From owner-chemistry@ccl.net Mon Sep 4 05:24:00 2006 From: "Egon Willighagen e.willighagen-#-science.ru.nl" To: CCL Subject: CCL: Chemoinformatics Blogs Message-Id: <-32475-060904045639-28057-KuhEjaYj32HnfSd5p9qGfQ_-_server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Sep 2006 10:14:32 +0200 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [e.willighagen*o*science.ru.nl] Dear CCL-readers, it is my great pleasure to announce Planet Blue Obelisk [1], a blog aggregator for the Blue Obelisk Movement [2,3]. It is a bit like the CCL mailing list, but different in some ways: first, a blog is a HTML page with small day-to-day notes by a specific author, often including images to make things more visual. Additionally, blogs often have thoughts instead of questions. The planet [1] has contributions from 10 scientists from all over the world, and discusses chemoinformatics (including bits of modeling) from a rather practical point of few (code snippets) to philisophical thoughts. Most authors welcome comments and the planet provides link to allow that. Looking forward to seeing you on the planet! Kind regards, Egon Willighagen 1.http://www.blueobelisk.org/planetbo/ 2.http://dx.doi.org/10.1021/ci050400b 3.http://www.blueobelisk.org/ -- e.willighagen||science.ru.nl Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Mon Sep 4 05:58:00 2006 From: "Tanja van Mourik tanja.vanmourik() st-andrews.ac.uk" To: CCL Subject: CCL:G: BSSE and Counterpoise method Message-Id: <-32476-060904053148-5984-EbHVymuh/WfVbFbFLvF5IQ]~[server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Sep 2006 09:55:12 +0100 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik%st-andrews.ac.uk] Dear Fuji, > I found the following model input for the counterpoise method in gaussian manual. In this, counterpoise=2 means this system is composed by two molecules, or HF---HF. The numbers on the right means that this atom belongs to the molecule 1 or 2. > Now, in order to calculate BSSE, I want to specify ghost atoms (NewBq key word) for the molecule 2 . Can any one tell me how to do this? I mean I need the syntax. > You do not need to specify the ghost orbitals when using the Counterpoise keyword; Gaussian automatically calculates the dimer, monomer1+ghost, monomer2+ghost, and monomer-without-ghost energies (all at the geometry of the dimer) - five energies in total for a two-fragment system. The monomer+ghost energies are indicated by "DCBS" (dimer centred basis set), the monomer-without-ghost energies by "MCBS" (monomer centred basis set). Gaussian uses these energies to calculate the CP-corrected dimer energy and BSSE energy, which are printed at the end of the output. Hope that helps, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik]|[st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= From owner-chemistry@ccl.net Mon Sep 4 07:46:01 2006 From: "Rene Thomsen rt-#-molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2006 v1.5 Message-Id: <-32477-060904074336-9463-XaIfD05ozq7VN1FcwXffMg,server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 4 Sep 2006 07:43:36 -0400 Sent to CCL by: "Rene Thomsen" [rt\a/molegro.com] Aarhus, Denmark, September 4th, 2006 - Molegro is pleased to announce a new release of Molegro Virtual Docker 2006, an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 1.5 (since version 1.1): * Grid-based version of the MolDock scoring function (4-5 times speedup) * New MolDock SE (simplex evolution) search algorithm (technology preview) * Workspace Finder (for easy browsing and inspection of molecular structures) * Sequence Viewer * Cartoon rendering (secondary structure visualization) * Faster wireframe visualization * New RMSD measure that takes any potential symmetries into account For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt],[molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon Sep 4 08:34:00 2006 From: "Abrash, Samuel sabrash_+_richmond.edu" To: CCL Subject: CCL:G: vibrational frequency output of GO3W Message-Id: <-32478-060904083259-2637-ocJHkatGDOQhb0/7z2zEGA]^[server.ccl.net> X-Original-From: "Abrash, Samuel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Sep 2006 08:32:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash%richmond.edu] What Errol was saying (below) is that by animating the vibration, you can see with your eyes which motions are dominant, and can therefore assign them as C-H stretch, scissor etc. Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash#%#richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash "The time it takes to do a scientific project is given by the equation t = 2a + b, where a is the original estimate of the length of the project, 2 is a correction factor, and b is a number large compared to 2a." -----Original Message----- > From: owner-chemistry#%#ccl.net [mailto:owner-chemistry#%#ccl.net] Sent: Sunday, September 03, 2006 12:26 PM To: Abrash, Samuel Subject: CCL:G: vibrational frequency output of GO3W Sent to CCL by: "neeraj misra" [misraneeraj[-]gmail.com] ------=_Part_44335_29083124.1157296455377 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks for the reply! Actually it is not that I want to animate the vibrations, instead I wish to write the different modes corresponding to a particular frequency.How to identify the modes for example whether it is a C=O stretch or C-C stretch etc.Any help would be a big help. Thanks in advance On 9/3/06, errol lewars elewars^-^trentu.ca wrote: > > Sent to CCL by: errol lewars [elewars!=!trentu.ca] > 2006 Sept 3 > > Hello, > > If what you mean is that you want to see what kind of atomic motion each > vibrational frequency corresponds to (stretch, bend, torsional, or some > combination of these), then you should use a program that can animate > the vibrations, such as GaussView; there are also free programs that can > do this. You may be able to puzzle out the motions from the "direction > vectors" (Cartesian components of the atomic motions) that Gaussian > prints out, but this is much less satisfactory. > > E. Lewars > ==== > > > neeraj misra misraneeraj/./gmail.com wrote: > > >Sent to CCL by: "neeraj misra" [misraneeraj#,#gmail.com] > >Dear ccl'ers, I would be grateful if someone of you could advise me how > to pick up the assignments (potential energy distributions) in the > vibrational analysis output of a gaussian 03 W run.I have done the > vibrational analysis but how to know that which mode (i.e stretch, angle > bend, wag, torsion) is having significant contribution at a particular > frequency.Anyone who can explain with a gaussian vibrational freq example > would be a big help.I realise its a trivial question but it does matter to > someone like me who has just started in this. > > thanks in advance > > neeeraj> > > > -- Neeraj Misra PhD Assoc.Prof in Physics Lucknow University 226007 Phone 0522-2740410 (O) 0522-2335914 (R) ------=_Part_44335_29083124.1157296455377 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Thanks for the reply! Actually it is not that I want to animate the vibrations, instead I wish to write the different modes corresponding to a particular frequency.How to identify the modes for example whether it is a C=O stretch or C-C stretch etc.Any help would be a big help.
           & nbsp;    Thanks in advance

