From owner-chemistry@ccl.net Tue Jul 10 03:33:00 2007 From: "Noel M O Boyle baoilleach*gmail.com" To: CCL Subject: CCL: ANN: openbabel-python 1.2.1 for Windows Message-Id: <-34700-070710032952-11164-8p3/62L4ZFLtKBdTWfs0pA ~ server.ccl.net> X-Original-From: "Noel M O Boyle" Date: Tue, 10 Jul 2007 03:29:48 -0400 Sent to CCL by: "Noel M O Boyle" [baoilleach!A!gmail.com] Announcing the release of the OpenBabel module for Python, version 1.2.1, for Windows, available from http://openbabel.sourceforge.net/wiki/Install. OpenBabel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. This Python module allows you to access this popular C++ library in your Python scripts. New features in 1.2.1: (1) Descriptor values for LogP, MR and PSA can be calculated (2) Incorporates all bug fixes included in the recent OpenBabel 2.1.1 New features in 1.2: (1) Data fields in file formats like MOL2 and SDF can now be accessed and edited (2) Unit cell data in crystallographic file formats such as CIF can now be accessed (3) A list of all detected input and output file formats can be accessed Core features: (1) Read and write over 80 molecular file formats (2) Access molecular properties like molecular weight, formula, charge (3) Daylight-type fingerprints and calculation of the Tanimoto coefficient (4) SMARTS pattern matching (5) Graph algorithms such as the Smallest Set of Smallest Rings (SSSR) and Depth-First Iteration over atoms Documentation: (1) The Python module: http://openbabel.sourceforge.net/wiki/Python (2) The C++ toolkit: http://openbabel.sourceforge.net/api/2.1.0/index.shtml (3) The OpenBabel web site: http://openbabel.sourceforge.net Support: (1) If you have any questions, send an email to openbabel-scripting++lists.sourceforge.net (2) Report a bug at http://sourceforge.net/tracker/?atid=428740&group_id=40728 Regards, baoilleach (on behalf of the OpenBabel development team) From owner-chemistry@ccl.net Tue Jul 10 04:07:01 2007 From: "makowskm : chemia.uj.edu.pl" To: CCL Subject: CCL:G: Nuclear repulsion energy Message-Id: <-34701-070709090046-22897-lyMXarAeT178SMbS3XKKkg=server.ccl.net> X-Original-From: makowskm_._chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Mon, 9 Jul 2007 14:24:22 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm(0)chemia.uj.edu.pl Is your molecule treated as belonging to C1 symmetry group? If not, the possible reason is symmetrization that Gaussian does. Means the atoms can be slightly moved to fit the symmetry group found and as the effect the standard orientation geometry used in actual calculations can non-trivially differ from input one. On opposite Gamess has no symmetry finder and will keep your geometry only translating to center of mass and rotating to the main axes of inertia tensor. I dont know a bit about ORCA in this respect. Regards, Marcin From owner-chemistry@ccl.net Tue Jul 10 06:01:01 2007 From: "Dhurairaj Senthilnathan zenthil03!^!yahoo.co.in" To: CCL Subject: CCL:G: Frequency symmetry problem Message-Id: <-34702-070709041403-28850-yFp4oqOFGPa1RbDFWoey0A]*[server.ccl.net> X-Original-From: Dhurairaj Senthilnathan Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-387292924-1183965202=:18034" Date: Mon, 9 Jul 2007 08:13:22 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Dhurairaj Senthilnathan [zenthil03(_)yahoo.co.in] --0-387292924-1183965202=:18034 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear mike, I think, there is no directe connection between optimized structure and symmetry. result of this structure will be the energy minima structure your given symmetry and geometry. zero-point energy will be printed in this gepmetry out file. thank you senthilnathan "Mike hang mikehang2007]|[yahoo.com" wrote: Dear CCL users I have perform Opt+Freq calculation with Gaussian 03 and the frequency symmetry obtained is ?A. what does this mean and how do I formally represent this frequency symmetry. Any help will be greatly appreciated thanks mike --------------------------------- Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. ________________________________________________________________________ Mr.D.SENTHILNATHAN , Research Scholar, School of Chemistry, Bharathidasan University, TIRUCHIRAPPALLI - 620 024, TamilNadu, INDIA http://chemthilchem.googlepages.com/whoiami Phone : + 91 431 2407053(office) + 94 437 81355 (Mobile) E-mail: zenthil03 _ yahoo.co.in chemthilchem _ gmail.com Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php --0-387292924-1183965202=:18034 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Dear mike,
               I think, there is no directe connection between optimized structure and symmetry. result of this structure will be the energy minima structure your given symmetry and geometry. zero-point energy will be printed in this gepmetry out file.
 
