Avogadro-Discuss Digest, Vol 46, Issue 6

Dear Co-Ordinator,

        I am using Avagadro for obtaining the first three lowest energy conformers of trimethyl phosphine. When I tried to optimise using conformer search I got 26 structures. I had to optimize one by one to obtain the three lowest energy conformers. But they are not matching with the one quoted in literature as the stable conformers at room temperature. Is it that the stable transformers at room temperature need not be corresponding to the ones wth lowest energy?

Please suggest me a way to use Avagadro to just how to put constraints on optimization. Somehow I could not do it ( may be a sample file of any molecule including the constraints).
Also I request you address the other problem

regards

Raja


From: "avogadro-discuss-request@lists.sourceforge.net" avogadro-discuss-request@lists.sourceforge.net
To: avogadro-discuss@lists.sourceforge.net
Sent: Friday, 31 May 2013, 8:51
Subject: Avogadro-Discuss Digest, Vol 46, Issue 6

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Today’s Topics:

  1. Calculation of molecular dimensions (Arnout D’Haese)
  2. Re: Calculation of molecular dimensions (Geoffrey Hutchison)
  3. Re: Calculation of molecular dimensions (lgontran@caspur.it)
  4. Re: Calculation of molecular dimensions (lgontran@caspur.it)
  5. creating *.mol file (Brent Friesen)
  6. Re: creating *.mol file (David Lonie)
  7. Question about Avogadro bonds display (Tir)
  8. Re: Question about Avogadro bonds display (Geoffrey Hutchison)

Message: 1
Date: Sat, 25 May 2013 23:43:18 +0200
From: Arnout D’Haese Arnout.DHaese@UGent.be
Subject: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
20130525234318.Horde.2DqOWFyqiOZRoTB2l7EVjaA@webmail.ugent.be
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; DelSp=Yes

Dear Avogadro discussion list members,

For research purposes, I’m looking for a software package that is able
to calculate the size of organic molecules with weights ranging from
200 to 500 g/mole, as either an equivalent spherical diameter, or
dimensions along the 3 axes. Is there a tool within Avogadro that
calculates molecular size ?

Kind regards, Arnout


Message: 2
Date: Tue, 28 May 2013 09:44:33 -0400
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: Arnout D’Haese Arnout.DHaese@UGent.be
Cc: avogadro-discuss@lists.sourceforge.net
Message-ID: D81DFB46-E179-4016-9489-15F4974C4F22@gmail.com
Content-Type: text/plain; charset=windows-1252

Avogadro does have a measure tool, which allows you to measure between atoms, and several features (e.g., the align tool) that allow you to align a molecule to a particular reference frame.

For research purposes, I’m looking for a software package that is able
to calculate the size of organic molecules with weights ranging from

calculates molecular size ?

But your question makes it sound like you want to do this for a large batch of molecules. If so, I?d suggest you look at writing a little script, e.g., with Pybel:
http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_Pybel.html

Hope that helps,
-Geoff


Message: 3
Date: Mon, 27 May 2013 05:49:48 +0200 (CEST)
From: lgontran@caspur.it
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 20130527034948.A93A5C6AA2@smtp.caspur.it
Content-Type: text/plain; charset=“iso-8859-1”; format=flowed

Gentile mittente, questa ? una risposta automatica. La informo che il mio
nuovo indirizzo di posta elettronica ?: ‘‘lorenzo.gontrani@gmail.com’’.
Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati
all’indirizzo lorenzo.gontrani@gmail.com. Successivamente a questa data
l’indirizzo l.gontrani@caspur.it non esister? pi?.
Grazie
Lorenzo Gontrani
Dear Sir or Madam, this is an automatic response to inform you that my new
email address is: ‘‘lorenzo.gontrani@gmail.com’’.
Until June 29, 2013 all the emails will be automatically forwarded to
lorenzo.gontrani@gmail.com. After this date the address l.gontrani@caspur.it
will no longer exist.
Regards
Lorenzo Gontrani


