From owner-chemistry@ccl.net Wed Jul 19 04:20:02 2006 From: "Raji Raji raji,anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: DNA-Ligand crystallisation Message-Id: <-32182-060719041845-30256-SHUlq+CX5rZ9M+UUOBFUlw]=[server.ccl.net> X-Original-From: "Raji Raji" Date: Wed, 19 Jul 2006 04:18:43 -0400 Sent to CCL by: "Raji Raji" [raji=-=anal.chem.tohoku.ac.jp] Dear CCL Members, Sorry, my question is not directly related to Computational chemistry. Can any one suggest me some useful references or DATA bases about how to crystallise a short (11 or 23 meric) DNA-Ligand complex for X-Ray crystallographical studies? Thank you very much in advance. Best Regards, Raji. From owner-chemistry@ccl.net Wed Jul 19 04:55:00 2006 From: "Eduardo Lemos de Sa edulsa]![quimica.ufpr.br" To: CCL Subject: CCL: summary about force field parameters Message-Id: <-32183-060719042117-30576-i7ceaU76D5Fs4eZDtlP91Q^^server.ccl.net> X-Original-From: "Eduardo Lemos de Sa" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 19 Jul 2006 04:27:11 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: "Eduardo Lemos de Sa" [edulsa,quimica.ufpr.br] Sirs and Ladies Last monday I sent to CCL this email: "Is there a non-commercially available source-code that accepts a user defined force-field and has a built in geometry optimizer that allows to superimpose valence constraints such as fixed torsion angles etc?" I am gratefull to G. M. Arantes, Geoffrey Hutchison and Andrey V Khavryuchenko for their suggestion. After here, the answers goes: 1) I don't know how much coding you're willing to do. The Ghemical/libghemical project does have support for force fields, a built-in optimizer, and support for constraints like fixed torsion angles. On the other hand, "user-defined" would probably require some coding in C++ -- you can edit parameterization for the current force fields, but not a completely user-defined model. To do that, you'd need to write some code for a new model. Ghemical/libghemical is under the GNU GPL, so it's free, open source, and non-commercial. http://www.uku.fi/~thassine/projects/ghemical/ Cheers, -Geoff 2)You may try MMTK (http://www.python.net/crew/hinsen/MMTK/) > from Andrey V Khavryuchenko 3) Arantes suggest me to use DYNAMO (is a free code). My best wishes Eduardo -- Eduardo Lemos de Sa edulsa{:}quimica.ufpr.br Professor Adj. IV - Departamento de Quimica Universidade Federal do Parana C. P. 19081 81531-990 Curitiba/PR - Brazil Fone (41) 3361 3300 From owner-chemistry@ccl.net Wed Jul 19 06:43:00 2006 From: "Noel O Boyle no228^^^cam.ac.uk" To: CCL Subject: CCL:G: ANNOUNCE: cclib 0.5 released Message-Id: <-32184-060719054510-21885-6EcaXVDyVUTrvgKN6rN2Tg ~~ server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 19 Jul 2006 10:01:03 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228__cam.ac.uk] cclib 0.5 is now available for download from http://cclib.sf.net. cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS (US), Gaussian, and PC GAMESS. (Support for Jaguar and GAMESS UK is being added.) Among other data, cclib extracts: * coordinates * atomic orbital information * molecular orbital information * information on vibrational modes * the results of a TD-DFT calculation (For a complete list see http://cclib.sf.net/wiki/index.php/Parsed_Data). cclib also provides some calculation methods for interpreting some electronic properties of molecules using analyses such as: * Mulliken population analysis * Overlap population analysis * Calculation of Mayer's bond orders. For information on how to use cclib, see http://cclib.sf.net/wiki/index.php/Using_cclib. If you need help, find a bug, want new features or have any questions, please send an email to our mailing list: https://lists.sourceforge.net/lists/listinfo/cclib-users Regards, The cclib development team From owner-chemistry@ccl.net Wed Jul 19 07:45:00 2006 From: "gas5x\a/bancorp.ru" To: CCL Subject: CCL: MM Force field parameters for thia-calixarenes? Message-Id: <-32185-060719042232-30816-9N2ibROBQDE+5nCBqjQjIg++server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="KOI8-R"; format="flowed" Date: Wed, 19 Jul 2006 11:22:16 +0400 MIME-Version: 1.0 Sent to CCL by: [gas5x*bancorp.ru] Hello All, Could anybody hint if there are any Molecular Mechanics parameters for calixarenes, escpecially thia-calixarenes (i.e., Ar-S-Ar fragments etc) for commonly used force fields like MM2/MM3, AMBER, OPLS developed? -- Grigory Shamov, Kazan Science Centre of RAS From owner-chemistry@ccl.net Wed Jul 19 09:23:00 2006 From: "Mateusz Witkowski big_mateo-#-inbox.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32186-060718183252-14326-pElK/rACLh62eAuIIHjQ0Q[A]server.ccl.net> X-Original-From: Mateusz Witkowski Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 18 Jul 2006 13:27:19 -0800 Mime-Version: 1.0 Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] Hi, I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? TIA Mateo From owner-chemistry@ccl.net Wed Jul 19 11:11:00 2006 From: "Andreas Klamt klamt[a]cosmologic.de" To: CCL Subject: CCL:G: How to visualize a lone pair Message-Id: <-32187-060719110747-19962-rDZ+NNnoYQUAirXSZG9J9w^-^server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 19 Jul 2006 16:04:34 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt=cosmologic.de] Dear Mateo, lone pairs and their directionalities can be very well identified in the VRML visualizations of the COSMO polarization charge density sigma on the COSMO surface. Many examples are given under http://www.cosmologic.de/ChemicalEngineering/visualization.html (Please note that these are zipped VRML files. Normally they should simply open when you double click them from a browser which has a VRML plug in (e.g. CORTONA viewer from Parallel Graphics) Just look at the first example, phenoxymethyl-oxirane_sig, or at benzaldehyde, where you easily identify the lone-pair directions as red hot spots. Look at et3n (you have to rotate) and you will see the lonepair almost hidden between the et groups. Many more examples are given there. You can generate such VRMLs with our COSMOtherm software based on DFT COSMO tiles from TURBOMOLE, Gaussian03, or DMol. Our COSMO-RS method quite clearly turns out that some additional interaction (beyond electrostatics) is required for molecular surface with sigma> 0.008 e/Ang^2, strongly increasing with sigma. Substantial hydrogen bonding only only occurs for sigma> 0.012 e/Ang^2. This can be found on lone pair regions of O, N, and S. Andreas > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > Hi, > I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. > Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? > What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? > > TIA > Mateo> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt : cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jul 19 11:46:00 2006 From: "XunLei Ding dxl#%#ustc.edu.cn" To: CCL Subject: CCL:G: NBO Message-Id: <-32188-060719052540-19115-QifFECbARPJ6iHCzbGr76Q^server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Wed, 19 Jul 2006 16:52:58 +0800 Sent to CCL by: "XunLei Ding" [dxl]|[ustc.edu.cn] It seems that, if you have not bought NBO5, "pop=nboread $nbo bndidx $end" will still use NBO3.1 in the calculation. Not as what is said in the manual. In your mail: >From: "vishal rai vishaliitb-,-gmail.com" >Reply-To: "CCL Subscribers" >To: "Xunlei, Ding " >Subject: CCL:G: NBO >Date:Tue, 11 Jul 2006 23:26:30 -0400 > >Sent to CCL by: "vishal rai" [vishaliitb..gmail.com] > Check out the link >http://www.gaussian.com/g_ur/k_population.htm > > >-- >Vishal Rai, >Graduate Student of Dr. I. N. N. Namboothiri, >Organic Synthesis and Physical Organic Chemistry Group, >Department of Chemistry, >Indian Institute of Technology Bombay, >Powai, Mumbai - 400 076 >India. > > >On 7/11/06, Dipankar Roy dipankarroy,iitb.ac.in >wrote: >> >> Sent to CCL by: "Dipankar Roy" [dipankarroy.]