid A 139 229



mobilizer Rigid

mobilizer Default A 145 145

singleBondMobility A 144 O3* Free A 145 P

singleBondMobility A 145 O3* Free A 146 P



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 147 147

singleBondMobility A 146 O3* Free A 147 P

singleBondMobility A 147 O3* Free A 148 P



mobilizer Rigid

mobilizer Default A 80 80

singleBondMobility A 79 O3* Free A 80 P

singleBondMobility A 80 O3* Free A 81 P



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 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 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 139 Superimpose B 176 Superimpose Cis

baseInteraction A 140 Superimpose B 177 Superimpose Cis

baseInteraction A 141 Superimpose B 178 Superimpose Cis

baseInteraction A 142 Superimpose B 179 Superimpose Cis

baseInteraction A 143 Superimpose B 180 Superimpose Cis

baseInteraction A 144 Superimpose B 181 Superimpose Cis

baseInteraction A 145 Superimpose B 182 Superimpose Cis

baseInteraction A 146 Superimpose B 183 Superimpose Cis

baseInteraction A 147 Superimpose B 184 Superimpose Cis

baseInteraction A 148 Superimpose B 185 Superimpose Cis

baseInteraction A 149 Superimpose B 186 Superimpose Cis

baseInteraction A 150 Superimpose B 187 Superimpose Cis

baseInteraction A 151 Superimpose B 188 Superimpose Cis

baseInteraction A 152 Superimpose B 189 Superimpose Cis

baseInteraction A 153 Superimpose B 190 Superimpose Cis

baseInteraction A 154 Superimpose B 191 Superimpose Cis

baseInteraction A 155 Superimpose B 192 Superimpose Cis

baseInteraction A 156 Superimpose B 193 Superimpose Cis

baseInteraction A 157 Superimpose B 194 Superimpose Cis

baseInteraction A 158 Superimpose B 195 Superimpose Cis

baseInteraction A 159 Superimpose B 196 Superimpose Cis

baseInteraction A 160 Superimpose B 197 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 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.6.pdb :
https://www.dropbox.com/s/876ke5pvabd1yg2/last.6.pdb

trajectory.6.pdb:
https://www.dropbox.com/s/ajyiml4rq0jgd ... tory.6.pdb


When we see the last.6.pdb and trajectory.6.pdb, there dont seem to be much changes in the morphing/conformation of the model chain A compared to last.1.pdb.
Is it because the threading is not finished yet? or some other reason? because there are not much changes in the trajectories too.

Please let me know about your suggestions.

cheers!
Deepak
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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 » Sun Dec 29, 2013 1:55 am

Sorry, Christmas is a busy time of year and I guess I composed a long-winded response and never hit "Submit."

Is this the Group I Intron? If so, you may be able to get some structural insight from my PSB paper on multiple-template homology modeling.

In any event I think you've made good progress. To avoid cognitive overload I would continue going step by step. The next easiest target for improvement is, in my opinion, the region around residue 145 in chain A. You already have the "threading" command that you need, I would add more flexibility. After that I would go after the partner chain in the helix, around residue 185. Or you could try to repair them both together.

I don't know what to do with the 5' terminus yet, but we can discuss that afterwards.

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 » Sun Dec 29, 2013 7:43 am

Thanks.

Can you please give me the link to the paper you mentioned.

and In chain A I have 2 major regions to morph well, region 1-32 and 103-138 . In last.6.pdb the region around 145 and 185 are also to be repaired as you suggested.

also, I wanted to ask that in the attached files as we see the flexible regions dont move as if they are rigid but i have them free in the command file. Can you please tell me what could be the reason for this behavior?

Any further suggestions on the steps you mentioned in last message will make it more clear for me because i dont understand what you mean by "adding more flexibility" and suggestions on repairing the regions.

Thanks.
cheers
Deepak
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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 » Sun Dec 29, 2013 9:49 am

group I intron threading paper:
http://xray.bmc.uu.se/flores/Papers_fil ... eprint.pdf

firstly, you should check you alignment. For example, you have residue 142, chain A, being threaded onto residue 179, chain B. It looks to me like it should be threaded onto residue 178, chain B. But that's not the only problem with this alignment. I think the chain A stem-loop, residues 142 to 158 or so, is shorter than that of chain B. So you need to be very careful about what residues you align. This is like the RNA threading example in the tutorial, in which the modeled stem-loop is shorter than that in the template.

secondly, by flexibility I just mean letting chain A, residues 142 to 158 be flexible, e.g.:
mobilizer Rigid
mobilizer Default A 142 158
Don't worry about the rest of the molecule, just fix this bit first.