Message: 4
Date: Tue, 28 May 2013 15:45:38 +0200 (CEST)
From: lgontran@caspur.it
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 20130528134538.63C6553BD8@smtp.caspur.it
Content-Type: text/plain; charset=“iso-8859-1”; format=flowed

Gentile mittente, questa ? una risposta automatica. La informo che il mio
nuovo indirizzo di posta elettronica ?: ‘‘lorenzo.gontrani@gmail.com’’.
Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati
all’indirizzo lorenzo.gontrani@gmail.com. Successivamente a questa data
l’indirizzo l.gontrani@caspur.it non esister? pi?.
Grazie
Lorenzo Gontrani
Dear Sir or Madam, this is an automatic response to inform you that my new
email address is: ‘‘lorenzo.gontrani@gmail.com’’.
Until June 29, 2013 all the emails will be automatically forwarded to
lorenzo.gontrani@gmail.com. After this date the address l.gontrani@caspur.it
will no longer exist.
Regards
Lorenzo Gontrani


Message: 5
Date: Wed, 29 May 2013 13:28:48 -0500
From: Brent Friesen ochemonline@gmail.com
Subject: [Avogadro-Discuss] creating *.mol file
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CABmRHAV2aNBhXJ=cWRT4NwU8r71D0LpyhrGKaTbVM_2rR6j6zQ@mail.gmail.com
Content-Type: text/plain; charset=“iso-8859-1”

I would like to use Avogadro as a way to create energy-minimized molecular
conformations for an NMR prediction platform called PERCH.
PERCH will only accept 3D structure files in *.mol or *.mms format.
How can I save the Avogadro-generated 3 structure as a *.mol file?
Thanks
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Message: 6
Date: Thu, 30 May 2013 10:24:38 -0400
From: David Lonie david.lonie@kitware.com
Subject: Re: [Avogadro-Discuss] creating *.mol file
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CA+=e1ovjjJzOEUrbR4PuJj13mtFfjvAXcFppnq7H0m-PAe2bNw@mail.gmail.com
Content-Type: text/plain; charset=“iso-8859-1”

Hi Brent,

Did you try:
File >> Save as >> “mymolecule.mol”?

Best,
Dave

On Wed, May 29, 2013 at 2:28 PM, Brent Friesen ochemonline@gmail.comwrote:

I would like to use Avogadro as a way to create energy-minimized molecular
conformations for an NMR prediction platform called PERCH.
PERCH will only accept 3D structure files in *.mol or *.mms format.
How can I save the Avogadro-generated 3 structure as a *.mol file?
Thanks


Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
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Message: 7
Date: Fri, 31 May 2013 15:17:07 +0200
From: Tir tir303@me.com
Subject: [Avogadro-Discuss] Question about Avogadro bonds display
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 57340C05-E328-4F64-A41C-91C4DCD6DFEF@me.com
Content-Type: text/plain; charset=us-ascii

hello,

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Thanks!


Message: 8
Date: Fri, 31 May 2013 11:50:52 -0400
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] Question about Avogadro bonds display
To: Tir tir303@me.com
Cc: "avogadro-discuss@lists.sourceforge.net"
avogadro-discuss@lists.sourceforge.net
Message-ID: 89D10E00-3FEC-4B1E-82BC-9766941C148D@gmail.com
Content-Type: text/plain; charset=us-ascii

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Good question. At the moment, no. I see that you’re using a @me.com address. If you’d like this, I can code it up in a few minutes and add it to the nightly Mac build tonight?

http://avogadro.openmolecules.net/nightly/mac/unstable/

-Geoff



Get 100% visibility into Java/.NET code with AppDynamics Lite
It’s a free troubleshooting tool designed for production
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
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Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
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End of Avogadro-Discuss Digest, Vol 46, Issue 6



From: Raja Sekhar indus2006@yahoo.co.uk
To: "avogadro-discuss@lists.sourceforge.net" avogadro-discuss@lists.sourceforge.net
Sent: Friday, 31 May 2013, 19:25
Subject: Re: Avogadro-Discuss Digest, Vol 46, Issue 6

Dear Co-Ordinator,

        I am using Avagadro for obtaining the first three lowest energy conformers of trimethyl phosphine. When I tried to optimise using conformer search I got 26 structures. I had to optimize one by one to obtain the three lowest energy conformers. But they are not matching with the one quoted in literature as the stable conformers at room temperature. Is it that the stable transformers at room temperature need not be corresponding to the ones wth lowest energy?