*[.iitb.ac.in] >> Hi, >> ROUTE section use pop=nboread >> and at the end (end of geometry specification) put a line gap and use >> $nbo bndidx $end >> That will do. >> -dipankar Roy >> >> > Sent to CCL by: "Gilles Frapper" [gilles.frapper*_*univ-poitiers.fr] >> > Dear all, >> > >> > What are the keywords to calculate the bond orders using NBO 3.1 in G03 >> ? >> > >> > (keywords: pop=nboread ; >> > end of the section: nbo ????? end) >> > >> > in what section of the output may I read the informations ? >> > >> > Merci. >> > >> > Gilles> >> > >> > >> > >> >> >> *********************************************** >> Dipankar Roy >> Graduate Student of Prof. R. B. Sunoj >> Computational Chemistry Laboratoty >> Dept. of Chemistry >> Indian Institute of Technology, Bombay >> India - 400076 >> Phone: +91-22-2576-4130(lab) >> URL: http://www.geocities.com/dipankar_roy79/dipankar.html >> *********************************************** >> >> GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE >> GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. >> - PROF. LEN SHAPIRO, NDSU> >> >> >> From owner-chemistry@ccl.net Wed Jul 19 12:20:00 2006 From: "XunLei Ding dxl,+,ustc.edu.cn" To: CCL Subject: CCL:G: NBO Message-Id: <-32189-060719054556-21983-EZc6uatuoOj4crhQYtWZvw]![server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Wed, 19 Jul 2006 16:39:14 +0800 Sent to CCL by: "XunLei Ding" [dxl|ustc.edu.cn] Yes, it seems that using nboread will using NBO 5, not NBO3. The following is from the web page of Gaussian manual. The following input file requests a bond order analysis using NBO 5: # B3LYP/6-31G(d,p) Pop=NBORead Example of NBO bond orders 0 1 C 0.000000 0.665676 0.000000 0.919278 1.237739 0.000000 H -0.919239 1.237787 0.000000 C 0.000000 -0.665676 0.000000 H -0.919278 -1.237739 0.000000 H 0.919239 -1.237787 0.000000 $nbo bndidx $end In your mail: >From: "vishal rai vishaliitb-,-gmail.com" >Reply-To: "CCL Subscribers" >To: "Xunlei, Ding " >Subject: CCL:G: NBO >Date:Tue, 11 Jul 2006 23:26:30 -0400 > >Sent to CCL by: "vishal rai" [vishaliitb..gmail.com] > Check out the link >http://www.gaussian.com/g_ur/k_population.htm > > >-- >Vishal Rai, >Graduate Student of Dr. I. N. N. Namboothiri, >Organic Synthesis and Physical Organic Chemistry Group, >Department of Chemistry, >Indian Institute of Technology Bombay, >Powai, Mumbai - 400 076 >India. > > >On 7/11/06, Dipankar Roy dipankarroy,iitb.ac.in >wrote: >> >> Sent to CCL by: "Dipankar Roy" [dipankarroy.]*[.iitb.ac.in] >> Hi, >> ROUTE section use pop=nboread >> and at the end (end of geometry specification) put a line gap and use >> $nbo bndidx $end >> That will do. >> -dipankar Roy >> >> > Sent to CCL by: "Gilles Frapper" [gilles.frapper*_*univ-poitiers.fr] >> > Dear all, >> > >> > What are the keywords to calculate the bond orders using NBO 3.1 in G03 >> ? >> > >> > (keywords: pop=nboread ; >> > end of the section: nbo ????? end) >> > >> > in what section of the output may I read the informations ? >> > >> > Merci. >> > >> > Gilles> >> > >> > >> > >> >> >> *********************************************** >> Dipankar Roy >> Graduate Student of Prof. R. B. Sunoj >> Computational Chemistry Laboratoty >> Dept. of Chemistry >> Indian Institute of Technology, Bombay >> India - 400076 >> Phone: +91-22-2576-4130(lab) >> URL: http://www.geocities.com/dipankar_roy79/dipankar.html >> *********************************************** >> >> GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE >> GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. >> - PROF. LEN SHAPIRO, NDSU> >> >> >> From owner-chemistry@ccl.net Wed Jul 19 12:55:00 2006 From: "Marius Retegan marius.retegan^^^yahoo.com" To: CCL Subject: CCL: nonbond parameters for Zn and Fe Message-Id: <-32190-060719111454-22578-wVy+niNOuqFBnw2vsON/jQ..server.ccl.net> X-Original-From: Marius Retegan Content-Type: multipart/alternative; boundary="0-690878600-1153318490=:88629" Date: Wed, 19 Jul 2006 15:14:50 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Marius Retegan [marius.retegan.-x-.yahoo.com] --0-690878600-1153318490=:88629 Content-Type: text/plain; charset=us-ascii Hello I need some help with finding the nonbonded parameters for Zn and Fe for the Amber force field. I would appreciate any reference or a method to derive these parameters from other force fields. Thank you Marius Retegan --0-690878600-1153318490=:88629 Content-Type: text/html; charset=us-ascii
Hello
I need some help with finding the nonbonded parameters for Zn and Fe for the Amber force field.
I would appreciate any reference or a method to derive these parameters from other force fields.
Thank you
Marius Retegan
--0-690878600-1153318490=:88629-- From owner-chemistry@ccl.net Wed Jul 19 13:30:00 2006 From: "shalini k shalinikbio[A]yahoo.com" To: CCL Subject: CCL: MM Force field parameters for thia-calixarenes? Message-Id: <-32191-060719095514-6752-n0asYBP4nbJQbTIdHkygFA~!~server.ccl.net> X-Original-From: shalini k Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-792799394-1153313707=:35144" Date: Wed, 19 Jul 2006 05:55:07 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: shalini k [shalinikbio|yahoo.com] --0-792799394-1153313707=:35144 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello all I am shalini...can any one give one good web addess,where I can learn Molecular docking . I am into building protein networks.. I am very keen on learning Docking. I am basically MSc Biotech. Regards Sent to CCL by: [gas5x*bancorp.ru] Hello All, Could anybody hint if there are any Molecular Mechanics parameters for calixarenes, escpecially thia-calixarenes (i.e., Ar-S-Ar fragments etc) for commonly used force fields like MM2/MM3, AMBER, OPLS developed? -- Grigory Shamov, Kazan Science Centre of RAShttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-792799394-1153313707=:35144 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello all
 
