Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond orders?).

File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't parse that (seems valid to me, FWTW).


On 22/09/16 11:15, Amit singh wrote:

Files a.pdb and b.pdb are from RDKit test data (working fine)

Files 1.pdb and 2.pdb (other than test data, which are giving error)

On Thu, Sep 22, 2016 at 3:03 PM, Greg Landrum < <>> wrote:

    HI Amit,

    On Thu, Sep 22, 2016 at 9:23 AM, Amit singh <
    <>> wrote:

        I am a new entry in this discussion forum and also for RDKit


        I am trying to calculate shape tanimoto and rms between two
        molecules (PDB files) from 3D functionality of RDKit.
        Code is working fine for the pdb files given in test data.
        But gives error whenever I uses other pdb files

        >>> rms = rdMolAlign.AlignMol(mol1, mol2)
        Traceback (most recent call last):
          File "<stdin>", line 1, in <module>
        RuntimeError: std::exception
        It looks like there is a problem in input files, but help required

    In order to be able to answer the question, we need a bit more
    information. Can you please share what files you loaded mol1 and
    mol2 from so that we can reproduce the problem?



Dr. Amit Kumar
Scientist B
National Institute of Cancer Prevention and Research
(Formly Institute of Cytology and Preventive Oncology)
 I-7, Sector - 39, Noida - 201301 Uttar Pradesh


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