Please suggest me a way to use Avagadro to just how to put constraints on optimization. Somehow I could not do it ( may be a sample file of any molecule including the constraints).
Also I request you address the other problem

regards

Raja


From: "avogadro-discuss-request@lists.sourceforge.net" avogadro-discuss-request@lists.sourceforge.net
To: avogadro-discuss@lists.sourceforge.net
Sent: Friday, 31 May 2013, 8:51
Subject: Avogadro-Discuss Digest, Vol 46, Issue 6

Send Avogadro-Discuss mailing list submissions to
avogadro-discuss@lists.sourceforge.net

To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
or, via email, send a message with subject or body ‘help’ to
avogadro-discuss-request@lists.sourceforge.net

You can reach the person managing the list at
avogadro-discuss-owner@lists.sourceforge.net

When replying, please edit your Subject line so it is more specific
than “Re: Contents of Avogadro-Discuss digest…”

Today’s Topics:

  1. Calculation of molecular dimensions (Arnout D’Haese)
  2. Re: Calculation of molecular dimensions (Geoffrey Hutchison)
  3. Re: Calculation of molecular dimensions (lgontran@caspur.it)
  4. Re: Calculation of molecular dimensions (lgontran@caspur.it)
  5. creating *.mol file (Brent Friesen)
  6. Re: creating *.mol file (David Lonie)
  7. Question about Avogadro bonds display (Tir)
  8. Re: Question about
    Avogadro bonds display (Geoffrey Hutchison)

Message: 1
Date: Sat, 25 May 2013 23:43:18 +0200
From: Arnout D’Haese Arnout.DHaese@UGent.be
Subject: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
20130525234318.Horde.2DqOWFyqiOZRoTB2l7EVjaA@webmail.ugent.be
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; DelSp=Yes

Dear Avogadro discussion list members,

For research
purposes, I’m looking for a software package that is able
to calculate the size of organic molecules with weights ranging from
200 to 500 g/mole, as either an equivalent spherical diameter, or
dimensions along the 3 axes. Is there a tool within Avogadro that
calculates molecular size ?

Kind regards, Arnout


Message: 2
Date: Tue, 28 May 2013 09:44:33 -0400
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: Arnout D’Haese Arnout.DHaese@UGent.be
Cc: avogadro-discuss@lists.sourceforge.net
Message-ID: D81DFB46-E179-4016-9489-15F4974C4F22@gmail.com
Content-Type: text/plain; charset=windows-1252

Avogadro does have a measure tool, which allows you to measure between atoms, and several features (e.g., the align tool) that allow you to align a molecule to a particular reference frame.

For research purposes, I’m looking for a software package that is able
to calculate the size of organic molecules with weights ranging from

calculates molecular size ?

But your question makes it sound like you want to do this for a large batch of molecules. If so, I?d suggest you look at writing a little script, e.g., with Pybel:
http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_Pybel.html

Hope that helps,
-Geoff


Message: 3
Date: Mon, 27 May 2013 05:49:48 +0200 (CEST)
From: lgontran@caspur.it
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 20130527034948.A93A5C6AA2@smtp.caspur.it
Content-Type: text/plain; charset=“iso-8859-1”; format=flowed

Gentile mittente, questa ? una risposta automatica. La informo che il
mio
nuovo indirizzo di posta elettronica ?: ‘‘lorenzo.gontrani@gmail.com’’.
Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati
all’indirizzo lorenzo.gontrani@gmail.com. Successivamente a questa data
l’indirizzo l.gontrani@caspur.it non esister? pi?.
Grazie
Lorenzo Gontrani
Dear Sir or Madam, this is an automatic response to inform you that my new
email address is: ‘‘lorenzo.gontrani@gmail.com’’.
Until June 29, 2013 all the emails will be automatically forwarded to
lorenzo.gontrani@gmail.com. After this date the address l.gontrani@caspur.it
will no longer exist.
Regards
Lorenzo Gontrani


