Conformer Search vs. Conformer Generation

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Conformer Search vs. Conformer Generation

kcpearce
I am new to OpenBabel and I am trying to generate numerous conformers of a certain compound. In the documentation, I read that the conformer searching can be done systematically, with a random rotor search, a weighted random search, or with genetic algorithm. However, I also read that conformer generation can only be done with the systematic or genetic algorithm approach. Is there no way to generate numerous conformers of a particular compound using the weighted random rotor search? I appreciate any and all feedback/suggestions.

Thanks,
Kirk Pearce
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Re: Conformer Search vs. Conformer Generation

Geoff Hutchison
The weighted random rotor search does not generate an ensemble of conformers, no. It’s intended to find the lowest energy conformer.

Hope that helps,
-Geoff

> On Jan 4, 2017, at 12:16 PM, kcpearce <[hidden email]> wrote:
>
> I am new to OpenBabel and I am trying to generate numerous conformers of a
> certain compound. In the documentation, I read that the conformer searching
> can be done systematically, with a random rotor search, a weighted random
> search, or with genetic algorithm. However, I also read that conformer
> generation can only be done with the systematic or genetic algorithm
> approach. Is there no way to generate numerous conformers of a particular
> compound using the weighted random rotor search? I appreciate any and all
> feedback/suggestions.
>
> Thanks,
> Kirk Pearce
>
>
>
> --
> View this message in context: http://forums.openbabel.org/Conformer-Search-vs-Conformer-Generation-tp4659653.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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Re: Conformer Search vs. Conformer Generation

kcpearce
Hi Geoff:

Thanks for your response!

I have seen that by using the `--writeconformers` option, you can write the coordinates of all of the conformers that are searched during the weighted random rotor search. And I have also seen that you can get detailed energy output for each of the corresponding conformers by using the `--log` option. Is there a way to save the energy information and sort the searched conformers by their total energy?

Essentially, I am starting with one compound and I want to do an exhaustive conformational search and keep all conformers below a certain threshold of relative energy to conduct further QM calculations with. Do you see any convenient way to do this using Open Babel?

Any and all feedback is greatly appreciated.

Thanks,
Kirk
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Re: Conformer Search vs. Conformer Generation

Noel O'Boyle
Administrator
You have just described what Confab does.
http://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html

On 5 January 2017 at 15:20, kcpearce <[hidden email]> wrote:

> Hi Geoff:
>
> Thanks for your response!
>
> I have seen that by using the `--writeconformers` option, you can write the
> coordinates of all of the conformers that are searched during the weighted
> random rotor search. And I have also seen that you can get detailed energy
> output for each of the corresponding conformers by using the `--log` option.
> Is there a way to save the energy information and sort the searched
> conformers by their total energy?
>
> Essentially, I am starting with one compound and I want to do an exhaustive
> conformational search and keep all conformers below a certain threshold of
> relative energy to conduct further QM calculations with. Do you see any
> convenient way to do this using Open Babel?
>
> Any and all feedback is greatly appreciated.
>
> Thanks,
> Kirk
>
>
>
> --
> View this message in context: http://forums.openbabel.org/Conformer-Search-vs-Conformer-Generation-tp4659653p4659656.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

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Re: Conformer Search vs. Conformer Generation

kcpearce
Correct. But as far as I can tell, Confab only works for a systematic approach or a genetic algorithm approach. Am I correct in my understanding that Confab cannot be used with a weighted random rotor approach?

Thanks,
Kirk
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Re: Conformer Search vs. Conformer Generation

Noel O'Boyle
Administrator
That's right. But that's not an "exhaustive conformational search" if
that's what you want.

- Noel

On 5 January 2017 at 21:09, kcpearce <[hidden email]> wrote:

> Correct. But as far as I can tell, Confab only works for a systematic
> approach or a genetic algorithm approach. Am I correct in my understanding
> that Confab cannot be used with a weighted random rotor approach?
>
> Thanks,
> Kirk
>
>
>
> --
> View this message in context: http://forums.openbabel.org/Conformer-Search-vs-Conformer-Generation-tp4659653p4659658.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

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Re: Conformer Search vs. Conformer Generation

kcpearce
That is true. Thanks for your help!