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/* -------------------------------------------------------------------------- *
* SimTK Core: SimTK Simbody(tm) *
* -------------------------------------------------------------------------- *
* This is part of the SimTK Core biosimulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2006-7 Stanford University and the Authors. *
* Authors: Christopher Bruns *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "SimTKmolmodel.h"
#include "molmodel/internal/Pdb.h"
#include <sstream>
using namespace SimTK;
using namespace std;
int main() {
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
dumm.loadAmber99Parameters();
try
{
String inputPdb=""
"ATOM 1 O5' G B 1 -9.159 -10.595 12.585 1.00 0.00 O\n"
"ATOM 2 C5' G B 1 -10.504 -10.828 12.144 1.00 0.00 C\n"
"ATOM 3 C4' G B 1 -11.413 -9.637 12.402 1.00 0.00 C\n"
"ATOM 4 O4' G B 1 -11.529 -9.358 13.803 1.00 0.00 O\n"
"ATOM 5 C3' G B 1 -10.853 -8.372 11.768 1.00 0.00 C\n"
"ATOM 6 O3' G B 1 -11.450 -8.222 10.474 1.00 0.00 O\n"
"ATOM 7 C2' G B 1 -11.366 -7.276 12.681 1.00 0.00 C\n"
"ATOM 8 O2' G B 1 -12.692 -6.870 12.323 1.00 0.00 O\n"
"ATOM 9 C1' G B 1 -11.337 -7.955 14.044 1.00 0.00 C\n"
"ATOM 10 N9 G B 1 -10.055 -7.715 14.737 1.00 0.00 N\n"
"ATOM 11 C8 G B 1 -9.097 -8.600 15.109 1.00 0.00 C\n"
"ATOM 12 N7 G B 1 -8.062 -8.138 15.727 1.00 0.00 N\n"
"ATOM 13 C5 G B 1 -8.349 -6.771 15.783 1.00 0.00 C\n"
"ATOM 14 C6 G B 1 -7.594 -5.706 16.345 1.00 0.00 C\n"
"ATOM 15 O6 G B 1 -6.520 -5.759 16.912 1.00 0.00 O\n"
"ATOM 16 N1 G B 1 -8.239 -4.486 16.187 1.00 0.00 N\n"
"ATOM 17 C2 G B 1 -9.460 -4.306 15.567 1.00 0.00 C\n"
"ATOM 18 N2 G B 1 -9.911 -3.053 15.508 1.00 0.00 N\n"
"ATOM 19 N3 G B 1 -10.177 -5.303 15.036 1.00 0.00 N\n"
"ATOM 20 C4 G B 1 -9.568 -6.502 15.177 1.00 0.00 C\n"
"ATOM 21 H5' G B 1 -10.920 -11.665 12.687 1.00 0.00 H\n"
"ATOM 22 H5'' G B 1 -10.482 -11.059 11.069 1.00 0.00 H\n"
"ATOM 23 H4' G B 1 -12.402 -9.841 11.995 1.00 0.00 H\n"
"ATOM 24 H3' G B 1 -9.764 -8.388 11.720 1.00 0.00 H\n"
"ATOM 25 HO2' G B 1 -12.766 -6.945 11.369 1.00 0.00 H\n"
"ATOM 26 H1' G B 1 -12.156 -7.577 14.656 1.00 0.00 H\n"
"ATOM 27 H8 G B 1 -9.198 -9.663 14.894 1.00 0.00 H\n"
"ATOM 28 H1 G B 1 -7.762 -3.680 16.564 1.00 0.00 H\n"
"ATOM 29 H21 G B 1 -9.367 -2.301 15.908 1.00 0.00 H\n"
"ATOM 30 H22 G B 1 -10.795 -2.855 15.063 1.00 0.00 H\n"
"ATOM 31 HO5' G B 1 -8.573 -10.999 11.941 1.00 0.00 H\n"
"ATOM 32 P G B 2 -10.655 -7.494 9.276 1.00 0.00 P\n"
"ATOM 33 OP1 G B 2 -11.450 -7.642 8.036 1.00 0.00 O\n"