Message: 4
Date: Tue, 28 May 2013 15:45:38 +0200 (CEST)
From: lgontran@caspur.it
Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 20130528134538.63C6553BD8@smtp.caspur.it
Content-Type: text/plain; charset=“iso-8859-1”;
format=flowed

Gentile mittente, questa ? una risposta automatica. La informo che il mio
nuovo indirizzo di posta elettronica ?: ‘‘lorenzo.gontrani@gmail.com’’.
Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati
all’indirizzo lorenzo.gontrani@gmail.com. Successivamente a questa data
l’indirizzo l.gontrani@caspur.it non esister? pi?.
Grazie
Lorenzo Gontrani
Dear Sir or Madam, this is an automatic response to inform you that my new
email address is: ‘‘lorenzo.gontrani@gmail.com’’.
Until June 29, 2013 all the emails will be automatically forwarded
to
lorenzo.gontrani@gmail.com. After this date the address l.gontrani@caspur.it
will no longer exist.
Regards
Lorenzo Gontrani


Message: 5
Date: Wed, 29 May 2013 13:28:48 -0500
From: Brent Friesen ochemonline@gmail.com
Subject: [Avogadro-Discuss] creating *.mol file
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CABmRHAV2aNBhXJ=cWRT4NwU8r71D0LpyhrGKaTbVM_2rR6j6zQ@mail.gmail.com
Content-Type: text/plain; charset=“iso-8859-1”

I would like to use Avogadro as a way to create energy-minimized molecular
conformations for an NMR prediction platform called PERCH.
PERCH will only accept 3D structure files in *.mol or *.mms format.
How can I save the Avogadro-generated 3 structure as a *.mol file?
Thanks
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Message: 6
Date: Thu, 30 May 2013 10:24:38 -0400
From: David Lonie david.lonie@kitware.com
Subject: Re: [Avogadro-Discuss] creating *.mol file
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CA+=e1ovjjJzOEUrbR4PuJj13mtFfjvAXcFppnq7H0m-PAe2bNw@mail.gmail.com
Content-Type: text/plain; charset=“iso-8859-1”

Hi Brent,

Did you try:
File >> Save as >> “mymolecule.mol”?

Best,
Dave

On Wed, May 29, 2013 at 2:28 PM, Brent Friesen ochemonline@gmail.comwrote:

I would like to use Avogadro as a way to create energy-minimized molecular
conformations for an NMR prediction platform called PERCH.
PERCH will only accept 3D structure files in *.mol or *.mms format.
How can I save the
Avogadro-generated 3 structure as a *.mol file?
Thanks


Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1


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Message: 7
Date: Fri, 31 May 2013 15:17:07 +0200
From: Tir tir303@me.com
Subject: [Avogadro-Discuss] Question about Avogadro bonds display
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 57340C05-E328-4F64-A41C-91C4DCD6DFEF@me.com
Content-Type: text/plain; charset=us-ascii

hello,

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a
way to only display atoms and hide all bonds? Without manually removing each of them.

Thanks!


Message: 8
Date: Fri, 31 May 2013 11:50:52 -0400
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] Question about Avogadro bonds display
To: Tir tir303@me.com
Cc: "avogadro-discuss@lists.sourceforge.net"
avogadro-discuss@lists.sourceforge.net
Message-ID: 89D10E00-3FEC-4B1E-82BC-9766941C148D@gmail.com
Content-Type: text/plain; charset=us-ascii

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Good question. At the moment, no. I see that you’re using a @me.com address. If you’d like this, I can code it up in a few minutes and add it to the nightly Mac build tonight?

http://avogadro.openmolecules.net/nightly/mac/unstable/

-Geoff



Get 100% visibility into Java/.NET code with AppDynamics Lite
It’s a free troubleshooting tool designed for production
Get
down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap2



Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

End of Avogadro-Discuss Digest, Vol 46, Issue 6