Excellent, working perfectly now, many thanks. I used your calcrmsd.py
script from an earlier thread as a starting point for my scripts, so to
avoid any future problems a simple canonical conversion of the conformers
can be added in? This might be repetitive if done already but it would save
any potential problems.
Best wishes,
Scott
On 16 October 2012 16:40, Noel O'Boyle <baoille...@gmail.com> wrote:
> See the docs:
> "When aligning molecules, the atoms of the two molecules must be in
> the same order for the results to be sensible."
>
> Try rearranging the atoms into canonical order first:
> obabel C:\Users\noel\Desktop\conf1.mol2 -O tmp.mol2 --canonical
> obabel C:\Users\noel\Desktop\conf2.mol2 -O tmp2.mol2 --canonical
>
> - Noel
>
> On 16 October 2012 16:23, scott_m <js...@cam.ac.uk> wrote:
> > Dear all,
> >
> > I have been using OBAlign() to get rmsd values between conformers but
> just
> > came across an erroneous value of 3.14 for the molecule N-Acryloyl
> glycine,
> > the CSD function tormat gives a rmsd of 0 for the two conformers. Any
> idea
> > what is going wrong here? I've attached the two mol2 files.
> >
> > Thanks,
> >
> > Scott
> > conf1.mol2 <http://forums.openbabel.org/file/n4655579/conf1.mol2>
> > conf2.mol2 <http://forums.openbabel.org/file/n4655579/conf2.mol2>
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/OBAlign-error-tp4655579.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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