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

     I removed  CONECT records from Files a.pdb and b.pdb. still code is
running fine

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

     Also tried to run by removing BR43 from the file. Still same error.


Amit


On Thu, Sep 22, 2016 at 4:26 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:

>
>
> File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't
> parse that (seems valid to me, FWTW).
>
> Paul
>
>
>
> On 22/09/16 11:15, Amit singh wrote:
>
> Hi
>
> 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 <greg.land...@gmail.com>
> wrote:
>
>> HI Amit,
>>
>>
>> On Thu, Sep 22, 2016 at 9:23 AM, Amit singh <amitbioi...@gmail.com>
>> wrote:
>>
>>>
>>> I am a new entry in this discussion forum and also for RDKit
>>>
>>
>> Welcome!
>>
>>
>>> 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?
>>
>> -greg
>>
>>
>
>
>
>
>
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