From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon Mar 26 2018 - 11:39:28 CDT
Dear NAMD users,
I am running well-tempered metadynamics in NAMD, to predict the binding
site between two proteins. At first, four binding sites are predicted using
docking. I have used the distance between the group of atoms forming
hydrogen bonds in these two proteins as the colvar variable. I have run
metadynamics around 40ns using initial structure from one of the docking
result. But the two proteins did not move from each other. So I thought may
be this initial structure corresponds to the lowest energy binding site,
that's why it is hard to move the proteins from each other from this
initial structure. Later I have started running metadynamics with another
initial structure from another docking result to see if the two proteins
move and run around 92ns. I still can not see any significant relative
movement of the two proteins.
Can anyone please give me suggestions what should I do?
Here is the colvar file that I am using-
colvarsTrajFrequency 1000
colvarsRestartFrequency 1000
colvar {
name r1
lowerBoundary 0.0
upperBoundary 50.0
width 2
distance {
group1 { atomnumbers {2818 2820 2841 1975 1977 1998 1218 1220 1231 1268
1270 1281 1153 1155 1164 1282 1284 1293 3289 3291 3298 1430 1432 1439 1201
1203 1217 2793 2795 2807 943 945 957 2080 2082 2086 2087
2089 2093 1232 1234 1250 2897 2899 2915 3342 3344 3362 1165 1167 1183 2875
2877 2896 1100 1102 1121 1185 1187 1200 1251 1253 1266 1365 1367 1381 1470
1472 1486 2773 2775 2792 2046 2048 2065 2066 2068
2079 2739 2741 2748 1403 1405 1413 1945 1947 1958 1344 1346 1364 2859 2861
2874 1454 1456 1467
}
}
group2 { atomnumbers {296 298 305 184 186 207 224 226 247 262 264 285 47
549 570 578 580 601 668 670 691 46 48 57 286 288 295 352 354 361 512 514
521 447 449 463 93 95 109 1 3 7 248 250 261 255 257 260
571 573 577 8 10 26 27 29 45 322 324 340 362 364 380 74 76 92 395 397 416
490 492 511 602 604 623 110 112 131 381 183 394 341 343 351 522 524 532 533
535 546 60 62 73 153 155 173 132 134 152 208 210 221
306 308 321}
}
}
}
metadynamics {
name metadyn_dist1
colvars r1
hillWeight 0.01 # Default is 0.01 - higher numbers = faster
dumpFreeEnergyFile yes
newHillFrequency 500 # Default is 100 - lower numbers = faster
writeHillsTrajectory on
hillwidth 1.0
wellTempered on
biasTemperature 1490
}
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