Hi Geoff,
When I tried to convert a multimolecule pdb file (output from obminimize)
to an sdf file, only the first molecule was converted.
I wrote my own script to split the file into multiple pdbs and put them
together as single sdf using obabel.
But any solution using obabel to that in single step i.e. converting
multimolecular pdb to sdf?
Thanks,
Sundar
On Thu, Oct 19, 2017 at 8:01 PM, Sundar Jubilant <jubilantsun...@gmail.com>
wrote:
> Thanks. I will try that.
>
> Sundar Thangapandian
>
> > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
> >
> > The obminimize program does not have all the features of the obabel
> command. You can naturally convert a PDB file to SDF:
> >
> > obabel file.pdb -O file.sdf
> >
> >> I tried -osdf filename.sdf and it didn't work. How can I get it in sdf
> format?
> >> Or how can I convert multimolecule pdb file to an sdf file?
> >
> > You can also use the --minimize flag with obabel to minimize molecules.
> > http://open-babel.readthedocs.io/en/latest/Command-line_
> tools/babel.html?highlight=minimize#forcefield-energy-and-minimization
> >
> > Hope that helps,
> > -Geoff
>
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