"ATOM 34 OP2 G B 2 -9.248 -7.952 9.308 1.00 0.00 O\n"
"ATOM 35 O5' G B 2 -10.689 -5.944 9.713 1.00 0.00 O\n"
"ATOM 36 C5' G B 2 -11.850 -5.146 9.440 1.00 0.00 C\n"
"ATOM 37 C4' G B 2 -11.678 -3.694 9.863 1.00 0.00 C\n"
"ATOM 38 O4' G B 2 -11.419 -3.590 11.266 1.00 0.00 O\n"
"ATOM 39 C3' G B 2 -10.481 -3.050 9.181 1.00 0.00 C\n"
"ATOM 40 O3' G B 2 -10.924 -2.423 7.974 1.00 0.00 O\n"
"ATOM 41 C2' G B 2 -10.085 -1.969 10.167 1.00 0.00 C\n"
"ATOM 42 O2' G B 2 -10.882 -0.790 10.004 1.00 0.00 O\n"
"ATOM 43 C1' G B 2 -10.357 -2.648 11.503 1.00 0.00 C\n"
"ATOM 44 N9 G B 2 -9.145 -3.330 11.991 1.00 0.00 N\n"
"ATOM 45 C8 G B 2 -8.821 -4.645 11.961 1.00 0.00 C\n"
"ATOM 46 N7 G B 2 -7.681 -4.993 12.454 1.00 0.00 N\n"
"ATOM 47 C5 G B 2 -7.164 -3.763 12.870 1.00 0.00 C\n"
"ATOM 48 C6 G B 2 -5.926 -3.463 13.497 1.00 0.00 C\n"
"ATOM 49 O6 G B 2 -5.036 -4.227 13.814 1.00 0.00 O\n"
"ATOM 50 N1 G B 2 -5.797 -2.102 13.744 1.00 0.00 N\n"
"ATOM 51 C2 G B 2 -6.740 -1.143 13.429 1.00 0.00 C\n"
"ATOM 52 N2 G B 2 -6.432 0.114 13.748 1.00 0.00 N\n"
"ATOM 53 N3 G B 2 -7.907 -1.418 12.839 1.00 0.00 N\n"
"ATOM 54 C4 G B 2 -8.055 -2.738 12.589 1.00 0.00 C\n"
"ATOM 55 H5' G B 2 -12.691 -5.536 9.997 1.00 0.00 H\n"
"ATOM 56 H5'' G B 2 -12.064 -5.200 8.363 1.00 0.00 H\n"
"ATOM 57 H4' G B 2 -12.581 -3.135 9.623 1.00 0.00 H\n"
"ATOM 58 H3' G B 2 -9.675 -3.764 9.008 1.00 0.00 H\n"
"ATOM 59 H2' G B 2 -9.021 -1.742 10.071 1.00 0.00 H\n"
"ATOM 60 HO2' G B 2 -10.518 -0.117 10.584 1.00 0.00 H\n"
"ATOM 61 H1' G B 2 -10.681 -1.907 12.234 1.00 0.00 H\n"
"ATOM 62 H8 G B 2 -9.493 -5.380 11.521 1.00 0.00 H\n"
"ATOM 63 H1 G B 2 -4.939 -1.812 14.187 1.00 0.00 H\n"
"ATOM 64 H21 G B 2 -5.549 0.320 14.193 1.00 0.00 H\n"
"ATOM 65 H22 G B 2 -7.081 0.860 13.544 1.00 0.00 H\n"
"ATOM 66 P C B 3 -9.944 -2.320 6.701 1.00 0.00 P\n"
"ATOM 67 OP1 C B 3 -10.708 -1.742 5.573 1.00 0.00 O\n"
"ATOM 68 OP2 C B 3 -9.258 -3.622 6.537 1.00 0.00 O\n"
"ATOM 69 O5' C B 3 -8.854 -1.235 7.180 1.00 0.00 O\n"
"ATOM 70 C5' C B 3 -9.116 0.164 7.039 1.00 0.00 C\n"
"ATOM 71 C4' C B 3 -7.921 1.010 7.472 1.00 0.00 C\n"
"ATOM 72 O4' C B 3 -7.587 0.777 8.845 1.00 0.00 O\n"
"ATOM 73 C3' C B 3 -6.673 0.649 6.681 1.00 0.00 C\n"
"ATOM 74 O3' C B 3 -6.580 1.521 5.552 1.00 0.00 O\n"
"ATOM 75 C2' C B 3 -5.552 0.993 7.643 1.00 0.00 C\n"
"ATOM 76 O2' C B 3 -5.209 2.382 7.575 1.00 0.00 O\n"
"ATOM 77 C1' C B 3 -6.164 0.634 8.992 1.00 0.00 C\n"
"ATOM 78 N1 C B 3 -5.806 -0.744 9.381 1.00 0.00 N\n"
"ATOM 79 C2 C B 3 -4.572 -0.943 9.986 1.00 0.00 C\n"