I am shalini...can any one give one good web addess,where I can learn Molecular docking . I am into building protein networks.. I am very keen on learning Docking.
I am basically MSc Biotech.
 
 
 
Regards

Sent to CCL by: [gas5x*bancorp.ru]
Hello All,

Could anybody hint if there are any Molecular Mechanics
parameters for calixarenes, escpecially thia-calixarenes
(i.e., Ar-S-Ar fragments etc) for commonly used force
fields like MM2/MM3, AMBER, OPLS developed?

--
Grigory Shamov,
Kazan Science Centre of RAS


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http://mail.yahoo.com --0-792799394-1153313707=:35144-- From owner-chemistry@ccl.net Wed Jul 19 14:05:00 2006 From: "Mark Zottola mzottola|gmail.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32192-060719105606-15499-Jz8tNgdJdn/jEYXBKSzjhQ,+,server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_146453_2977020.1153318334733" Date: Wed, 19 Jul 2006 10:12:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola===gmail.com] ------=_Part_146453_2977020.1153318334733 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Mateusz, In order for there to be a hydrogen bond, there has to be a bond between donor and acceptor. In order for there to be a bond between any two atoms, there must be: i) An accumulation of charge between the two atoms, and ii) Along the path of maximal electron density between the two atoms must exist a point of mininimum electron density, a bond critical point. If, after reaching an equilibrium structure, such conditions exist between donor and acceptor, you have a hydrogen bond. There is significant reason to believe that close contacts between hydrogen bond donor and acceptor at either long distance or tighter (100 - 120) valence angles are due not to electrostatics, but other molecular features. Both AIM and NBO are effective tools for studying the systems you are interested in. HTH. Best Regards, Mark Zottola On 7/19/06, Mateusz Witkowski big_mateo-#-inbox.com wrote: > > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > Hi, > I'm interested in the directionality of O,N,S lone pairs in creation of > hydrogen bonds. > Is it possible to visualize a lone pair from QM results? If so, what > should be done, which software should be used? > What is your general impression about hydrogen bonds with XH-A angle > ~100-120deg? Is there any border between HB and purely electrostatic > interaction? > > TIA > Mateo> > > > ------=_Part_146453_2977020.1153318334733 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Mateusz,
 
In order for there to be a hydrogen bond, there has to be a bond between donor and acceptor.  In order for there to be a bond between any two atoms, there must be:
i) An accumulation of charge between the two atoms, and
ii) Along the path of maximal electron density between the two atoms must exist a point of mininimum electron density, a bond critical point.  If, after reaching an equilibrium structure, such conditions exist between donor and acceptor, you have a hydrogen bond.
 