thank you
senthilnathan 
"Mike hang mikehang2007]|[yahoo.com" <owner-chemistry _ ccl.net> wrote:
Dear CCL users

I have perform Opt+Freq calculation with Gaussian 03 and the frequency symmetry obtained is ?A. what does this mean and how do I formally represent this frequency symmetry.
Any help will be greatly appreciated
thanks
mike
Building a website is a piece of cake.
Yahoo! Small Business gives you all the tools to get online.



________________________________________________________________________

Mr.D.SENTHILNATHAN ,
Research Scholar,
School of Chemistry,
Bharathidasan University,
TIRUCHIRAPPALLI - 620 024,
TamilNadu, INDIA
http://chemthilchem.googlepages.com/whoiami

Phone : + 91 431 2407053(office)
+ 94 437 81355 (Mobile)

E-mail: zenthil03 _ yahoo.co.in
chemthilchem _ gmail.com

Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php --0-387292924-1183965202=:18034-- From owner-chemistry@ccl.net Tue Jul 10 06:35:01 2007 From: "Jerome Kieffer jerome.Kieffer * terre-adelie.org" To: CCL Subject: CCL:G: Visualizing vibrational data Message-Id: <-34703-070710032154-10174-/Qz+Uktv3h07QkbiwYlZ3g^server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 10 Jul 2007 08:26:16 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer%x%terre-adelie.org] On Mon, 9 Jul 2007 13:49:40 -0400 "Raoul E Correa raoul##berkeley.edu" wrote: > I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode. I usually convert the output logfile from G03 (and others) into an input file for CAChe (the software for visualization) using the cclib library and babel, cclib and babel are free, and cclib is a python library available from sourceforge. > Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help! hyperchem and spartan have animations for vibration, I like CAChe because motions are showed by vectors, easier for paper reports Regards. -- Jérôme KIEFFER : http://www.terre-adelie.org À vélo, prendre une rue à contre-sens est moins dangeureux que prendre un boulevard dans le sens légal. À qui la faute ? From owner-chemistry@ccl.net Tue Jul 10 08:12:00 2007 From: "Soren Eustis soren(_)jhu.edu" To: CCL Subject: CCL: Visualizing vibrational data Message-Id: <-34704-070709233559-985-Q273KA54uBemTnHAVaNKSg .. server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 9 Jul 2007 22:33:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren(~)jhu.edu] ChemCraft is a wonderful visualization program for this purpose. www.chemcraftprog.com -----Original Message----- > From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net] Sent: Monday, July 09, 2007 1:50 PM To: Eustis, Soren Subject: CCL: Visualizing vibrational data Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] Hello, I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode. Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help! Raoulhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 10 08:55:00 2007 From: "allouche allouche~~lasim.univ-lyon1.fr" To: CCL Subject: CCL: Visualizing vibrational data Message-Id: <-34705-070710082538-14448-1syzsBS8HQP9jc2zlCvYAg ~~ server.ccl.net> X-Original-From: allouche Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 10 Jul 2007 13:55:08 +0200 MIME-Version: 1.0 Sent to CCL by: allouche [allouche[a]lasim.univ-lyon1.fr] Raoul E Correa raoul##berkeley.edu a écrit : >Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] >Hello, > >I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode. > >Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help! > > Hello, Gabedit (version 2.0.11) can read and visualize geometry, vibrational modes and Molecular orbitals from Q-Chem output file. You can download Gabedit from gabedit.sf.net Regards. -- Abdul-Rahman ALLOUCHE Tel : + (33) (0) 472431929 Fax : + (33) (0) 472431507 Email : allouche..lasim.univ-lyon1.fr Web : lasim.univ-lyon1.fr/allouche From owner-chemistry@ccl.net Tue Jul 10 10:24:00 2007 From: "ss537^_^drexel.edu" To: CCL Subject: CCL: Visualizing vibrational data Message-Id: <-34706-070710091827-18824-rXia8BH+rVdq9qlwJXAGtQ]~[server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 10 Jul 2007 08:20:36 -0400 MIME-Version: 1.0 Sent to CCL by: [ss537!