Hi Albert,
> I am just wondering is it possible for babel to generate multiple
> conformation for a ligand and return the energy for each conformation?
>
> I only found:
>
> http://openbabel.org/wiki/Obconformer
>
> It can generate one lowest energy conformation.....
>
> I also found this:
>
> http://open-babel.readthedocs.org/en/latest/3DStructureGen/multipleconformers.html
>
> When I followed the command, it generate many conformation with serious
> atom clashes....
>
> I am just wondering can we use obconformer generate multiple low energy
> conformation?
I recommend using a variant of the following command-line (bash syntax for multi
line command):
obabel -i INTYPE INFILE -o OUTTYPE -O OUTFILE \
--conformer --nconf NUMBER_CONFORMERS --mutability MUTABILITY \
--children NUMBER_CHILDREN --convergence CONVERGENCE --score SCORE \
--writeconformers
By doing "obabel -L conformer" you can have a look at what the options do. It is
very important to use "--writeconformers" (I recommend as the last option, but I
don't know whether that's necessary), otherwise you'll get only one conformer in
OUTFILE but no error message. The help message is also wrong since it states to
use --converge while the programme itself looks for the key --convergence, again
you won't get an error message but not the behaviour you want. I already told
the devs some time ago but afaik it has not been corrected yet. I might create a
pull request sometime in the future.
If energy is the criterion you want to optimize, choose "--score energy".
Minenergy means that after the minimum energy conformers have been generated
(this is what --score energy does), the current force-field will be used to
minimize each conformer (I think for 500 steps), hence "min".
Steric clashes should be filtered out, but you might have to tweak the filter in
the source. At least I had to do that for very big molecules.
Hope this helps. Cheers,
Torsten
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