Error during conformational search

Hi David,

thanks so much for your quick reply.
Please find in attachment the molecule that caused the crash.

I’m a Phd student and I’ll have to do 'systematic research of rotors’
even for much larger molecules.

Tanks again for your help
Federica

Def. Quota David Lonie loniedavid@gmail.com:

Hi Federica,

On Tue, Mar 13, 2012 at 5:28 AM, fbisignano@unical.it wrote:

I’m doing the research of the conformers with Avogadro.
I made a ‘systematic research of rotors’ for a molecule of 36 atoms
and 8 rotatable bonds. This one has been successful.
But when I did the same operation for one molecule of 45 atoms and 11
rotatable bonds, I found the following error:

   Microsoft Visual C++ Runtime Library

RUNTIME ERROR!
Program: C:\Programmi_1\Avogadro\bin\avogadro.exe
This application has requested the Runtime to terminate it in an
unusual way.
Please contact the application’s support team for more information.

Can you send a copy of the molecule that caused this crash? This will
be much easier to track down and fix if we can reproduce the problem.

Thanks,

Dave


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Dear all,

I’m doing the research of the conformers with Avogadro.
I made a ‘systematic research of rotors’ for a molecule of 36 atoms
and 8 rotatable bonds. This one has been successful.
But when I did the same operation for one molecule of 45 atoms and 11
rotatable bonds, I found the following error:

Microsoft Visual C++ Runtime Library

RUNTIME ERROR!
Program: C:\Programmi_1\Avogadro\bin\avogadro.exe
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application’s support team for more information.

I am running Avogadro 1.0.3 on a 64-bit Windows operating system
(Intel ® Core ™ i5 CPU M460@ 2.53 GHz 2.53 GHz; RAM: 6.00 GB).

If someone may help me solve this problem, I would be very grateful.
Thank you for your attention.
Best regards
Federica


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In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e’ vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio.

Hi Federica,

On Tue, Mar 13, 2012 at 5:28 AM, fbisignano@unical.it wrote:

I’m doing the research of the conformers with Avogadro.
I made a ‘systematic research of rotors’ for a molecule of 36 atoms
and 8 rotatable bonds. This one has been successful.
But when I did the same operation for one molecule of 45 atoms and 11
rotatable bonds, I found the following error:

   Microsoft Visual C++ Runtime Library

RUNTIME ERROR!
Program: C:\Programmi_1\Avogadro\bin\avogadro.exe
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application’s support team for more information.

Can you send a copy of the molecule that caused this crash? This will
be much easier to track down and fix if we can reproduce the problem.

Thanks,

Dave

I’m a Phd student and I’ll have to do ‘systematic research of rotors’ even for much larger molecules.

You may want to investigate the genetic-algorithm and Monte Carlo weighted search options in Open Babel (which are used by Avogadro). These can be accessed from the babel command-line and GUI.

http://openbabel.org/docs/dev/Command-line_tools/babel.html#generating-conformers-for-structures

Hope that helps,
-Geoff

On Thu, Mar 15, 2012 at 11:52 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I’m a Phd student and I’ll have to do ‘systematic research of rotors’ even for much larger molecules.

You may want to investigate the genetic-algorithm and Monte Carlo weighted search options in Open Babel (which are used by Avogadro). These can be accessed from the babel command-line and GUI.

http://openbabel.org/docs/dev/Command-line_tools/babel.html#generating-conformers-for-structures

I agree with Geoff – that molecule would generate quite a few
conformers, at least 10,000 (the GUI cuts off there – there are
probably many more potential conformers for this flexible of a
molecule). I started the search and within seconds the search had
consumed over 2GB of RAM to store the conformer data. This is probably
what caused your crash – if I had not stopped avogadro on my system,
I would have quickly run out of memory and crashed, too.

Unfortunately Avogadro doesn’t currently have any utilities to
generate this many conformers in a memory efficient way, which would
require writing to disk as more conformers generated. Your options
here are to use a different search algorithm (random/Monte Carlo or
GA) to try just sampling some of the conformational space, or try to
find a computer with an enormous RAM reserve.

If you really do need to generate all 10,000+ conformers, you’ll
probably need to use the commandline openbabel interface. The Avogadro
interface is only capable of generating 10,000 conformers. I doubt
that the raw babel CLI interface has such a restriction, but I’m not
100% sure on that.

Hope this helps,

Dave

On Thu, 15 Mar 2012 15:52:00 -0000, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

I’m a Phd student and I’ll have to do ‘systematic research of rotors’ even for much larger molecules.

You may want to investigate the genetic-algorithm and Monte Carlo weighted search options in Open Babel (which are used by Avogadro). These can be accessed from the babel command-line and GUI.

http://openbabel.org/docs/dev/Command-line_tools/babel.html#generating-conformers-for-structures

Metadynamics and umbrella sampling might also be worth a look, especially since you’re moving to larger molecules. Maybe take a look at PLUMED 1 and the codes it integrates with.

-Ian Kirker