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generating conformers with open babel

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generating conformers with open babel

Francois Berenger-2
Hello,

I am running Open Babel 2.3.2.

I naively thought that the command:

obabel input.mol2 -O output.mol2 --confab --conf 50

Would give me in output.mol2 the 50 lowest energy conformers
of each molecule in input.mol2.

Unfortunately not (output.mol2 is equal to input.mol2).

What is the proper way to call confab ?

Thanks,
F.

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Re: generating conformers with open babel

mwojcikowski
Hello,

I think that Confab is available only in current development branch. Check "obabel -L confab" to see if it's there. If not then you'd have to use conda or compile it yourself.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
[hidden email]

2016-05-03 12:14 GMT+02:00 Francois Berenger <[hidden email]>:
Hello,

I am running Open Babel 2.3.2.

I naively thought that the command:

obabel input.mol2 -O output.mol2 --confab --conf 50

Would give me in output.mol2 the 50 lowest energy conformers
of each molecule in input.mol2.

Unfortunately not (output.mol2 is equal to input.mol2).

What is the proper way to call confab ?

Thanks,
F.

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Re: generating conformers with open babel

Francois Berenger-2
On 05/03/2016 02:57 PM, Maciek Wójcikowski wrote:
> Hello,
>
> I think that Confab is available only in current development branch.
> Check "obabel -L confab" to see if it's there.

It's not there. Thanks for the advice.

> If not then you'd have to
> use conda or compile it yourself.
>
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> [hidden email] <mailto:[hidden email]>
>
> 2016-05-03 12:14 GMT+02:00 Francois Berenger <[hidden email]
> <mailto:[hidden email]>>:
>
>     Hello,
>
>     I am running Open Babel 2.3.2.
>
>     I naively thought that the command:
>
>     obabel input.mol2 -O output.mol2 --confab --conf 50
>
>     Would give me in output.mol2 the 50 lowest energy conformers
>     of each molecule in input.mol2.
>
>     Unfortunately not (output.mol2 is equal to input.mol2).
>
>     What is the proper way to call confab ?
>
>     Thanks,
>     F.
>
>     ------------------------------------------------------------------------------
>     Find and fix application performance issues faster with Applications
>     Manager
>     Applications Manager provides deep performance insights into
>     multiple tiers of
>     your business applications. It resolves application problems quickly and
>     reduces your MTTR. Get your free trial!
>     https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
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>     OpenBabel-discuss mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

--
Regards,
Francois.
"When in doubt, use more types"

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