Here is how to create 3 conformers starting from a SMILES string....
>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)
C:\Temp>obabel -:CC(CC)CC(=O)Cl -O tmp.mol --gen3d
1 molecule converted
C:\Temp>obabel tmp.mol --conformer -O tmp.sdf --nconf 3 --writeconformers
... random text ...
1 molecule converted
C:\Temp>obabel tmp.sdf -osmi
C[C@@H](CC)CC(=O)Cl
C[C@@H](CC)CC(=O)Cl
C[C@@H](CC)CC(=O)Cl
3 molecules converted
On 9 May 2014 10:30, Chris Swain <sw...@mac.com> wrote:
>
>
> Message: 2
> Date: Wed, 7 May 2014 05:45:46 -0700 (PDT)
> From: Douglas Houston <dhous...@staffmail.ed.ac.uk>
> Subject: Re: [Open Babel] Generating a diverse set of conformers
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <1399466746210-4657403.p...@n4.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> So I've recompiled obabel with eigen, but the output of obabel -L ops has
> not
> changed:
>
> 0xout <file.xxx> Additional file output
> addfilename Append input filename to title
> AddInIndex Append input index to title
> AddPolarH Adds hydrogen to polar atoms only
> canonical Canonicalize the atom order
> energy ForceField Energy Evaluation (not displayed in GUI)
> fillUC Fill the unit cell (strict or keepconnect)
> gen2D Generate 2D coordinates
> gen3D Generate 3D coordinates
> largest # <descr> Output # mols with largest values
> minimize ForceField Energy Minimization (not displayed in GUI)
> partialcharge <method> Calculate partial charges by specified method
> readconformer Adjacent conformers combined into a single molecule
> s Isomorphism filter(-s, -v options replacement)(not displayed in GUI)
> smallest # <descr> Output # mols with smallest values of descriptor(not
> displayed in GUI)
> sort <desc> Sort by descriptor(~desc for reverse)
> unique [param] remove duplicates by descriptor;default inchi
> v Isomorphism filter(-s, -v options replacement)(not displayed in GUI)
>
> obabel still writes only 1 conformer (with no error messages) no matter the
> options I use.
>
>
>
> I think this is the expected result. The obconformer tool can be used as
> part of a conformational study by generating random conformers using a
> Monte Carlo search. The best conformer out of the batch of conformers will
> be output, after taking the supplied number of geometry optimization steps.
> By default, obconformer uses the MMFF94 <http://openbabel.org/wiki/MMFF94>
> force
> field.
> So to generate the best conformer (out of 250) of baseconformer.sdf and
> write it to rotamer1.sdf after 100 geometry optimization steps:
>
> obconformer 250 100 baseconformer.sdf >conformer.sdf
>
> The output is a single conformation
>
>
>
>
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