Furthermore, why do I get no co-ordinates?
obabel ligand.babel.smi -O ligand.babel.sdf --conformer --nconf 20
--weighted
Using OpenBabel 2.3.1
==============================
*** Open Babel Warning in WriteMolecule
No 2D or 3D coordinates exist. Any stereochemical information will be
lost. To generate 2D or 3D coordinates use --gen2D or --gen3d.
1 molecule converted
And using your command also gives me one no-coordinates molecule.
obabel ligand.babel.smi -O test.sdf --conformer --nconf 50 --score energy
Is this something related to smiles input?
-
Jean-Paul Ebejer
Early Stage Researcher
On 9 December 2011 17:55, JP <jeanpaul.ebe...@inhibox.com> wrote:
> yes Geoff, this does help *a lot* - especially considering the call from
> the command line.
>
> One more question and a suggestion please.
>
> Q: The weighted rotor conformer gives only one conformer (lowest energy)?
> What happens when you specify the num of conformers to say 50 ?
>
> S: Also a suggestion obabel --help totally ignores the fact that there is
> this wealth of functionality available.
>
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 9 December 2011 17:12, Geoffrey Hutchison <ge...@geoffhutchison.net>wrote:
>
>> > Specifically, I was wondering if there is an example of how to use
>> OBConformerSearch from Python (and is there a way how to use this directly
>> from the command line?).
>>
>> Sorry the documentation isn't online -- we should definitely fix that.
>> It's easy to use from the command-line:
>>
>> obabel -L conformer
>> One of the ops
>> conformer Conformer Searching (not displayed in GUI)
>> Typical usage: obabel infile.xxx -O outfile.yy --conformer --nconf
>> options: description
>> --log output a log of the energies (default = no log)
>> --nconf # number of conformers to generate
>> forcefield based methods for finding stable conformers:
>> --systematic systematically generate all conformers
>> --random randomly generate conformers
>> --weighted weighted rotor search for lowest energy conformer
>> --ff # select a forcefield (default = MMFF94)
>> genetic algorithm based methods (default):
>> --children # number of children to generate for each parent (default
>> = 5)
>> --mutability # mutation frequency (default = 5)
>> --converge # number of identical generations before convergence is
>> reached
>> --score # scoring function [rmsd|energy] (default = rmsd)
>>
>> For example:
>> # generate 50 conformers, scoring with MMFF94 energies, but default
>> children, etc.
>> obabel EtOT5D.cml -O EtOT5D0.xyz --conformer --nconf 50 --score energy
>>
>> As far as Python, I haven't tried, but the code is "wrapped" so it should
>> be available. If you want some example code, I can probably whip something
>> up based on the C++ (e.g., src/ops/conformer.cpp).
>>
>> > Also, do the conformers undergo some form of energy minimization in
>> this GA approach?
>>
>> As of yet, no. That could be done new scoring function (e.g., minenergy)
>> which determines the energy after some minimization. It's a good idea.
>>
>> > Also, I can see I can generate a fixed number of conformers (e.g. 50)
>> using Weighted Rotor Score, what is a decent parameter for geomSteps in
>> > WeightedRotorSearch (unsigned int conformers, unsigned int geomSteps) ?
>> Why do the other structure methods have a default for 2500 and this one
>> has not?
>> > Is this an oversight?
>>
>> I usually use a few hundred geomSteps, maybe 250 or 500. IMHO, the point
>> isn't to produce a fully converged structure, but to quickly minimize
>> steric collisions generated from a particular rotamer. Once I have some
>> low-energy conformers, I'll minimize the low-energy set to find more
>> converged energies and geometries.
>>
>> Hope that helps,
>> -Geoff
>
>
>
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