I've never used OBConstraints, but just as general advice: when
setting up the forcefield, you should ensure that (a) the atoms have
3D coordinates, (b) hydrogens have already been added, and (c) that
calling the Setup function is successful.
// We pass the constraints as argument for Setup()
if (!pFF->Setup(mol, constraints)) {
cerr << "ERROR: could not setup force field." << endl;
}
- Noel
On 25 June 2010 01:03, Christopher Wassman <[email protected]> wrote:
> 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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