Dear Noel,
>> if you don't include bond orders and hydrogens.
Thanks a lot, your suggestion indeed worked. I obtained mol2 from pdb (with
hydrogens) using babel and corrected bond order (bond types) in mol2 file
where they were wrong. Now I am getting correct canonical order
regards,
On Thu, Apr 25, 2013 at 5:31 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> As you may be aware, it may not be a good idea to store chemical
> information in PDB files as you need to guess the structure from the
> 3D coordinates if you don't include bond orders and hydrogens.
>
> If you open them both in Avogadro, you will see that Open Babel
> detects a double bond in one case but not the other. Or just do:
> obabel a.pdb b.pdb -O tmp.smi
>
> [N](CCO[P@@](=O)(O)OC[C@H
> ](OC(=O)CCCCCCC/C=C\CCCCCCCC)COC(=O)CCCCCCCCCCC/C=C/CC)(C)(C)C
> a.pdb
> [N](CCO[P@@](=O)(O)OC[C@H
> ](OC(=O)CCCCCCC/C=C\CCCCCCCC)COC(=O)CCCCCCCCCCCCCCC)(C)(C)C
> b.pdb
>
> So, different structure, different canonicalisation.
>
> - Noel
>
> On 25 April 2013 13:41, gromacs query <gromacsqu...@gmail.com> wrote:
> > Dear All,
> >
> > I have some query related to canonical option in babel and am new to
> babel
> >
> > I have two pdb files (a.pdb and b.pdb). These include just heavy atoms
> but
> > are pdbs for same structure.
> >
> > a.pdb and b.pdb have same atom names but different atom number and
> > coordinates.
> >
> > What I expect is canonical output should remain same. But both gives me
> > different canonical order. Is this bug or something I am missing.
> >
> > I use this command:
> >
> > babel --canonical -ipdb a.pdb -opdb a_cano.pdb
> > babel --canonical -ipdb b.pdb -opdb b_cano.pdb
> >
> > I get different canonical ouput in both pdbs. Should not be the order
> remain
> > same?
> >
> > Please suggest
> >
> > regards,
> > Jiom
> >
> >
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