From chemistry-request@ccl.net Wed Dec 3 23:15:33 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB44F2xp010587 for ; Wed, 3 Dec 2003 23:15:02 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 44B1E9AC9; Thu, 4 Dec 2003 05:15:02 +0100 (CET) To: chemistry:at:ccl.net Subject: Hydrogen bonds Message-ID: <1070511302.3fceb4c631282:at:webmail.u-picardie.fr> Date: Thu, 04 Dec 2003 05:15:02 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I am looking for references describing intra or inter-molecular Hydrogen bonds (life time for example) observed in small organic molecules, peptides or nucleic acids during ... some experiments (for instance during molecular dynamics simulations). Thanks, best regards, Francois From chemistry-request@ccl.net Thu Dec 4 02:13:58 2003 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB47DQxp015902 for ; Thu, 4 Dec 2003 02:13:26 -0500 Received: from cosmologic.de (xdsl-213-168-110-252.netcologne.de [213.168.110.252]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id ABX68099 (AUTH klamt{at}cosmologic.de); Thu, 4 Dec 2003 08:13:18 +0100 (CET) Message-ID: <3FCEDE89.7030607{at}cosmologic.de> Date: Thu, 04 Dec 2003 08:13:13 +0100 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Laurence Cuffe CC: yonyang , chemistry{at}ccl.net Subject: Re: CCL:keto/enolate TS structure in Solvation model References: <3FCE14DE.13452.B1FB4@localhost> Content-Type: multipart/alternative; boundary="------------090304010302020002010306" X-Spam-Status: No, hits=0.2 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_00_10,HTML_MESSAGE,REFERENCES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --------------090304010302020002010306 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Laurence, dear Yong, although I have not too much experience in searching TS, but based on all my COSMO experience - I strongly disagree with the opinion that it makes any sense to use simple spherical or ellipsoidal cavity Onsager models for TS search in solution. The solvation energies strongly depend on the size, orientation and position of the cavity relative to the molecule, that these kinds of cavities anyway only make sense of quite spherical or ellipsoidal molecules. For all others you could as well use a random number generator, with the only difference that the sign of the dielectric energy correction will always be right. This is so much more true for TS, which tend to be very "non-spherical", and the degree of deviation from a spherical shape changes strongly along the reaction path. For TS search in continuum solvation models everything else than a good molecular shaped cavity is useless. I am not absolutely convinced that the way of smoothing between atomic spheres with auxiliary spheres as done in PCM (GEPOL) is optimal, because each of the auxiliary spheres has the wrong curvature (convex), while in the interpolation region (crevices) we need a concave surface. In our more advanced COSMO implementations in TURBOMOLE, GAMESS (not yet officially released), and MOPAC98/2000/2002 we have a better interpolation for those regions, which become of special importance during reactions. Another point of importance in the application of dielectric continuum solvation methods to TS is the choice of radii for the cavity construction. United atom definitions and atom-type based definitions are quite useless, because the atoms loose their clear bond partners and atom types during a reaction. In our COSMO and COSMO-RS parameterizations we only use element specific radii, which should keep valid during a reaction. This set of radii is also available in Gaussion03 now. The fact that DFT might not be optimal for TS at all is a different issue. Use of more refined schemes like COSMO-RS (COSMOtherm program) for corrections beyond the dielectric level (including hydrogen bonding) may be required as well. So I agree, that TS search in solution is still a very demanding area of research, and no turn key solutions exist here. But going back to the Onsager level is the wrong direction! Andreas Laurence Cuffe wrote: >On 1 Dec 2003, at 14:46, yonyang wrote: > > > >>Dear CCL users: >>I am playing around with a keto/enolate formation reaction catalyzed by >>gernal acid and base(methyl amine/ammonium ion). I would like to locate >>the TS structure in organic solvent such as THF or cyclohexane based on >>the TS structure previously located in gas phase. Despite semi-empirical >>method AM1 in spartan was able to locate the initial strucuture in >>organic >>solvation, but further optimization in Gaussian was unsuccesful and >>failed >>many times. >> >> >Dear Yong >you may find our paper: >"Experimental and theoretical studies of rotational barriers in aceto, >n-methylaceto and n-phenylacetohydroxamic acid" >David A. Brown, Laurence P, Cuffe, Geraldine M. Fitzpatrick, Noel >J. fitzpatrick, William K. Glass and Kara M. Herlihy >in the collection of Czechoslovak Chemical Communications > 2001, 66(1), 99-108 >of interest. I think there's an abstract on the webpage: >http://cccc.uochb.cas.cz/Vol/66/No01/20010099.html >Finding solvated Transistion states is not easy and when we did >find them we did not find the barrier heights reliable using DFT and >PCM, although this may have changed with the new version of >Gaussian. If your molecule has a dipole moment you might >consider using the Onsager method, Its old fashioned, but also >computationaly cheap and it seemed to improve over gas phase >results for our systems. It may also provide a better starting point >for more complex calculations. >Hope this helps >All the best >Laurence Cuffe > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY{at}ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl{at}ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt{at}cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- --------------090304010302020002010306 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Laurence, dear Yong,