There is significant reason to believe that close contacts between hydrogen bond donor and acceptor at either long distance or tighter (100 - 120) valence angles are due not to electrostatics, but other molecular features. 
 
Both AIM and NBO are effective tools for studying the systems you are interested in.  HTH.
 
Best Regards,
 
 
Mark Zottola

 
On 7/19/06, Mateusz Witkowski big_mateo-#-inbox.com <owner-chemistry- -ccl.net> wrote:
Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com]

Hi,
I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds.
Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used?
What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction?

TIA
Mateo



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------=_Part_146453_2977020.1153318334733-- From owner-chemistry@ccl.net Wed Jul 19 14:41:01 2006 From: "Shobe, David dshobe{=}sud-chemieinc.com" To: CCL Subject: CCL:G: How to visualize a lone pair Message-Id: <-32193-060719120546-31286-LcGpFIc45uGYSkfShCiqtw_+_server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 19 Jul 2006 18:05:32 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe++sud-chemieinc.com] Mateo, You don't really need COSMO-RS (a nice and useful program, so I'm told, but rather expensive) to find the lone pair direction. All you need is a program that analyzes the electron density and finds the maximum of the Laplacian, which can usually be identified with an electron pair. This maximum will be at a particular point in space, so the lone pair directionality follows naturally. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] Sent: Wednesday, July 19, 2006 11:24 AM To: Shobe, David Subject: CCL:G: How to visualize a lone pair Sent to CCL by: Andreas Klamt [klamt=cosmologic.de] Dear Mateo, lone pairs and their directionalities can be very well identified in the VRML visualizations of the COSMO polarization charge density sigma on the COSMO surface. Many examples are given under http://www.cosmologic.de/ChemicalEngineering/visualization.html (Please note that these are zipped VRML files. Normally they should simply open when you double click them from a browser which has a VRML plug in (e.g. CORTONA viewer from Parallel Graphics) Just look at the first example, phenoxymethyl-oxirane_sig, or at benzaldehyde, where you easily identify the lone-pair directions as red hot spots. Look at et3n (you have to rotate) and you will see the lonepair almost hidden between the et groups. Many more examples are given there. You can generate such VRMLs with our COSMOtherm software based on DFT COSMO tiles from TURBOMOLE, Gaussian03, or DMol. Our COSMO-RS method quite clearly turns out that some additional interaction (beyond electrostatics) is required for molecular surface with sigma> 0.008 e/Ang^2, strongly increasing with sigma. Substantial hydrogen bonding only only occurs for sigma> 0.012 e/Ang^2. This can be found on lone pair regions of O, N, and S. Andreas > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > Hi, > I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. > Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? > What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? > > TIA > Mateo> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt:-:cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -----------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jul 19 15:16:01 2006 From: "Shobe, David dshobe.###.sud-chemieinc.com" To: CCL Subject: CCL:G: Gaussian03 to AIM2000 Message-Id: <-32194-060719121347-31897-9cfvMiG/rvUVqDWTB51E6A###server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C6AB4E.4B8FE977" Date: Wed, 19 Jul 2006 18:13:38 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C6AB4E.4B8FE977 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I have recently purchased both of these programs, and I am having trouble s= omewhere. (I had been using Gaussian98 earlier). If I generate a wfn file= with Gaussian03 and then try to calculate atomic properties in AIM2000, I = encounter the following problems 1. Equivalent hydrogens have different atomic electron populations. 2. Atomic electron populations do not add up to an integer. 3. Atomic electron populations add up to a sum significantly less than the = total number of electrons. 4. Atomic electron populations sometimes change if the molecule is translat= ed or rotated. How can I tell where the problem is, in AIM2000, or in Gaussian03's wfn fil= e generating routine, or if I'm doing something wrong? Has anyone on CCL h= ad similar problems with either Gaussian03 or AIM2000? --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C6AB4E.4B8FE977 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Gaussian03 to AIM2000

I have recently purchased both of these pr= ograms, and I am having trouble somewhere.  (I had been using Gaussian= 98 earlier).  If I generate a wfn file with Gaussian03 and then try to= calculate atomic properties in AIM2000, I encounter the following problems=

1. Equivalent hydrogens have different ato= mic electron populations.
2. Atomic electron populations do not add= up to an integer.
3. Atomic electron populations add up to = a sum significantly less than the total number of electrons.
4. Atomic electron populations sometimes = change if the molecule is translated or rotated.

How can I tell where the problem is, in AI= M2000, or in Gaussian03's wfn file generating routine, or if I'm doing some= thing wrong?  Has anyone on CCL had similar problems with either Gauss= ian03 or AIM2000?

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a fire= wall.




