[Open Babel] Still having problems with OBConformerSearch

[Alessandro Nascimento]

Hi OB folks,

I am still having some problems with the GA algorithm for conformer
generation. My purpose is to generate a set of conformers 'on-the-fly'
on a C++ program for binding energy evaluation.

So, I opened the mol2 file, minimized it with steepest descent and
used OBConformerSearch as described in the example on the API web
page. However, I aways get the error message "Initial conformer does
not pass filter! Initial conformer count: 0". I used methotrexate, as
in the API example,
(http://zinc11.docking.org/fget.pl?l=0&z=57082260&f=m) but could not
make it work. Other molecules resulted in the same behavior.

The full output of the program is attached.

Any clues/hints?


Thanks in advance



The code:
################################################################################
        OBconv->SetInAndOutFormats("mol2", "mol2");
        bool file_read = OBconv->ReadFile(OBmol, molfile);
        if (!file_read){
                printf("Could not open file %s for reading.\n", 
molfile.c_str());
                exit(1);
        }

        double total=0.00;
        FOR_ATOMS_OF_MOL(atom, OBmol){
                total+=atom->GetPartialCharge();
        }
        OBmol->SetTotalCharge(int(total));

        OBff->Setup(*OBmol);
        OBff->SteepestDescent(10000, 1.0e-10);
        cout << "First minimization done!" << endl;
        if (!OBff->GetCoordinates(*OBmol)){
                cout << "Could not get coordinates from OBff. Check 
Conformer.cpp
file." << endl;
        }
        OBconv->WriteFile(OBmol, "teste.mol2");
        OBConformerSearch* OBconf = new OBConformerSearch;
        OBconf->Setup(*OBmol, 30, 5, 5, 25);
        OBconf->Search();
        OBconf->GetConformers(*OBmol);
        printf("Number of conformers: %d.\n", OBmol->NumConformers());
// always = 1;
        ...
################################################################################





-- 
[ ]s

--alessandro

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