"ATOM 80 O2 C B 3 -3.819 -0.005 10.168 1.00 0.00 O\n"
"ATOM 81 N3 C B 3 -4.233 -2.208 10.357 1.00 0.00 N\n"
"ATOM 82 C4 C B 3 -5.067 -3.235 10.145 1.00 0.00 C\n"
"ATOM 83 N4 C B 3 -4.704 -4.460 10.526 1.00 0.00 N\n"
"ATOM 84 C5 C B 3 -6.338 -3.035 9.520 1.00 0.00 C\n"
"ATOM 85 C6 C B 3 -6.665 -1.780 9.156 1.00 0.00 C\n"
"ATOM 86 H5' C B 3 -9.978 0.427 7.652 1.00 0.00 H\n"
"ATOM 87 H5'' C B 3 -9.343 0.379 5.995 1.00 0.00 H\n"
"ATOM 88 H4' C B 3 -8.150 2.065 7.332 1.00 0.00 H\n"
"ATOM 89 H3' C B 3 -6.659 -0.403 6.395 1.00 0.00 H\n"
"ATOM 90 H2' C B 3 -4.681 0.364 7.446 1.00 0.00 H\n"
"ATOM 91 HO2' C B 3 -5.283 2.738 8.463 1.00 0.00 H\n"
"ATOM 92 H1' C B 3 -5.805 1.330 9.750 1.00 0.00 H\n"
"ATOM 93 H41 C B 3 -3.808 -4.607 10.967 1.00 0.00 H\n"
"ATOM 94 H42 C B 3 -5.325 -5.242 10.374 1.00 0.00 H\n"
"ATOM 95 H5 C B 3 -7.018 -3.868 9.344 1.00 0.00 H\n"
"ATOM 96 H6 C B 3 -7.623 -1.590 8.672 1.00 0.00 H\n"
"END\n";
std::istringstream inStream(inputPdb);
PdbStructure pdbStructure(inStream, PdbStructure::InputType::PDB);
RNA myRNA("GGC");
myRNA.setPdbChainId("B");
myRNA.writeDefaultPdb(cout); // OK
Compound::AtomTargetLocations atomTargets = myRNA.createAtomTargets(pdbStructure);
cout << atomTargets.size() << endl;
SimTK_ASSERT_ALWAYS( (atomTargets.size() == 95), "Wrong number of atom matches" ); // pdb lacks H2', has HO5'
cout << atomTargets.size() << endl;
// assert(atomTargets.size() == 16);
myRNA.writeDefaultPdb(cout);
// Four steps to a perfect match
myRNA.matchDefaultBondLengths(atomTargets);
myRNA.matchDefaultBondAngles(atomTargets);
myRNA.matchDefaultDihedralAngles(atomTargets);
myRNA.matchDefaultTopLevelTransform(atomTargets);
Real residual = myRNA.getTransformAndResidual(atomTargets).residual;
cout << "residual = " << residual << " nanometers" << endl;
myRNA.assignBiotypes();
myRNA.writeDefaultPdb(cout);
system.adoptCompound(myRNA);
system.modelCompounds();
system.realizeTopology();
const State& state = system.getDefaultState();
VerletIntegrator study(system);
study.initialize(state);
study.setAccuracy(0.01);
TimeStepper myTimeStepper(system,study);
Real mytime=0;
Real interval = 0.02; //picoseconds
for (int k=0; k<3; k++) {
cout<< "step "<<k<<endl;
mytime = k*interval;
while (myTimeStepper.getTime() < mytime)
myTimeStepper.stepTo(mytime);
cout << "check 9"<<endl;
myRNA.writePdb(myTimeStepper.getState(), cout);
}
cout << "PASSED" << endl;
return 0;
}
catch (const std::exception& e)
{
printf("EXCEPTION THROWN: %s\n", e.what());
}
catch (...)
{
printf("UNKNOWN EXCEPTION THROWN\n");
} return 0;
}
|