although I have not too much experience in searching TS, but based on all my COSMO experience -  I strongly disagree with the opinion that it makes any sense to use simple spherical or ellipsoidal cavity Onsager models for TS search in solution. The solvation energies strongly depend on the size, orientation and position of the cavity relative to the molecule, that these kinds of cavities anyway only make sense of quite spherical or ellipsoidal molecules. For all others you could as well use a random number generator, with the only difference that the sign of the dielectric energy correction will always be right.  This is so much more true for TS, which tend to be very "non-spherical", and the degree of deviation from a spherical shape changes strongly along the reaction path.

For TS search in continuum solvation models everything else than a good molecular shaped cavity is useless. I am not absolutely convinced that the way of smoothing between atomic spheres with auxiliary spheres as done in PCM (GEPOL) is optimal, because each of the auxiliary spheres has the wrong curvature (convex), while in the interpolation region (crevices) we need a concave surface. In our more advanced COSMO implementations in TURBOMOLE, GAMESS (not yet officially released), and MOPAC98/2000/2002 we have a better interpolation for those regions, which become of special importance during reactions.

Another point of importance in the application of dielectric continuum solvation methods to TS is the choice of radii for the cavity construction. United atom definitions and atom-type based definitions are quite useless, because the atoms loose their clear bond partners and atom types during a reaction. In our COSMO and COSMO-RS parameterizations we only use element specific radii, which should keep valid during a reaction. This set of radii is also available in Gaussion03 now.

The fact that DFT might not be optimal for TS at all is a different issue. Use of more refined schemes like COSMO-RS (COSMOtherm program) for corrections beyond the dielectric level (including hydrogen bonding) may be required as well.
So I agree, that TS search in solution is still a very demanding area of research, and no turn key solutions exist here. But going back to the Onsager level is the wrong direction!

Andreas

Laurence Cuffe wrote:
On 1 Dec 2003, at 14:46, yonyang wrote:

  
Dear CCL users:
I am playing around with a keto/enolate formation reaction catalyzed by
gernal acid and base(methyl amine/ammonium ion). I would like to locate
the TS structure in organic solvent such as THF or cyclohexane based on
the TS structure previously located in gas phase. Despite semi-empirical
method AM1 in spartan was able to locate the initial strucuture in
organic
solvation, but further optimization in Gaussian was unsuccesful and
failed
many times.
    
Dear Yong 
you may find our paper:
"Experimental and theoretical studies of rotational barriers in aceto, 
n-methylaceto and n-phenylacetohydroxamic acid"
David A. Brown, Laurence P, Cuffe, Geraldine M. Fitzpatrick, Noel 
J. fitzpatrick, William K. Glass and Kara M. Herlihy
in  the collection of Czechoslovak Chemical Communications
 2001, 66(1), 99-108
of interest.  I think there's an abstract on the webpage:
http://cccc.uochb.cas.cz/Vol/66/No01/20010099.html
Finding solvated Transistion states is not easy and when we did 
find them we did not find the barrier heights reliable using DFT and 
PCM, although this may have changed with the new version of 
Gaussian.  If your molecule has a dipole moment you might 
consider using the Onsager method,  Its old fashioned, but also 
computationaly cheap and it seemed to improve over gas phase 
results for our systems. It may also provide a better starting point 
for more complex calculations. 
Hope this helps
All the best
Laurence Cuffe