This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.
------_=_NextPart_001_01C6AB4E.4B8FE977-- From owner-chemistry@ccl.net Wed Jul 19 15:50:00 2006 From: "rachelle joyce bienstock biensto1[a]niehs.nih.gov" To: CCL Subject: CCL: CHARMM patch type question Message-Id: <-32195-060719130509-32309-9NwgrM30ql1TaCwCoLOVlQ##server.ccl.net> X-Original-From: "rachelle joyce bienstock" Date: Wed, 19 Jul 2006 13:05:09 -0400 Sent to CCL by: "rachelle joyce bienstock" [biensto1=-=niehs.nih.gov] I am running an RDOCK job within the Accelrys software and have encountered this CHARMM error CHARMM> READ SEQU PDB UNIT 17 MAINIO> Sequence information being read from unit 17. TITLE> * RESIDUE SEQUENCE -- 10 RESIDUES LEU ARGNLYSNLEU ARGNLYSNARGNLEU ACE CAMD CHARMM> GENERATE LIG1 SETUP ***** ERROR in GENIC ***** Residue 'CAMD ' has the wrong patch type The patch types are defined within the Accelrys AMINO.RTF file. CAMD is a defined type within this file as a C-terminus amide- which is what this small peptide has an amidated C-terminus. Can someone shed some light for me on how to fix this CHARMM error? Thanks, Dr. Rachelle J. Bienstock Molecular Modeling and Structural Biochemistry National Institutes of Health (NIH) National Institute of Environmental Health Sciences (NIEHS) ITSS P.O. Box 12233 MD F0-011 Research Triangle Park, NC 27709, USA biensto1[A]niehs.nih.gov From owner-chemistry@ccl.net Wed Jul 19 16:25:01 2006 From: "Stradella, Omar omar.stradella,+,intel.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32196-060719113059-2315-3bMyOfKH7ok6n7Bjyh5K8g-,-server.ccl.net> X-Original-From: "Stradella, Omar" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 19 Jul 2006 09:58:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Stradella, Omar" [omar.stradella__intel.com] Take a look at AIMPAC from Richard Bader group (http://www.chemistry.mcmaster.ca/aim/aim_0.html). You can use the location of critical points in the Laplacian of the electronic density to find the center of lone pairs distributions. You can also try to use the existence and properties of saddle points in the electron distribution to characterize the nature and existence of hydrogen bonds. Omar Stradella, PhD Life Sciences Applications Engineer Intel Corp. 77 Reed Rd. Hudson, MA 01749 Email: omar.stradella!=!intel.com Phone: +1 978-553-5388 -----Original Message----- > From: owner-chemistry!=!ccl.net [mailto:owner-chemistry!=!ccl.net] Sent: Wednesday, July 19, 2006 9:30 AM To: Stradella, Omar Subject: CCL: How to visualize a lone pair Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] Hi, I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? TIA Mateohttp://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 Wed Jul 19 17:00:00 2006 From: "Jim Kress ccl_nospam===kressworks.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32197-060719122512-3677-uW/xQ0noPpIXXjXpDupVCA],[server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 19 Jul 2006 12:24:58 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam],[kressworks.com] NBO analysis offers an excellent technique for visualization of lone pairs as well as other orbitals. You can get more information here: http://www.chem.wisc.edu/~nbo5/ Jim > -----Original Message----- > From: Mateusz Witkowski big_mateo-#-inbox.com > [mailto:owner-chemistry|,|ccl.net] > Sent: Wednesday, July 19, 2006 9:27 AM > To: Kress, Jim > Subject: CCL: How to visualize a lone pair > > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > Hi, > I'm interested in the directionality of O,N,S lone pairs in > creation of hydrogen bonds. > Is it possible to visualize a lone pair from QM results? If > so, what should be done, which software should be used? > What is your general impression about hydrogen bonds with > XH-A angle ~100-120deg? Is there any border between HB and > purely electrostatic interaction? > > TIA > Mateo > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the |,| sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Wed Jul 19 17:35:00 2006 From: "Tapas Kar tapaskar__cc.usu.edu" To: CCL Subject: CCL:G: How to visualize a lone pair Message-Id: <-32198-060719155343-32312-B10U4LYyCmLfYRoqqkkpdw|,|server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 19 Jul 2006 13:53:33 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar,,cc.usu.edu] Hi I used Boys localization scheme to locate lone and all bond pairs including multi-center bonds in classical and non-classical molecules. Remarkable stability of LiBH2 and HBeBH2 dimers. B=B double bond or multicenter bonds? Tapas Kar and K. Jug, Chem. Phys. Lett., 214 (1993) 615. Is there any three-center CBC bond in 1,5-C2B3H5 and 1,3-C2B3H3 ? Tapas Kar and Karl Jug, Int. J. Quantum Chem.,.53 (1995) 407. If you are interested, I will arrange to send you the code which can