 
On 9/3/06, errol lewars elewars^-^trentu.ca <owner-chemistry(a)ccl.net> ; wrote:
Sent to CCL by: errol lewars [elewars!=!trentu.ca]
2006 Sept 3

Hello,

If what you mean is that you want to see what kind of atomic motion each
vibrational frequency corresponds to (stretch, bend, torsional, or some
combination of these), then you should use a program that can animate
the vibrations, such as GaussView; there are also free programs that can
do this. You may be able to puzzle out the motions from the "direction
vectors" (Cartesian components of the atomic motions) that Gaussian
prints out, but this is much less satisfactory.

E. Lewars
====


neeraj misra misraneeraj/./gmail.com wrote:

>Sent to CCL by: "neeraj  misra" [misraneeraj#,#gmail.com]
>Dear ccl'ers, I would be grateful if someone of you could advise me how to pick up the assignments (potential energy distributions) in the vibrational analysis output of a gaussian 03 W run.I have done the vibrational analysis but how to know that which mode (i.e stretch, angle bend, wag, torsion) is having significant contribution at a particular frequency.Anyone who can explain with a gaussian vibrational freq example would be a big help.I realise its a trivial question but it does matter to someone like me who has just started in this.
>           ;             ;         thanks in advance
>         &nb sp;           &nb sp;           &nb sp;           &nb sp;    neeeraj>
>
>
>
>



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--
Neeraj Misra PhD
Assoc.Prof in Physics
Lucknow University 226007
Phone 0522-2740410 (O)
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