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-- 
--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  
Fax:  +49-2171-73168-9
e-mail: klamt{at}cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
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        Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------------

--------------090304010302020002010306-- From chemistry-request@ccl.net Thu Dec 4 11:13:14 2003 Received: from web21208.mail.yahoo.com (web21208.mail.yahoo.com [216.136.175.205]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hB4GCgxp027721 for ; Thu, 4 Dec 2003 11:12:42 -0500 Message-ID: <20031204161241.81684.qmail:at:web21208.mail.yahoo.com> Received: from [129.109.59.107] by web21208.mail.yahoo.com via HTTP; Thu, 04 Dec 2003 08:12:41 PST Date: Thu, 4 Dec 2003 08:12:41 -0800 (PST) From: IEJMD Subject: CCL : IECMD 2003 - Program for December 4, 2003 To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.4 required=7.0 tests=MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Internet Electronic Conference of Molecular Design 2003 IECMD 2003 - Program for December 4, 2003 Full papers available from: http://www.biochempress.com To post a message, send an E-mail to: iecmd2003:at:yahoogroups.com Send a confidential comment about a paper to: iejmd:at:yahoo.com 1. IECMD 2003, paper 41 Internal Rotation Of NO2 Group In Lower Nitroalkanes From Quantum Chemical Calculations Yu. I. Tarasov, A. V. Stepanova, D. M. Kovtun, I. V. Kochikov, B. K. Novosadov, N. Vogt, and J. Vogt 2. IECMD 2003, paper 49 Avoided Curves Crossings of the Rydberg [(AHa+)(e-)Rydberg] (a=2-4) Radical Jong Keun Park 3. IECMD 2003, paper 34 Use of an Expert System in Lignan Skeleton Prediction from 1H NMR Data Mara B. Costantin, Marcelo J. P. Ferreira, Gilberto V. Rodrigues, and Vicente P. Emerenciano 4. IECMD 2003, paper 42 QSPR Modeling The Aqueous Solubility Of Polychlorinated Biphenyls By Optimization Of Correlation Weights Of Local And Global Graph Invariants E. A. Castro, A. A. Toropov, A. I. Nesterova, and O. M. Nabiev 5. IECMD 2003, paper 53 Novel Method for Discrimination of Conserved Genes through Numerical Characterization of DNA Sequences Ashesh Nandy 6. IECMD 2003, paper 56 TUNCUR: Sequential Codes for Semiempirical Quantum-Chemical Calculations of Tunneling Current Valentin A. Zayets and Elena F. Sheka ===== Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-1157 USA __________________________________ Do you Yahoo!? Free Pop-Up Blocker - Get it now http://companion.yahoo.com/ From chemistry-request@ccl.net Thu Dec 4 12:01:09 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4H0bxp028915 for ; Thu, 4 Dec 2003 12:00:37 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id hB4H0aLP020981 for ; Thu, 4 Dec 2003 12:00:36 -0500 (EST) Message-Id: <200312041700.hB4H0aLP020981:at:copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 04 Dec 2003 11:52:53 -0500 Subject: Re: Elec. Excited States From: "Olga Dmitrenko" To: chemistry:at:ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 0.9 DEAR_SOMEBODY,SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Steve, Probably MOLPRO is the right choice. I would recommend to follow the approach of 2001 paper by Ram. CASSCF optimizations and MP2 corrections can be done using Gamess which is a little bit more user-friendly program (on my opinion). But MRCI - it's MOLPRO business,.. and it's not easy. Best regards, Olga From chemistry-request@ccl.net Thu Dec 4 11:41:44 2003 Received: from smtp1.uh.cu (smtp1.uh.cu [200.55.139.212]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4Gf1xp028393 for ; Thu, 4 Dec 2003 11:41:09 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by smtp1.uh.cu (Postfix) with ESMTP id C5A30350A8 for ; Thu, 4 Dec 2003 09:28:54 -0500 (CST) Received: from fq.uh.cu (canaria.qct.fq.oc.uh.cu [192.168.3.4]) by smtp1.uh.cu (Postfix) with ESMTP id 9411935098 for ; Thu, 4 Dec 2003 09:28:54 -0500 (CST) Received: from fq.uh.cu (yaquelin.qct.fq.oc.uh.cu [192.168.3.40]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id hB49S7hb012609 for ; Thu, 4 Dec 2003 09:28:10 GMT Message-ID: <3FCF52BA.8774BB80:at:fq.uh.cu> Date: Thu, 04 Dec 2003 09:28:58 -0600 From: Juan Alexander Padron X-Mailer: Mozilla 4.78 [es] (Win98; U) X-Accept-Language: es MIME-Version: 1.0 To: CCL Subject: A note of disappointment Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, hits=0.3 