be used with Gaussian as substituted L601. This code will provide bond order for 2 and 3-center cases also. It will generate coordinates of electron-pairs after localization. You have to use a visual program (such as Chem3D, molden, xmol etc) to see the location of electron pairs. In general, H-bonds stabilized due to dipole-dipole, charge-dipole interactions and polarization, charge transfer (in addition to electrostatic) also contribute significantly. Morokuma analysis (in GAMESS) can provide such information. Thanks Tapas -----Original Message----- > From: owner-chemistry^^^ccl.net [mailto:owner-chemistry^^^ccl.net] Sent: Wednesday, July 19, 2006 7:25 AM To: Kar, Tapas Subject: CCL: How to visualize a lone pair Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] Hi, I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? TIA Mateohttp://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 Wed Jul 19 18:10:01 2006 From: "Dmitry A. Olefir oxyran+/-mail.ru" To: CCL Subject: CCL:G: Gaussian03 to AIM2000 Message-Id: <-32199-060719165418-3963-u3mJlqaW0h+vwaGqKTlRPA]=[server.ccl.net> X-Original-From: "Dmitry A. Olefir" Date: Wed, 19 Jul 2006 16:54:17 -0400 Sent to CCL by: "Dmitry A. Olefir" [oxyran-*-mail.ru] Dear David! Problems about which you write are not caused by bugs in G03 or AIM2000. :) If you wish to gain accurate results using the AIM theory you should pay attention to quantity of Laplacian, which might equal to zero (in theory). In practice good results are gained if absolute value of L less than 0.001. Sorry for my bad English, and best regards. Olefir Dmitry From owner-chemistry@ccl.net Wed Jul 19 18:46:01 2006 From: "D. Afanasyev dafanasiev:_:ukr.net" To: CCL Subject: CCL:G: Gaussian03 to AIM2000 Message-Id: <-32200-060719170231-7956-qH/fEtcguGbk5YqyfhQIQg||server.ccl.net> X-Original-From: "D. Afanasyev" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Date: Wed, 19 Jul 2006 23:22:15 +0300 Mime-Version: 1.0 Sent to CCL by: "D. Afanasyev" [dafanasiev*o*ukr.net] Hello, You could try to analyze wfn file produced by G03 with original Bader's program PROAIMV, at first. As to the problems you mentioned, you probably know that AIM2000 uses numerical integration algorithms, so there is always some numerical error in integrated properties. Moreover, these integration algorithms (largely PROAIMV and PROMEGA) are flexible enough and can be controlled by means of several options; AIM2000 defaults are not always good, depending on your particular system. When you mentioned "equivalent hydrogens", what kind of equivalency did you mean? I personally used AIM2000 and PROAIMV with Gaussian03 Rev. B02 and C01 without any problems before. Dmytro. ************************************** * Dmytro Afanasyev * * Undergraduate Researcher * * Prof. H.F. Schaefer III group * *Center for Computational Chemistry* * University of Georgia * * Athens, GA, 30602 * ************************************** -----Original Message----- > From: "Shobe, David dshobe.!A!.sud-chemieinc.com" To: "Afanasyev, Dmitriy " Date: Wed, 19 Jul 2006 15:27:03 -0400 Subject: CCL:G: Gaussian03 to AIM2000 > Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com] > This is a multi-part message in MIME format. > ------_=_NextPart_001_01C6AB4E.4B8FE977 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > I have recently purchased both of these programs, and I am having trouble s= > omewhere. (I had been using Gaussian98 earlier). If I generate a wfn file= > with Gaussian03 and then try to calculate atomic properties in AIM2000, I = > encounter the following problems > > 1. Equivalent hydrogens have different atomic electron populations. > 2. Atomic electron populations do not add up to an integer. > 3. Atomic electron populations add up to a sum significantly less than the = > total number of electrons. > 4. Atomic electron populations sometimes change if the molecule is translat= > ed or rotated. > > How can I tell where the problem is, in AIM2000, or in Gaussian03's wfn fil= > e generating routine, or if I'm doing something wrong? Has anyone on CCL h= > ad similar problems with either Gaussian03 or AIM2000? > > --David Shobe, Ph.D., M.L.S. > S=FCd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > This e-mail message may contain confidential and / or privileged informatio= > n. If you are not an addressee or otherwise authorized to receive this mess= > age, you should not use, copy, disclose or take any action based on this e-= > mail or any information contained in the message. If you have received this= > material in error, please advise the sender immediately by reply e-mail an= > d delete this message.=20 > Thank you. > ------_=_NextPart_001_01C6AB4E.4B8FE977 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > 1"> > > Gaussian03 to AIM2000 > > > > >