^!drexel.edu] Hi Raoul You could try using Macmolplt, it has been very useful for visualizing output files from vibrational frequency calculations, it is free for download as well. http://www.scl.ameslab.gov/~brett/MacMolPlt/ Cheers Sriraj SRIRAJ SRINIVASAN PhD STUDENT DEPARTMENT OF CHEMICAL AND BIOLOGICAL ENGINEERING DREXEL UNIVERSITY, PHILADELPHIA,PA. PHONE: 215-895-5938 ----- Original Message ----- > From: "Raoul E Correa raoul##berkeley.edu" Date: Monday, July 9, 2007 1:49 pm Subject: CCL: Visualizing vibrational data > > Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] > Hello, > > I was wondering if there is software which helps one visualize the > motions of atoms along a vibrational mode, such as those described > by a frequency calculation in any computational package. I run > simulations on QChem but haven't found a program that will take > the output and create animations of the actual vibrational mode. > > Does anyone know of such a stand-alone program? Or maybe a way to > convert the output into something that another program (e.g. > Molekel) could use? Thanks for the help! > > Raoul > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the - - sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Tue Jul 10 12:11:00 2007 From: "Stephen.Garrison . srnl.doe.gov" To: CCL Subject: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies Message-Id: <-34707-070710110225-28616-phJiqL7NtSN3xfAj8T1q5g!A!server.ccl.net> X-Original-From: Stephen.Garrison+/-srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 004EEF8D85257314_=" Date: Tue, 10 Jul 2007 10:21:58 -0400 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison/./srnl.doe.gov This is a multipart message in MIME format. --=_alternative 004EEF8D85257314_= Content-Type: text/plain; charset="US-ASCII" Has anyone seen G03 perform a transition state optimization (with CalcAll) with no constraints, find a stationary point with one non-zero, negative eigenvalue (in this case -0.00447), and then find NO imaginary frequencies? Does anyone have an idea of what went wrong or what is happening? Here are some snippets from the end fo the file: Berny optimization. Use GDIIS/GDPIS optimizer. Internal Forces: Max 0.000014071 RMS 0.000002532 Search for a saddle point. Step number 39 out of a maximum of 46 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- analytic derivatives used. Eigenvalues --- -0.00447 0.00391 0.00510 0.01026 0.02635 Eigenvalues --- 0.03313 0.03457 0.04197 0.04777 0.05408 Eigenvalues --- 0.07590 0.09529 0.12116 0.13685 0.22436 Eigenvalues --- 0.22531 0.23190 0.28322 0.37711 0.46845 Eigenvalues --- 0.530671000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.00000 Item Value Threshold Converged? Maximum Force 0.000014 0.000015 YES RMS Force 0.000003 0.000010 YES Maximum Displacement 0.000020 0.000060 YES RMS Displacement 0.000007 0.000040 YES Low frequencies --- -12.5184 -6.3209 -0.0001 0.0005 0.0008 2.6758 Low frequencies --- 70.3933 92.5242 122.4695 Thanks for your help. --=_alternative 004EEF8D85257314_= Content-Type: text/html; charset="US-ASCII"
Has anyone seen G03 perform a transition state optimization (with CalcAll) with no constraints, find a stationary point with one non-zero, negative eigenvalue (in this case -0.00447), and then find NO imaginary frequencies? Does anyone have an idea of what went wrong or what is happening?