I'm appending my command file, to show you what I mean about flexibility. Note that I don't believe the threading below is correct -- that part you should fix, for chain A residues 142 to 158. Let me know how it goes. Once this part looks good we can worry about the rest.

Sam


firstStage 7
lastStage 7
reportingInterval .5
numReportingIntervals 200
removeRigidBodyMomentum False

# "target" fragment

RNA B 1 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG


# "threaded" fragment

RNA A 1 GAGCCUUUAUACAGUAAUGUAUAUCGAAAAAUCCUCUAAUUCAGGGAACACCUAAGGCAAUCCUGAGCUAAGCUCUUAGUAAUAAGAGAAAGUGCAACGACUAUUCCGAUAGGAAGUAGGGUCAAGUGACUCGAAAUGGGGAUUACCCUUCUAGGGUAGUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUCCGUAACAUAAUUG


mobilizer Rigid B
leontisWesthofInFileName parameters.csv
temperature 1.0

#Threading forces
threading A 32 48 B 3 19 300
threading A 53 78 B 106 131 300
threading A 83 102 B 152 171 300
threading A 139 160 B 176 197 300
threading A 165 187 B 211 233 300
threading A 220 229 B 238 247 300


mobilizer Rigid
mobilizer Default A 142 158


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 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 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 139 Superimpose B 176 Superimpose Cis
baseInteraction A 140 Superimpose B 177 Superimpose Cis
baseInteraction A 141 Superimpose B 178 Superimpose Cis
baseInteraction A 142 Superimpose B 179 Superimpose Cis
baseInteraction A 143 Superimpose B 180 Superimpose Cis
baseInteraction A 144 Superimpose B 181 Superimpose Cis
baseInteraction A 145 Superimpose B 182 Superimpose Cis
baseInteraction A 146 Superimpose B 183 Superimpose Cis
baseInteraction A 147 Superimpose B 184 Superimpose Cis
baseInteraction A 148 Superimpose B 185 Superimpose Cis
baseInteraction A 149 Superimpose B 186 Superimpose Cis
baseInteraction A 150 Superimpose B 187 Superimpose Cis
baseInteraction A 151 Superimpose B 188 Superimpose Cis
baseInteraction A 152 Superimpose B 189 Superimpose Cis
baseInteraction A 153 Superimpose B 190 Superimpose Cis
baseInteraction A 154 Superimpose B 191 Superimpose Cis
baseInteraction A 155 Superimpose B 192 Superimpose Cis
baseInteraction A 156 Superimpose B 193 Superimpose Cis
baseInteraction A 157 Superimpose B 194 Superimpose Cis
baseInteraction A 158 Superimpose B 195 Superimpose Cis
baseInteraction A 159 Superimpose B 196 Superimpose Cis
baseInteraction A 160 Superimpose B 197 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 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
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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 » Sun Dec 29, 2013 8:59 pm

Thanks Sam.

I understand what you mean now. There was mistake in threading , I have corrected it now. The region 142-158 seems to have improved . Plz let me know your comments/suggestions? The remaining regions iam trying to remodel well are 1-32 and 103-139 and 188-219. I am also attaching the native structure (apart from the template chain B) of the model to which i eventually have to superpose the model to have a good RMSD between 8-10A

I am attaching the result of the run based on this modified command file:

# Put chain A and B in last.1.pdb
firstStage 2
lastStage 3
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 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
mobilizer Default A 145 145
singleBondMobility A 144 O3* Free A 145 P
singleBondMobility A 145 O3* Free A 146 P

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 147 147
singleBondMobility A 146 O3* Free A 147 P
singleBondMobility A 147 O3* Free A 148 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 138 Superimpose B 174 Superimpose Cis
baseInteraction A 139 Superimpose B 175 Superimpose Cis
baseInteraction A 140 Superimpose B 176 Superimpose Cis
baseInteraction A 141 Superimpose B 177 Superimpose Cis
baseInteraction A 142 Superimpose B 178 Superimpose Cis
baseInteraction A 143 Superimpose B 179 Superimpose Cis
baseInteraction A 144 Superimpose B 180 Superimpose Cis
baseInteraction A 145 Superimpose B 181 Superimpose Cis
baseInteraction A 146 Superimpose B 192 Superimpose Cis
baseInteraction A 147 Superimpose B 193 Superimpose Cis
baseInteraction A 148 Superimpose B 194 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.1.pdb :
https://www.dropbox.com/s/drt9q3f4njei3a2/last.1.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

model-native-structure:
https://www.dropbox.com/s/t1sbi1rx3qfm0 ... native.pdb

Thnaks,
cheers!
Deepak
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