Conformer search

Hi list,

Is there currently a GUI-based method to generate and view
conformations of a molecule? Using the forcefield extension, I appear
to be generating the conformers, but in View > Properties > Conformer
Properties, only a single entry shows up.

We would like to do this as part of a lab, so we need a GUI-based,
student-friendly way to generate and compare conformations. Does
anyone know if such a workflow is possible using existing tools?

Thanks,
Dave

Hi avogadro users,

recently I’ve started to use Avogadro to design my initial molecules in my
projects, however I’m trying to find the Conformer Isomers of my molecules,
the point is that trying the follow procedure: Extensions -> Molecular
Mechanics -> Conformer search -> Random Rotor search (here I chose 5
conformers), Avogadro suddenly crashes. I attached the terminal message.
I’m running Avogadro 0.9.6 on Jaunty (Ubuntu). The other question is how can
I manipulate dihedral angles with Avogadro?

best regards,


leonardo

“I’m not questioning your powers of observation I’m merely remarking upon
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que muy poca gente se da cuenta”
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siempre os hace caer?"
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matar a alguien”
“Brick walls are there for a reason: they let us prove how badly we want
things”
“Las batallas contra las mujeres son las únicas que se ganan huyendo”
“El amor es el mejor motivo que existe para aprender un idioma”
“La soledad es una sed que la ilusión no satisface”
“El dolor es inevitable, el sufrimiento es opcional”
“El pensamiento es efímero, la imagen absoluta”
“Por mi raza hablará mi espíritu”
________________________________(_/)
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Hi,

On Wed, Sep 23, 2009 at 1:09 PM, Leonardo Andrés Espinosa Leal
espinosa.leal@gmail.com wrote:

Hi avogadro users,

recently I’ve started to use Avogadro to design my initial molecules in my
projects, however I’m trying to find the Conformer Isomers of my molecules,
the point is that trying the follow procedure: Extensions -> Molecular
Mechanics -> Conformer search -> Random Rotor search (here I chose 5
conformers), Avogadro suddenly crashes. I attached the terminal message.
I’m running Avogadro 0.9.6 on Jaunty (Ubuntu).

I fixed this bug in OpenBabel but I’m not sure when the ubuntu package
will be updated. LaserJock, Azeem?

The other question is how can
I manipulate dihedral angles with Avogadro?

The boncentric tool can be used for this.

best regards,


leonardo

“I’m not questioning your powers of observation I’m merely remarking upon
the paradox of asking a masked man who he is”
“El binomio de Newton es tan hermoso como la Venus de Milo: lo que pasa es
que muy poca gente se da cuenta”
"¡Oh seres humanos, hechos para alzar el vuelo!, ¿por qué una leve brisa
siempre os hace caer?"
“La música es como un cuchillo: puedes usarlo para cortar el pan o para
matar a alguien”
“Brick walls are there for a reason: they let us prove how badly we want
things”
“Las batallas contra las mujeres son las únicas que se ganan huyendo”
“El amor es el mejor motivo que existe para aprender un idioma”
“La soledad es una sed que la ilusión no satisface”
“El dolor es inevitable, el sufrimiento es opcional”
“El pensamiento es efímero, la imagen absoluta”
“Por mi raza hablará mi espíritu”
________________________________(_/)
tokbox: http://www.tokbox.com/leonardo646 (=’ .’=)
job: http://nano-bio.ehu.es/user/20 (“)
(”)
blog: http://cyosolo.blogspot.com/
myspace: http://www.myspace.com/cyosolo


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Hi, thanks for your replies,

anyway I update openbabel at 2.2.0 version and the problem still remains,
Avogadro suddenly crashes also using Systematic rotor search as steve
proposes. about dihedral angles I’ve not tried yet but I’ll ask you if I
have any other problems. I’d like to fix soon the problem with the
Conformer search, any help about this is welcome.


