Dear all,
I try to find conformers of the loop of a 9-mer peptide, with the N-terminal
(the 3 first residues) and the C-terminal end (the last 2 residues) fixed.
I have customized, for this purpose, the obconformer program this way:
int i,j;
unsigned int n;
OBResidue *residue=NULL;
vector<OBAtom*> atoms;
OBAtom *atom;
std::string atmtype;
OBFFConstraints constraints;
int fixlist[5]={1,2,3,8,9};
mol.Clear();
conv.Read(&mol);
for(i=0;i<5;i++)
{
residue=mol.GetResidue(fixlist[i]-1);
cout << residue->GetName()<<" ";
atoms=residue->GetAtoms();
for(j=0;j<4;j++) // only backbone is freezed
{
atom=atoms[j];
n=atom->GetIdx();
constraints.AddAtomConstraint(n);
}
}
cout << "\n";
OBForceField *pFF = OBForceField::FindForceField("MMFF94");
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
pFF->Setup(mol,constraints);
pFF->WeightedRotorSearch(weightSteps, geomSteps
pFF->ConjugateGradients(geomSteps); // final cleanup
pFF->UpdateCoordinates(mol);
conv.Write(&mol);
But When I fit the Nterminal ends of both molecules (initial conformer and the
result of the program), the C-terminal end is not superimposed. It looks as if
minimization can't deal with geometrical constraints. What's wrong in my
program?
Thanks for your help. Regards
François------------------------------------------------------------------------------
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