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Re: [Avogadro-Discuss] Avogadro-Discuss Digest, Vol 46, Issue 6
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From: Raja S. <ind...@ya...> - 2013-06-01 08:59:32
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________________________________ From: Raja Sekhar <ind...@ya...> To: "avo...@li..." <avo...@li...> 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: "avo...@li..." <avo...@li...> To: avo...@li... Sent: Friday, 31 May 2013, 8:51 Subject: Avogadro-Discuss Digest, Vol 46, Issue 6 Send Avogadro-Discuss mailing list submissions to avo...@li... 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 avo...@li... You can reach the person managing the list at avo...@li... 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 (lgo...@ca...) 4. Re: Calculation of molecular dimensions (lgo...@ca...) 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: avo...@li... Message-ID: <201...@we...> 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 <geo...@gm...> Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions To: Arnout D'Haese <Arnout.DHaese@UGent.be> Cc: avo...@li... Message-ID: <D81...@gm...> 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: lgo...@ca... Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions To: avo...@li... Message-ID: <201...@sm...> 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 ?: ''lor...@gm...''. Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati all'indirizzo lor...@gm.... Successivamente a questa data l'indirizzo l.g...@ca... non esister? pi?. Grazie Lorenzo Gontrani Dear Sir or Madam, this is an automatic response to inform you that my new email address is: ''lor...@gm...''. Until June 29, 2013 all the emails will be automatically forwarded to lor...@gm.... After this date the address l.g...@ca... will no longer exist. Regards Lorenzo Gontrani ------------------------------ Message: 4 Date: Tue, 28 May 2013 15:45:38 +0200 (CEST) From: lgo...@ca... Subject: Re: [Avogadro-Discuss] Calculation of molecular dimensions To: avo...@li... Message-ID: <201...@sm...> 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 ?: ''lor...@gm...''. Fino al 29 Giugno 2013 tutti i messaggi verrano automaticamente inoltrati all'indirizzo lor...@gm.... Successivamente a questa data l'indirizzo l.g...@ca... non esister? pi?. Grazie Lorenzo Gontrani Dear Sir or Madam, this is an automatic response to inform you that my new email address is: ''lor...@gm...''. Until June 29, 2013 all the emails will be automatically forwarded to lor...@gm.... After this date the address l.g...@ca... will no longer exist. Regards Lorenzo Gontrani ------------------------------ Message: 5 Date: Wed, 29 May 2013 13:28:48 -0500 From: Brent Friesen <och...@gm...> Subject: [Avogadro-Discuss] creating *.mol file To: avo...@li... Message-ID: <CABmRHAV2aNBhXJ=cWR...@ma...> 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 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 6 Date: Thu, 30 May 2013 10:24:38 -0400 From: David Lonie <dav...@ki...> Subject: Re: [Avogadro-Discuss] creating *.mol file To: avo...@li... Message-ID: <CA+=e1o...@ma...> 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 <och...@gm...>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 > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > Avogadro-Discuss mailing list > Avo...@li... > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 7 Date: Fri, 31 May 2013 15:17:07 +0200 From: Tir <ti...@me...> Subject: [Avogadro-Discuss] Question about Avogadro bonds display To: avo...@li... Message-ID: <573...@me...> 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 <geo...@gm...> Subject: Re: [Avogadro-Discuss] Question about Avogadro bonds display To: Tir <ti...@me...> Cc: "avo...@li..." <avo...@li...> Message-ID: <89D...@gm...> 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 Avo...@li... https://lists.sourceforge.net/lists/listinfo/avogadro-discuss End of Avogadro-Discuss Digest, Vol 46, Issue 6 *********************************************** |