Here are some snippets from the end fo the file:

 Berny optimization.
 Use GDIIS/GDPIS optimizer.
 Internal  Forces:  Max     0.000014071 RMS     0.000002532
 Search for a saddle point.
 Step number  39 out of a maximum of  46
 All quantities printed in internal units (Hartrees-Bohrs-Radians)
 Swaping is turned off.
 Second derivative matrix not updated -- analytic derivatives used.
     Eigenvalues ---   -0.00447   0.00391   0.00510   0.01026   0.02635
     Eigenvalues ---    0.03313   0.03457   0.04197   0.04777   0.05408
     Eigenvalues ---    0.07590   0.09529   0.12116   0.13685   0.22436
     Eigenvalues ---    0.22531   0.23190   0.28322   0.37711   0.46845
     Eigenvalues ---    0.530671000.000001000.000001000.000001000.00000
     Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000
     Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000
     Eigenvalues --- 1000.00000

         Item               Value     Threshold  Converged?
 Maximum Force            0.000014     0.000015     YES
 RMS     Force            0.000003     0.000010     YES
 Maximum Displacement     0.000020     0.000060     YES
 RMS     Displacement     0.000007     0.000040     YES

 Low frequencies ---  -12.5184   -6.3209   -0.0001    0.0005    0.0008    2.6758
 Low frequencies ---   70.3933   92.5242  122.4695