I have recently purchased both of these pr= > ograms, and I am having trouble somewhere.  (I had been using Gaussian= > 98 earlier).  If I generate a wfn file with Gaussian03 and then try to= > calculate atomic properties in AIM2000, I encounter the following problems= >

> >

1. Equivalent hydrogens have different ato= > mic electron populations. > >
2. Atomic electron populations do not add= > up to an integer. > >
3. Atomic electron populations add up to = > a sum significantly less than the total number of electrons. > >
4. Atomic electron populations sometimes = > change if the molecule is translated or rotated. >

> >

How can I tell where the problem is, in AI= > M2000, or in Gaussian03's wfn file generating routine, or if I'm doing some= > thing wrong?  Has anyone on CCL had similar problems with either Gauss= > ian03 or AIM2000?

> >

--David Shobe, Ph.D., M.L.S. > >
S=FCd-Chemie, Inc. > >
phone (502) 634-7409 > >
fax (502) 634-7724 >

> >

Don't bother flaming me: I'm behind a fire= > wall. >

>
>
>
> > >
> This e-mail message may contain confidential and / or privileged informatio= > n. If you are not an addressee or otherwise authorized to receive this mess= > age, you should not use, copy, disclose or take any action based on this e-= > mail or any information contained in the message. If you have received this= > material in error, please advise the sender immediately by reply e-mail an= > d delete this message.
> Thank you.
>
> > ------_=_NextPart_001_01C6AB4E.4B8FE977--> > > > > From owner-chemistry@ccl.net Wed Jul 19 19:20:00 2006 From: "D. Afanasyev dafanasiev~!~ukr.net" To: CCL Subject: CCL:G: How to visualize a lone pair Message-Id: <-32201-060719171351-21120-/zIMBxLz+DhXBJXOwOyQyA=-=server.ccl.net> X-Original-From: "D. Afanasyev" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Date: Wed, 19 Jul 2006 23:35:16 +0300 Mime-Version: 1.0 Sent to CCL by: "D. Afanasyev" [dafanasiev-*-ukr.net] Hello, you can't actually visualize a lone pair at all. It's a misinterpretation. What you can do is to visualize some orbital (say, NBO or PNBO of NBO analysis) which intuitively corresponds to a "lone pair" (and spatially resembles it, actually). You can do that either by means of GaussView or by means of NBOView. Or, alternatively, you can follow the way suggested by David and analyze the Laplacian field of your system. MOLDEN does some simple analysis of Laplacian from Gaussian/Gamess output files. AIM2000 also does stuff like that... Dmytro. ************************************** * Dmytro Afanasyev * * Undergraduate Researcher * * Prof. H.F. Schaefer III group * *Center for Computational Chemistry* * University of Georgia * * Athens, GA, 30602 * ************************************** -----Original Message----- > From: "Shobe, David dshobe{=}sud-chemieinc.com" To: "Afanasyev, Dmitriy " Date: Wed, 19 Jul 2006 15:07:06 -0400 Subject: CCL:G: How to visualize a lone pair > Sent to CCL by: "Shobe, David" [dshobe++sud-chemieinc.com] > Mateo, > > You don't really need COSMO-RS (a nice and useful program, so I'm told, but rather expensive) to find the lone pair direction. All you need is a program that analyzes the electron density and finds the maximum of the Laplacian, which can usually be identified with an electron pair. This maximum will be at a particular point in space, so the lone pair directionality follows naturally. > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] > Sent: Wednesday, July 19, 2006 11:24 AM > To: Shobe, David > Subject: CCL:G: How to visualize a lone pair > > Sent to CCL by: Andreas Klamt [klamt=cosmologic.de] Dear Mateo, > > lone pairs and their directionalities can be very well identified in the VRML visualizations of the COSMO polarization charge density sigma on the COSMO surface. Many examples are given under http://www.cosmologic.de/ChemicalEngineering/visualization.html > (Please note that these are zipped VRML files. Normally they should simply open when you double click them from a browser which has a VRML plug in (e.g. CORTONA viewer from Parallel Graphics) > > Just look at the first example, phenoxymethyl-oxirane_sig, or at benzaldehyde, where you easily identify the lone-pair directions as red hot spots. Look at et3n (you have to rotate) and you will see the lonepair almost hidden between the et groups. Many more examples are given there. You can generate such VRMLs with our COSMOtherm software based on DFT COSMO tiles from TURBOMOLE, Gaussian03, or DMol. > > Our COSMO-RS method quite clearly turns out that some additional interaction (beyond electrostatics) is required for molecular surface with sigma> 0.008 e/Ang^2, strongly increasing with sigma. Substantial hydrogen bonding only only occurs for sigma> 0.012 e/Ang^2. This can be found on lone pair regions of O, N, and S. > > Andreas > > > > > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > > > Hi, > > I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. > > Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? > > What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? > > > > TIA > > Mateo> > > > > > > > > > > > > > -- > ----------------------------------------------------------------------------- > Dr. habil. Andreas Klamt > COSMOlogic GmbH&CoKG > Burscheider Str. 515 > 51381 Leverkusen, Germany > > Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 > e-mail: klamt:-:cosmologic.de > web: www.cosmologic.de > ----------------------------------------------------------------------------- > COSMOlogic > Your Competent Partner for > Computational Chemistry and Fluid Thermodynamics > -----------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. > Thank you.> > > > > From owner-chemistry@ccl.net Wed Jul 19 19:55:00 2006 From: "Mark Zottola mzottola],[gmail.com" To: CCL Subject: CCL:G: Gaussian03 to AIM2000 Message-Id: <-32202-060719170954-17914-PD+CGK0Bwh32DBNRKreSAA_-_server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_157573_25003035.1153343389799" Date: Wed, 19 Jul 2006 17:09:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola++gmail.com] ------=_Part_157573_25003035.1153343389799 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline David, > From what you described, you have version D01 of Gaussian G03. This version has a bug which causes a mismatch between the atomic coordinates used to generate the wavefunction file and the atomic coordinates in the wavefunction file itself. You can either hand edit the wfn file to change the atomic coordinates from (IIRC) the standard orientation into input orientation. The second solution is to use version C02 of Gaussian03. I use the latter as hand editing a file seems fraught with error. I hope this helps. Mark Zottola On 7/19/06, Shobe, David dshobe.=-=.sud-chemieinc.com wrote: > > Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com] > This is a multi-part message in MIME format. > ------_=_NextPart_001_01C6AB4E.4B8FE977 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > I have recently purchased both of these programs, and I am having trouble > s= > omewhere. (I had been using Gaussian98 earlier). If I generate a wfn > file= > with Gaussian03 and then try to calculate atomic properties in AIM2000, I > = > encounter the following problems > > 1. Equivalent hydrogens have different atomic electron populations. > 2. Atomic electron populations do not add up to an integer. > 3. Atomic electron populations add up to a sum significantly less than the > = > total number of electrons. > 4. Atomic electron populations sometimes change if the molecule is > translat= > ed or rotated. > > How can I tell where the problem is, in AIM2000, or in Gaussian03's wfn > fil= > e generating routine, or if I'm doing something wrong? Has anyone on CCL > h= > ad similar problems with either Gaussian03 or AIM2000? > > --David Shobe, Ph.D., M.L.S. > S=FCd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > This e-mail message may contain confidential and / or privileged > informatio= > n. If you are not an addressee or otherwise authorized to receive this > mess= > age, you should not use, copy, disclose or take any action based on this > e-= > mail or any information contained in the message. If you have received > this= > material in error, please advise the sender immediately by reply e-mail > an= > d delete this message.=20 > Thank you. > ------_=_NextPart_001_01C6AB4E.4B8FE977 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > charset=3Diso-8859-= > 1"> > "> > Gaussian03 to AIM2000 > > > > >