required=7.0 tests=MAILTO_TO_SPAM_ADDR,USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL list: I am reluctant to use this list for any reason that differs from scientific exchange, but I feel that all my colleagues must be aware of the recent news regarding to my country. It have came to me the horrendous information that the ACS, compelled by the US government, has forbidden to authors of (by this precise order) Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > from my point of view, is the ultimate violation of the rights of the people that devote their life to the development of science. No political reasons are valid to exclude anyone from the scientific community, mostly if those are from third developed countries who are the ones who required all the help that they can get. In the case of my country they are no reason to declare such blockade, cause we are not a thread to anyone: instead of this they are thousands of Cubans in a lot of countries helping in fields like health care, agriculture, education and many others that are vital. My country is also the place of birth of lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. Finlay, Pedro Kourm, and many others that have make serious advances in different fields of knowledge. This is a dark precedent to the new generation of researches in my country, that sincerely appreciate the tremendous scientific capacities of the American science, and once again must feel excluded without reason. Be then this mail a note of disappointment and protest. Best Regards, -- &/////////////////////////////////////////////////// &Juan Alexander Padrsn-Garcma &Researcher, PhD Student &Laboratory of Computational & Theoretical Chemistry, &Chemistry Faculty Havana University, Cuba &padrongj:at:fq.uh.cu, alex2473:at:yahoo.es &http://www.fq.uh.cu/investigacion/lqct ____________ ///////////////////////////////////////// From chemistry-request@ccl.net Thu Dec 4 10:14:12 2003 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4FDfxp026135 for ; Thu, 4 Dec 2003 10:13:41 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.10/8.12.10) with SMTP id hB4FDb7F026968 for ; Thu, 4 Dec 2003 09:13:38 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Solvated TS Searches Date: Thu, 4 Dec 2003 09:13:36 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_021D_01C3BA46.E629C500" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.9 required=7.0 tests=HTML_20_30,HTML_MESSAGE,MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_021D_01C3BA46.E629C500 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit I am interested in the comments about seeking solvated Transition Structures. We recently completed a study of SN2 displacements in sugar analogues using B3LYP and both Onsager and IPCM solvation - the manuscripts are under review now for J Phys Chem A (the story of this research project is a very long and convoluted one and I won't get into it here). However, we did not have any particular difficulty in locating first-order saddle points using Onsager solvation. We did this work with Gaussian 98, which meant that we could not do geometry optimizations using IPCM (and the SC-IPCM didn't work). We simply took "gas phase" structures as starting points, and ran either Opt=TS or QST3 calculations from there using the Onsager solvation model. We then did single-point energy calculations using IPCM solvation at the Onsager geometries, assuming that the actual geometries would not be greatly different even though the energies would. The results we obtained using this approach seemed to us to be quite in line with expectations. I would be very interested in hearing how others have fared using IPCM, SC-IPCM or other higher-order continuum solvation models for geometry optimizations with Gaussian 03. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin$at$cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ ------=_NextPart_000_021D_01C3BA46.E629C500 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I am = interested in=20 the comments about seeking solvated Transition = Structures.
 
We = recently=20 completed a study of SN2 displacements in sugar analogues using B3LYP = and both=20 Onsager and IPCM solvation - the manuscripts are under review now for J = Phys=20 Chem A (the story of this research project is a very long and convoluted = one and=20 I won't get into it here).
 
