Dear Noel,
It worked out just fine. I put the two structures in one input file and
used the command line
obabel c.xyz -O final.xyz --align
The only issue that remains is the number of decimal places in the output
geometry. I really could make use of few more digits. Any way to increase
it?
Thank you very much!
Demetrio Filho
On Fri, May 31, 2013 at 5:16 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> See also --align for whole molecule alignment. This assumes that the
> atom orderings are the same in the two molecules.
>
>
> http://open-babel.readthedocs.org/en/latest/Command-line_tools/babel.html#aligning-molecules-or-substructures
>
> - Noel
>
> On 31 May 2013 00:18, Demetrio A. da Silva Filho <dasf....@gmail.com>
> wrote:
> > Hi Geoff,
> >
> > Thanks! I will give it another try.
> > Indeed, I can write an arbitrary number of decimals in the input file.
> But
> > will open babel write with the same number of decimals? If not, is there
> a
> > way to change it?
> >
> > Regards,
> > Demetrio Filho
> >
> >
> > On Thu, May 30, 2013 at 7:25 PM, Geoffrey Hutchison
> > <geoff.hutchi...@gmail.com> wrote:
> >>
> >> > molecules using open babel. The catch is: I wish I could loose
> accuracy
> >> > as
> >> > minimum as possible. I mean, I wish I could extract the two geometries
> >> > from
> >> > the fchk file keeping as many decimal digits as possible and then
> >> > generate
> >> > two new geometries with as many decimal digits as possible. How can I
> do
> >> > it?
> >> > Which format allow me to use the largest number of decimal digits?
> >>
> >> You can write out an arbitrary number of digits, e.g. with XYZ. If you
> >> want an existing format in Open Babel, I'd suggest DMol3, which I think
> uses
> >> 14 decimals (albeit in Bohr).
> >>
> >> > I have looked into the obfit code but I have another question. How the
> >> > two
> >> > molecules should enter? One after the other? Any separation? just cat
> >> > molecule1 molecule2 > moleculefit?
> >>
> >> No, obfit takes one molecule and fits it onto another, e.g.
> >>
> >> obfit molecule1.xyz molecule2.xyz >newfile.xyz
> >>
> >> http://openbabel.org/wiki/Obfit
> >>
> >> > Besides, I wish all atoms could be used in the alignment. Which SMILES
> >> > should I use?
> >>
> >> You'd pick a SMARTS that corresponds to the molecular SMILES. So, for
> >> example, if you wanted to superimpose two benzenes:
> >>
> >> c1ccccc1
> >>
> >> Hope that helps,
> >> -Geoff
> >
> >
> >
> >
> > --
> > Demétrio A. da Silva Filho
> > Instituto de Física - Universidade de Brasília
> > Multiuso II - Sala B1 11/4
> > Fone: (61)3107.6089
> >
> >
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>
--
Demétrio A. da Silva Filho
Instituto de Física - Universidade de Brasília
Multiuso II - Sala B1 11/4
Fone: (61)3107.6089
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