leonardo

“I’m not questioning your powers of observation I’m merely remarking upon
the paradox of asking a masked man who he is”
“El binomio de Newton es tan hermoso como la Venus de Milo: lo que pasa es
que muy poca gente se da cuenta”
"¡Oh seres humanos, hechos para alzar el vuelo!, ¿por qué una leve brisa
siempre os hace caer?"
“La música es como un cuchillo: puedes usarlo para cortar el pan o para
matar a alguien”
“Brick walls are there for a reason: they let us prove how badly we want
things”
“Las batallas contra las mujeres son las únicas que se ganan huyendo”
“El amor es el mejor motivo que existe para aprender un idioma”
“La soledad es una sed que la ilusión no satisface”
“El dolor es inevitable, el sufrimiento es opcional”
“El pensamiento es efímero, la imagen absoluta”
“Por mi raza hablará mi espíritu”
_________________________________ (_/)
tokbox: http://www.tokbox.com/leonardo646 (=’ .’=)
job: http://nano-bio.ehu.es/user/20 (“)
(”)
blog: http://cyosolo.blogspot.com/
myspace: http://www.myspace.com/cyosolo

Hi again,

I’m sorry this is embarrassing but it is necessary for feedback with other
users, I fixed the problem with the conformer search. I purged the OpenBabel
package installed and the Avogadro one, then I installed the 2.2 version of
OpenBabel and again the avogadro one. Now the search of conformers is
working perfectly!!! I’ll try the business with the dihedral angles later.

Thanks for your help,

leonardo


leonardo

“I’m not questioning your powers of observation I’m merely remarking upon
the paradox of asking a masked man who he is”
“El binomio de Newton es tan hermoso como la Venus de Milo: lo que pasa es
que muy poca gente se da cuenta”
"¡Oh seres humanos, hechos para alzar el vuelo!, ¿por qué una leve brisa
siempre os hace caer?"
“La música es como un cuchillo: puedes usarlo para cortar el pan o para
matar a alguien”
“Brick walls are there for a reason: they let us prove how badly we want
things”
“Las batallas contra las mujeres son las únicas que se ganan huyendo”
“El amor es el mejor motivo que existe para aprender un idioma”
“La soledad es una sed que la ilusión no satisface”
“El dolor es inevitable, el sufrimiento es opcional”
“El pensamiento es efímero, la imagen absoluta”
“Por mi raza hablará mi espíritu”
_________________________________ (_/)
tokbox: http://www.tokbox.com/leonardo646 (=’ .’=)
job: http://nano-bio.ehu.es/user/20 (“)
(”)
blog: http://cyosolo.blogspot.com/
myspace: http://www.myspace.com/cyosolo

On Sep 23, 2009, at 7:48 AM, Tim Vandermeersch wrote:

I fixed this bug in OpenBabel but I’m not sure when the ubuntu package
will be updated. LaserJock, Azeem?

For reference, what version of Open Babel has the fix?

The other question is how can
I manipulate dihedral angles with Avogadro?

The boncentric tool can be used for this.

You can also edit dihedral angles using the “Properties” tables. This
allows you to enter a specific value, which is somewhat hard to do
with the mouse tool.

Cheers,
-Geoff

Is there currently a GUI-based method to generate and view
conformations of a molecule? Using the forcefield extension, I appear
to be generating the conformers, but in View > Properties > Conformer
Properties, only a single entry shows up.

What conformer search are you using? The weighted search will just give you the lowest energy conformer, not generate new ones. Systematic searching should give you a set.

We would like to do this as part of a lab, so we need a GUI-based,
student-friendly way to generate and compare conformations. Does
anyone know if such a workflow is possible using existing tools?

Without much coding, yes. Open Babel has a new (v2.3) conformer search framework, which should probably replace the weighted search and will generate multiple conformations. Better yet, you can either pick low-energy conformers, or a diverse set (i.e., maximizing RMSD differences).

I just haven’t had time to splice the new framework into the forcefield extension. I also have some ideas about manual dihedral scans, but that will need someone with more programming time.

Hope that helps,
-Geoff

On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Is there currently a GUI-based method to generate and view
conformations of a molecule? Using the forcefield extension, I appear
to be generating the conformers, but in View > Properties > Conformer
Properties, only a single entry shows up.

What conformer search are you using? The weighted search will just give you the lowest energy conformer, not generate new ones. Systematic searching should give you a set.

Even with systematic and random search, I only get a single conformer
in the properties dialog. Is this a bug or am I missing a step?
(avogadro master and OB trunk)

We would like to do this as part of a lab, so we need a GUI-based,
student-friendly way to generate and compare conformations. Does
anyone know if such a workflow is possible using existing tools?

Without much coding, yes. Open Babel has a new (v2.3) conformer search framework, which should probably replace the weighted search and will generate multiple conformations. Better yet, you can either pick low-energy conformers, or a diverse set (i.e., maximizing RMSD differences).

I just haven’t had time to splice the new framework into the forcefield extension.

