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

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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.com>wrote:

> 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: 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


------------------------------

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