Tried to implement fixing atoms as part of a conformational search....
as a straightforward
modification of the 'obconformer' tool.... but perhaps I'm missing
something. I'm using the source from
openbabel-2.2.3
I simply added this (in the "while(ifs.peek() != EOF && ifs.good())" loop):
OBFFConstraints constraints;
int i = 0;
for (i=1; i<=3; i++) {
cout << " Fixing atom index " << i << "...\n";
OBAtom *atom;
atom = mol.GetAtom(i);
if (!atom->IsHydrogen())
{
constraints.AddAtomConstraint(i);
}
else
{
cerr << "Error! heavy atoms first !" << endl;
}
}
pFF->Setup(mol,constraints);
pFF->WeightedRotorSearch(weightSteps, geomSteps);
...
etc as in "tools/obconfomer.cpp"
and removed the old "pFF->Setup(mol);" statement
I tried this on a simple butane molecule (defined in a pdb), where the
first atoms listed are the carbon backbone, in linear order.
I'd expect this to "freeze" the first 3 carbon atoms, however, in the
output only 2 of the 4 carbon atoms are held in fixed position. (The
first and the last carbons moved.)
Trying this approach to freeze all 4 of the carbon atoms, results in a
conformer where only 1 of the carbon atoms have moved. (The first
carbon moved.)
Anyone able to shed some light on this for me? What am I missing?
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