>
> 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 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
------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