Thanks for your help.
--=_alternative 004EEF8D85257314_=-- From owner-chemistry@ccl.net Tue Jul 10 12:48:00 2007 From: "Andrew Orry andy..molsoft.com" To: CCL Subject: CCL: MolSoft ICM Workshop - Protein Structure and Drug Discovery - September 2007 Message-Id: <-34708-070710100724-6629-p1QPwjrIrL314PrmQgs/GA##server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 09 Jul 2007 17:53:40 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy||molsoft.com] Molsoft LLC (www.molsoft.com) would like to invite you to an ICM Workshop entitled "Protein Structure and Drug Discovery" to be held on September 20th – 21st 2007 in La Jolla, CA, USA. The workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate in this workshop. The workshop is presented by Prof. Ruben Abagyan (Scripps) and Dr. Maxim Totrov (MolSoft). This workshop consists of lectures, demonstrations and “hands-on” computational experiments and will cover: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, chemical clustering, searching, superposition ... - QSAR, machine learning - Protein-Protein Docking See www.molsoft.com/training.html for more information. “The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools.” Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy++molsoft.com or call (858)625 2000 ext.108. MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Tue Jul 10 13:30:00 2007 From: "Yingbin Ge yingbin.ge^^^gmail.com" To: CCL Subject: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies Message-Id: <-34709-070710132710-7059-suYs0sCwVKPnaZmanvpq3w/./server.ccl.net> X-Original-From: "Yingbin Ge" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 10 Jul 2007 12:27:02 -0500 MIME-Version: 1.0 Sent to CCL by: "Yingbin Ge" [yingbin.ge-.-gmail.com] It seems that you did not project out the translational and rotational modes. The first 6 lowest frequencies are close to zero; they are very likely due to the tran/rot modes. You may want to look at the motions of the first 6 modes. > Low frequencies --- -12.5184 -6.3209 -0.0001 0.0005 0.0008 > 2.6758 > Low frequencies --- 70.3933 92.5242 122.4695 Yingbin On 7/10/07, Stephen.Garrison . srnl.doe.gov wrote: > > Has anyone seen G03 perform a transition state optimization (with CalcAll) > with no constraints, find a stationary point with one non-zero, negative > eigenvalue (in this case -0.00447), and then find NO imaginary frequencies? > Does anyone have an idea of what went wrong or what is happening? > > Here are some snippets from the end fo the file: > > Berny optimization. > Use GDIIS/GDPIS optimizer. > Internal Forces: Max 0.000014071 RMS 0.000002532 > Search for a saddle point. > Step number 39 out of a maximum of 46 > All quantities printed in internal units (Hartrees-Bohrs-Radians) > Swaping is turned off. > Second derivative matrix not updated -- analytic derivatives used. > Eigenvalues --- -0.00447 0.00391 0.00510 0.01026 0.02635 > Eigenvalues --- 0.03313 0.03457 0.04197 0.04777 0.05408 > Eigenvalues --- 0.07590 0.09529 0.12116 0.13685 0.22436 > Eigenvalues --- 0.22531 0.23190 0.28322 0.37711 0.46845 > Eigenvalues --- > 0.530671000.000001000.000001000.000001000.00000 > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.00000 > > Item Value Threshold Converged? > Maximum Force 0.000014 0.000015 YES > RMS Force 0.000003 0.000010 YES > Maximum Displacement 0.000020 0.000060 YES > RMS Displacement 0.000007 0.000040 YES > > Low frequencies --- -12.5184 -6.3209 -0.0001 0.0005 0.0008 > 2.6758 > Low frequencies --- 70.3933 92.5242 122.4695 > > Thanks for your help. > From owner-chemistry@ccl.net Tue Jul 10 15:12:01 2007 From: "Abrash, Samuel sabrash===richmond.edu" To: CCL Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization Energies Message-Id: <-34710-070710150645-17932-jbP6fTte9h0bTMdhUivkUQ^server.ccl.net> X-Original-From: "Abrash, Samuel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 10 Jul 2007 10:55:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] Hi Folks, I have a question about both the appropriateness of G3MP2 for calculating vertical ionization energies, and in addition for the use of G03 frequency calculations for calculating zero point corrections for the ion in a vertical ionization energy calculation. Here are the details. I'm doing a series of calculations on adiabatic and vertical ionization energies of isomers of C6H6. I'd like to do them at both the UPBEPBE/aug-cc-pVDZ and G3MP2 levels. However, for the vertical ionization energies, there may be a problem with using G3MP2. Here's the problem. In the vertical ionization energy calculation I take the energy of the ion at the same geometry as the optimized neutral, and subtract the energy of the optimized neutral. The ion is therefore not at an equilibrium geometry. I am wondering if G3MP2 is a valid method for calculating the energy of an ion that is not at an equilibrium geometry. The reason is that a frequency calculation is a part of the G3MP2 method. The Gaussian website has this to say about frequency calculations: ""Vibrational frequencies are computed by determining the second derivatives of the energy with respect to the Cartesian nuclear coordinates and then transforming to mass-weighted coordinates. This transformation is only valid at a stationary point! Thus, it is meaningless to compute frequencies at any geometry other than a stationary point for the method used for frequency determination." This suggests that G3MP2 can't be used to calculate vertical ionization energies, and in addition, that Gaussian can't be used to calculate zero point corrections for calculations of vertical ionization energies. Am I correct that G3MP2 can't be used? If so, is there some kind of a fix? I'd appreciate your input. Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash(0)richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash "Rabbi Yitzhak said: At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from the darkness and they were joined together. Because of this, out of darkness came the light and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else...the good inclination and the evil inclination, the right and the left." - The Zohar -----Original Message----- > From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] Sent: Monday, July 09, 2007 8:24 AM To: Abrash, Samuel Subject: CCL:G: Nuclear repulsion energy Sent to CCL by: makowskm(0)chemia.uj.edu.pl Is your molecule treated as belonging to C1 symmetry group? If not, the possible reason is symmetrization that Gaussian does. Means the atoms can be slightly moved to fit the symmetry group found and as the effect the standard orientation geometry used in actual calculations can non-trivially differ from input one. On opposite Gamess has no symmetry finder and will keep your geometry only translating to center of mass and rotating to the main axes of inertia tensor. I dont know a bit about ORCA in this respect. Regards, Marcinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 10 15:47:00 2007 From: "Xiaobing Feng sxopowo(0)yahoo.co.uk" To: CCL Subject: CCL: Free Linux graphics software for viewing strucuture of molecules and wavefunction Message-Id: <-34711-070710122042-21953-nfHVRPZvFaQYxsq++xsyaw() server.ccl.net> X-Original-From: Xiaobing Feng Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1765752552-1184080828=:67825" Date: Tue, 10 Jul 2007 16:20:28 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Xiaobing Feng [sxopowo]*[yahoo.co.uk] --0-1765752552-1184080828=:67825 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, Could someone recommend a Free Linux graphics software for viewing the structure of a molecule and its wavefunctions, like LUMO, HOMO et al. Many thanks in advance. Xiaobing --------------------------------- Now you can scan emails quickly with a reading pane. Get the new Yahoo! Mail. --0-1765752552-1184080828=:67825 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers,

 Could someone recommend a Free Linux graphics software for viewing
the structure of a molecule and its wavefunctions, like LUMO, HOMO et al.
Many thanks in advance.