I have recently purchased both of these > pr= > ograms, and I am having trouble somewhere.  (I had been using > Gaussian= > 98 earlier).  If I generate a wfn file with Gaussian03 and then try > to= > calculate atomic properties in AIM2000, I encounter the following > problems= >

> >

1. Equivalent hydrogens have different > ato= > mic electron populations. > >
2. Atomic electron populations do not > add= > up to an integer. > >
3. Atomic electron populations add up to > = > a sum significantly less than the total number of electrons. > >
4. Atomic electron populations sometimes > = > change if the molecule is translated or rotated. >

> >

How can I tell where the problem is, in > AI= > M2000, or in Gaussian03's wfn file generating routine, or if I'm doing > some= > thing wrong?  Has anyone on CCL had similar problems with either > Gauss= > ian03 or AIM2000?

> >

--David Shobe, Ph.D., M.L.S. > >
S=FCd-Chemie, Inc. > >
phone (502) 634-7409 > >
fax (502) 634-7724 >

> >

Don't bother flaming me: I'm behind a > fire= > wall. >

>
>
>
> > >
> This e-mail message may contain confidential and / or privileged > informatio= > n. If you are not an addressee or otherwise authorized to receive this > mess= > age, you should not use, copy, disclose or take any action based on this > e-= > mail or any information contained in the message. If you have received > this= > material in error, please advise the sender immediately by reply e-mail > an= > d delete this message.
> Thank you.
>
> > ------_=_NextPart_001_01C6AB4E.4B8FE977--> > > > ------=_Part_157573_25003035.1153343389799 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
David,
 
From what you described, you have version D01 of Gaussian G03.  This version has a bug which causes a mismatch between the atomic coordinates used to generate the wavefunction file and the atomic coordinates in the wavefunction file itself.  You can either hand edit the wfn file to change the atomic coordinates from (IIRC) the standard orientation into input orientation.  The second solution is to use version C02 of Gaussian03. I use the latter as hand editing a file seems fraught with error.
 
I hope this helps.
 
 
Mark Zottola

 
On 7/19/06, Shobe, David dshobe.=-=.sud-chemieinc.com <owner-chemistry=-=ccl.net > wrote:
Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com]
This is a multi-part message in MIME format.
------_=_NextPart_001_01C6AB4E.4B8FE977
Content-Type: text/plain;
       charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

I have recently purchased both of these programs, and I am having trouble s=
omewhere.  (I had been using Gaussian98 earlier).  If I generate a wfn file=
with Gaussian03 and then try to calculate atomic properties in AIM2000, I =
encounter the following problems

1. Equivalent hydrogens have different atomic electron populations.
2. Atomic electron populations do not add up to an integer.
3. Atomic electron populations add up to a sum significantly less than the =
total number of electrons.
4. Atomic electron populations sometimes change if the molecule is translat=
ed or rotated.

How can I tell where the problem is, in AIM2000, or in Gaussian03's wfn fil=
e generating routine, or if I'm doing something wrong?  Has anyone on CCL h=
ad similar problems with either Gaussian03 or AIM2000?

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.




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<TITLE>Gaussian03 to AIM2000</TITLE>
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<P><FONT SIZE=3D2 FACE=3D"Arial">I have recently purchased both of these pr=
ograms, and I am having trouble somewhere.&nbsp; (I had been using Gaussian=
98 earlier).&nbsp; If I generate a wfn file with Gaussian03 and then try to=
calculate atomic properties in AIM2000, I encounter the following problems=
</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">1. Equivalent hydrogens have different ato=
mic electron populations.</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">2. Atomic electron populations do not add=
up to an integer.</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">3. Atomic electron populations add up to =
a sum significantly less than the total number of electrons.</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">4. Atomic electron populations sometimes =
change if the molecule is translated or rotated.</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">How can I tell where the problem is, in AI=
M2000, or in Gaussian03's wfn file generating routine, or if I'm doing some=
thing wrong?&nbsp; Has anyone on CCL had similar problems with either Gauss=
ian03 or AIM2000?</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">--David Shobe, Ph.D., M.L.S.</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">S=FCd-Chemie, Inc.</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">phone (502) 634-7409</FONT>

<BR><FONT SIZE=3D2 FACE=3D"Arial">fax (502) 634-7724</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Don't bother flaming me: I'm behind a fire=
wall.</FONT>
</P>
<BR>
<BR>
<BR>


<DIV>
This e-mail message may contain confidential and / or privileged informatio=
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age, you should not use, copy, disclose or take any action based on this e-=
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