I should be able to spend some time on this, since it will be related
to my PI’s lab course. I saw a GA search heuristic go into trunk, is
this the one you mean? I can replace the current weighted search in
the forcefield extension with that. Are the different fitness options
already incorporated into OB, or can it take a user supplied fitness
function callback? I can add some of these in if there’s time.

I also have some ideas about manual dihedral scans, but that will need someone with more programming time.

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

Dave

On 19 December 2011 19:54, David Lonie loniedavid@gmail.com wrote:

On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Is there currently a GUI-based method to generate and view
conformations of a molecule? Using the forcefield extension, I appear
to be generating the conformers, but in View > Properties > Conformer
Properties, only a single entry shows up.

What conformer search are you using? The weighted search will just give you the lowest energy conformer, not generate new ones. Systematic searching should give you a set.

Even with systematic and random search, I only get a single conformer
in the properties dialog. Is this a bug or am I missing a step?
(avogadro master and OB trunk)

At some point I changed the behaviour of systematic search to match
the weighted search. This was (a) for consistency, and (b) because the
systematic search uses up your memory if the molecule has several
rotatable bonds. Sorry if this was a mistake, but it seemed that the
goal of the systematic search was simply to find a single low energy
conformer.

We would like to do this as part of a lab, so we need a GUI-based,
student-friendly way to generate and compare conformations. Does
anyone know if such a workflow is possible using existing tools?

Without much coding, yes. Open Babel has a new (v2.3) conformer search framework, which should probably replace the weighted search and will generate multiple conformations. Better yet, you can either pick low-energy conformers, or a diverse set (i.e., maximizing RMSD differences).

I just haven’t had time to splice the new framework into the forcefield extension.

I should be able to spend some time on this, since it will be related
to my PI’s lab course. I saw a GA search heuristic go into trunk, is
this the one you mean? I can replace the current weighted search in
the forcefield extension with that. Are the different fitness options
already incorporated into OB, or can it take a user supplied fitness
function callback? I can add some of these in if there’s time.

I also have some ideas about manual dihedral scans, but that will need someone with more programming time.

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

Dave


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On Mon, Dec 19, 2011 at 2:54 PM, David Lonie loniedavid@gmail.com wrote:

On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Is there currently a GUI-based method to generate and view
conformations of a molecule? Using the forcefield extension, I appear
to be generating the conformers, but in View > Properties > Conformer
Properties, only a single entry shows up.

What conformer search are you using? The weighted search will just give you the lowest energy conformer, not generate new ones. Systematic searching should give you a set.

Even with systematic and random search, I only get a single conformer
in the properties dialog. Is this a bug or am I missing a step?
(avogadro master and OB trunk)

Found the problem: Commit fb544bfd0109bd0952b03d4d4f0e15009c1c3faa add
the ability to selectively enable/disable multiple conformers in the
prop dialogs, but it doesn’t seem to ever get enabled. I’ll push a
patch soon.

Dave

On Dec 19, 2011, at 2:54 PM, David Lonie wrote:

this the one you mean? I can replace the current weighted search in
the forcefield extension with that. Are the different fitness options
already incorporated into OB, or can it take a user supplied fitness
function callback? I can add some of these in if there’s time.

There are different fitness options already incorporated, and it can take a user-supplied fitness (e.g., in OB trunk, it offers an energy minimization option more like the weighted search). Take a look at src/ops/conformer.cpp for examples.

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

My game-plan would allow for scans of multiple dihedrals systematically – but you would pick the dihedrals to scan, rather than the automatic global systematic search.

-Geoff

On Dec 19, 2011, at 4:47 PM, Geoffrey Hutchison wrote:

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

Oh, but one thing the 3rd party extensions offers, which might be useful for a lab course – a graphical plot of conformer energy vs. conformer #, which enables you to click on a structure to switch the geometry in the main Avogadro window. That shouldn’t be too hard if you have free time. :slight_smile:

Cheers,
-Geoff

On Mon, Dec 19, 2011 at 4:48 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Dec 19, 2011, at 4:47 PM, Geoffrey Hutchison wrote:

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

Oh, but one thing the 3rd party extensions offers, which might be useful for a lab course – a graphical plot of conformer energy vs. conformer #, which enables you to click on a structure to switch the geometry in the main Avogadro window. That shouldn’t be too hard if you have free time. :slight_smile:

I can’t believe I forgot about that – thanks! :slight_smile:

Dave