Xiaobing

Now you can scan emails quickly with a reading pane. Get the new Yahoo! Mail. --0-1765752552-1184080828=:67825-- From owner-chemistry@ccl.net Tue Jul 10 16:28:00 2007 From: "John Merle jkmerle a yahoo.com" To: CCL Subject: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies Message-Id: <-34712-070710151142-18924-wi47wHlGVshWe6S2xH7wtg{:}server.ccl.net> X-Original-From: John Merle Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 10 Jul 2007 11:11:36 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: John Merle [jkmerle(_)yahoo.com] Hi Steve, Perhaps the mode was identified to be a translation or rotation. John Merle --- "Stephen.Garrison . srnl.doe.gov" wrote: > Has anyone seen G03 perform a transition state > optimization (with CalcAll) > with no constraints, find a stationary point with > one non-zero, negative > eigenvalue (in this case -0.00447), and then find NO > imaginary > frequencies? Does anyone have an idea of what went > wrong or what is > happening? > > Here are some snippets from the end fo the file: > > Berny optimization. > Use GDIIS/GDPIS optimizer. > Internal Forces: Max 0.000014071 RMS > 0.000002532 > Search for a saddle point. > Step number 39 out of a maximum of 46 > All quantities printed in internal units > (Hartrees-Bohrs-Radians) > Swaping is turned off. > Second derivative matrix not updated -- analytic > derivatives used. > Eigenvalues --- -0.00447 0.00391 0.00510 > 0.01026 0.02635 > Eigenvalues --- 0.03313 0.03457 0.04197 > 0.04777 0.05408 > Eigenvalues --- 0.07590 0.09529 0.12116 > 0.13685 0.22436 > Eigenvalues --- 0.22531 0.23190 0.28322 > 0.37711 0.46845 > Eigenvalues --- > 0.530671000.000001000.000001000.000001000.00000 > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- > 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.00000 > > Item Value Threshold > Converged? > Maximum Force 0.000014 0.000015 > YES > RMS Force 0.000003 0.000010 > YES > Maximum Displacement 0.000020 0.000060 > YES > RMS Displacement 0.000007 0.000040 > YES > > Low frequencies --- -12.5184 -6.3209 -0.0001 > 0.0005 0.0008 > 2.6758 > Low frequencies --- 70.3933 92.5242 122.4695 > > Thanks for your help. > ____________________________________________________________________________________ Get the Yahoo! toolbar and be alerted to new email wherever you're surfing. http://new.toolbar.yahoo.com/toolbar/features/mail/index.php From owner-chemistry@ccl.net Tue Jul 10 16:57:00 2007 From: "Reynier Suardiaz reynier.suardiaz- -gmail.com" To: CCL Subject: CCL:G: large NBO E2 energy values for antibonding-antibonding interactions Message-Id: <-34713-070710155329-12050-HGgAvPI5ITmk0fZk+geSvQ%x%server.ccl.net> X-Original-From: "Reynier Suardiaz" Date: Tue, 10 Jul 2007 15:53:26 -0400 Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz#gmail.com] Dear CCL I am obtaining large values of E2 for "antibonding-antibonding" interactions withing NBO methodology using NBO 3.0 in gaussian03. i.e. 120. BD*( 2) C 4 - C 5 /115. BD*( 2) C 2 - C 3 163.56 0.01 0.067 124. BD*( 2) C 6 - O 10 / 81. RY*( 6) C 6 1.49 0.80 0.114 124. BD*( 2) C 6 - O 10 / 99. RY*( 2) O 10 0.77 1.00 0.092 124. BD*( 2) C 6 - O 10 /115. BD*( 2) C 2 - C 3 164.68 0.01 0.079 E2 values of 163.56 and 164.68 kcal/mol... This is in O-O trans isomer of furfural, in O-O cis isomer there are not those large numbers. Which can be the meaning of this numbers? Are those numbers correct? any suggestion would be appreciated Best regards reynier From owner-chemistry@ccl.net Tue Jul 10 17:33:00 2007 From: "Soren Eustis soren_-_jhu.edu" To: CCL Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization Energies Message-Id: <-34714-070710154240-3526-uJ3bEazzPt7Q5faL5m7DeA**server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 10 Jul 2007 15:42:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren*|*jhu.edu] Good post. I had a similar question regarding the use of zero point corrections for adiabatic electron affinities and vertical electron affinities. Clearly, the use of ZPE corrections for the adiabatic case is needed. However for the vertical case it makes sense to use only the ZPE of the initial state (in my case the anion), since the energy level being accessed in the final state is indeed well above the ground state. However, I have found that for large molecules with significant degrees of freedom, the ZPE of the initial state is so large as to make the vertical energies very small. Thus, the calculation of vertical electron affinities only work if I use the non-ZPE corrected values for the anion and the neutral. This makes no chemical sense to me, but the numbers line up well this way. For your case I would say that calculating frequencies of a species that is not in a potential well is meaningless. I would suggest doing single point energy calculations for both species and then doing separate frequency calculations for the initial state. However, I am curious as to what the ZPE will do to your IP values. Anyone have any thoughts on this. It seems common in the literature that ZPE's are used for adiabatic calculations only, and they are completely ignored (even for the initial state) for vertical calculations. This seems to line up with experiment, but it is unsatisfying intellectually. Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University Remsen Hall 3400 N Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren^^jhu.edu -----Original Message----- > From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] Sent: Tuesday, July 10, 2007 10:56 AM To: Eustis, Soren Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization Energies Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] Hi Folks, I have a question about both the appropriateness of G3MP2 for calculating vertical ionization energies, and in addition for the use of G03 frequency calculations for calculating zero point corrections for the ion in a vertical ionization energy calculation. Here are the details. I'm doing a series of calculations on adiabatic and vertical ionization energies of isomers of C6H6. I'd like to do them at both the UPBEPBE/aug-cc-pVDZ and G3MP2 levels. However, for the vertical ionization energies, there may be a problem with using G3MP2. Here's the problem. In the vertical ionization energy calculation I take the energy of the ion at the same geometry as the optimized neutral, and subtract the energy of the optimized neutral. The ion is therefore not at an equilibrium geometry. I am wondering if G3MP2 is a valid method for calculating the energy of an ion that is not at an equilibrium geometry. The reason is that a frequency calculation is a part of the G3MP2 method. The Gaussian website has this to say about frequency calculations: ""Vibrational frequencies are computed by determining the second derivatives of the energy with respect to the Cartesian nuclear coordinates and then transforming to mass-weighted coordinates. This transformation is only valid at a stationary point! Thus, it is meaningless to compute frequencies at any geometry other than a stationary point for the method used for frequency determinatio! n." This suggests that G3MP2 can't be used to calculate vertical ionization energies, and in addition, that Gaussian can't be used to calculate zero point corrections for calculations of vertical ionization energies. Am I correct that G3MP2 can't be used? If so, is there some kind of a fix? I'd appreciate your input. 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 "Rabbi Yitzhak said: At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came from the darkness and they were joined together. Because of this, out of darkness came the light and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else...the good inclination and the evil inclination, the right and the left." - The Zohar -----Original Message----- > From: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net] Sent: Monday, July 09, 2007 8:24 AM To: Abrash, Samuel Subject: CCL:G: Nuclear repulsion energy Sent to CCL by: makowskm(0)chemia.uj.edu.pl Is your molecule treated as belonging to C1 symmetry group? If not, the possible reason is symmetrization that Gaussian does. Means the atoms can be slightly moved to fit the symmetry group found and as the effect the standard orientation geometry used in actual calculations can non-trivially differ from input one. On opposite Gamess has no symmetry finder and will keep your geometry only translating to center of mass and rotating to the main axes of inertia tensor. I dont know a bit about ORCA in this respect. Regards, Marcinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 10 18:08:01 2007 From: "Cory Pye cpye]~[crux.smu.ca" To: CCL Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization Energies Message-Id: <-34715-070710172630-15858-22G/Rq5f0xbq5PJ/13cigw_-_server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 10 Jul 2007 18:26:04 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye]_[crux.smu.ca] Hello, you are correct in asserting that the ZPE might not mean much high on the PES. What I would do is just do the calculation on the excited state at the ground state geometry, then manually substitute the ADIABATIC excited state ZPE for that which Gaussian calculates at the non-equilibrium geometry (since you are doing the adiabatic calculation as well, this should work). You could even ignore the ZPE contributions, but the result might not be as accurate. -Cory On Tue, 10 Jul 2007, Abrash, Samuel sabrash===richmond.edu wrote: > > Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] > Hi Folks, > > I have a question about both the appropriateness of G3MP2 for calculating > vertical ionization energies, and in addition for the use of G03 frequency > calculations for calculating zero point corrections for the ion in a vertical > ionization energy calculation. Here are the details. > > I'm doing a series of calculations on adiabatic and vertical ionization > energies of isomers of C6H6. I'd like to do them at both the > UPBEPBE/aug-cc-pVDZ and G3MP2 levels. > > However, for the vertical ionization energies, there may be a problem with > using G3MP2. Here's the problem. In the vertical ionization energy > calculation I take the energy of the ion at the same geometry as the > optimized neutral, and subtract the energy of the optimized neutral. The ion > is therefore not at an equilibrium geometry. I am wondering if G3MP2 is a > valid method for calculating the energy of an ion that is not at an > equilibrium geometry. The reason is that a frequency calculation is a part > of the G3MP2 method. The Gaussian website has this to say about frequency > calculations: ""Vibrational frequencies are computed by determining the > second derivatives of the energy with respect to the Cartesian nuclear > coordinates and then transforming to mass-weighted coordinates. This > transformation is only valid at a stationary point! Thus, it is meaningless > to compute frequencies at any geometry other than a stationary point for the > method used for frequency determination." This suggests that G3MP2 can't be > used to calculate vertical ionization energies, and in addition, that > Gaussian can't be used to calculate zero point corrections for calculations > of vertical ionization energies. > > Am I correct that G3MP2 can't be used? If so, is there some kind of a fix? > I'd appreciate your input. > > Samuel A. Abrash ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye- -crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Tue Jul 10 20:19:00 2007 From: "Lukasz Cwiklik cwiklik-x-gmail.com" To: CCL Subject: CCL:G: Free Linux graphics software for viewing strucuture of molecules and wavefunction Message-Id: <-34716-070710200025-25244-symDzLKxK28Vc1o5rFyrgA^-^server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 11 Jul 2007 01:59:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik|gmail.com] On 7/10/07, Xiaobing Feng sxopowo(0)yahoo.co.uk wrote: > Hi CCLers, > > Could someone recommend a Free Linux graphics software for viewing > the structure of a molecule and its wavefunctions, like LUMO, HOMO et al. > Many thanks in advance. > > Xiaobing Hi, You can use VMD which is a free software usually used for visualization of MD results. It can be easily employed for generation of both working version and high quality rendered visualizations of molecules and molecular orbitals based on Gaussian cube files. If you need further assistance, I can send you a quick howto. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Jul 10 21:41:00 2007 From: "Vlad vvv900[-]anusf.anu.edu.au" To: CCL Subject: CCL:G: Free Linux graphics software for viewing strucuture of molecules and wavefunction Message-Id: <-34717-070710213944-29967-giQin7GEz65XNRzxVM89Pg[-]server.ccl.net> X-Original-From: "Vlad" Content-description: Mail message body Content-transfer-encoding: 8BIT Content-type: text/plain; charset=WINDOWS-1251 Date: Wed, 11 Jul 2007 11:39:36 +1000 MIME-Version: 1.0 Sent to CCL by: "Vlad" [vvv900_+_anusf.anu.edu.au] Hi Xiaobing, > Could someone recommend a Free Linux graphics software for viewing > the structure of a molecule and its wavefunctions, like LUMO, HOMO et > al. You might want to try our program JMolEditor - http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html It supports all Gaussian input and output files + can visualize MOs, densities from the cube files. To run it on Linux you need to be sure that the Java version on your computer is >= 1.5 and you need download and install java3d for high-performance graphics. Program has several tutorials for the Gaussian users http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/in dex.html Best wishes, Vlad   ======================== Dr. Vladislav Vassiliev Supercomputer Facility The Australian National University Canberra, 0200, ACT, Australia Phone: +61 2 6125 9694 Fax: +61 2 6125 8199