However, we did=20 not have any particular difficulty in locating first-order saddle = points=20 using Onsager solvation.  We did this work with Gaussian 98, which = meant=20 that we could not do geometry optimizations using IPCM (and the SC-IPCM = didn't=20 work).  We simply took "gas phase" structures as starting points, = and ran=20 either Opt=3DTS or QST3 calculations from there using the Onsager = solvation=20 model.  We then did single-point energy calculations using IPCM = solvation=20 at the Onsager geometries, assuming that the actual geometries would not = be=20 greatly different even though the energies would.
 
The = results we=20 obtained using this approach seemed to us to be quite in line with=20 expectations.
 
I = would be very=20 interested in hearing how others have fared using IPCM, SC-IPCM or other = higher-order continuum solvation models for geometry optimizations with = Gaussian=20 03.

Dr. Philip G. Hultin
Associate Department Head=20 and
Associate Professor of Chemistry
University of = Manitoba
Winnipeg,=20 MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin$at$cc.umanitoba.ca<= BR>http://www.umanitoba.ca/chemistry/

 
------=_NextPart_000_021D_01C3BA46.E629C500-- From jkl@ccl.net Thu Dec 4 12:31:59 2003 -0500 Return-Path: Received: from web60507.mail.yahoo.com (web60507.mail.yahoo.com [216.109.116.128]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with SMTP id hB4HVxjl027271 for ; Thu, 4 Dec 2003 12:31:59 -0500 Message-ID: <20031204173150.75680.qmail^at^web60507.mail.yahoo.com> Received: from [139.19.34.3] by web60507.mail.yahoo.com via HTTP; Fri, 05 Dec 2003 01:31:50 CST Date: Fri, 5 Dec 2003 01:31:50 +0800 (CST) From: =?iso-8859-1?q?The=20August?= Subject: How good is ICM Dock for small flexible peptides? To: chemistry^at^ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Checker-Version: SpamAssassin 2.60 (1.212-2003-09-23-exp) on atlantis.ccl.net X-Spam-Status: No, hits=-0.9 required=9.0 tests=BAYES_10 autolearn=ham version=2.60 Hello CCLers, Can anybody tell me how's ICM Dock's( From MOLSOFT) ability to dock small flexible peptides (upto 10 amino acids long)? Any other comments on ICM Dock is highly solicited. Sincerely GED _______________________________________________________________________ > Do You Yahoo!? > Get your free @yahoo.com.hk address at http://mail.english.yahoo.com.hk _______________________________________________________________________ From chemistry-request@ccl.net Thu Dec 4 13:47:41 2003 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4IlAxp031990 for ; Thu, 4 Dec 2003 13:47:10 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Thu, 04 Dec 2003 13:47:29 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Thu, 04 Dec 2003 13:46:53 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:A note of disappointment Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=-0.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) List: Pardon my doubting Thomas nature. Can anyone confirm this. I have no doubt that the current gov't of the US might pull something like this and, unfortunately, I can figure out the reasons why the ACS might bow to the demand. However, this would truly be a black mark against ACS. Thanks. Pete Gannett >>> Juan Alexander Padron 12/04/03 10:28AM >>> Dear CCL list: I am reluctant to use this list for any reason that differs from scientific exchange, but I feel that all my colleagues must be aware of the recent news regarding to my country. It have came to me the horrendous information that the ACS, compelled by the US government, has forbidden to authors of (by this precise order) Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > from my point of view, is the ultimate violation of the rights of the people that devote their life to the development of science. No political reasons are valid to exclude anyone from the scientific community, mostly if those are from third developed countries who are the ones who required all the help that they can get. In the case of my country they are no reason to declare such blockade, cause we are not a thread to anyone: instead of this they are thousands of Cubans in a lot of countries helping in fields like health care, agriculture, education and many others that are vital. My country is also the place of birth of lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. Finlay, Pedro Kourm, and many others that have make serious advances in different fields of knowledge. This is a dark precedent to the new generation of researches in my country, that sincerely appreciate the tremendous scientific capacities of the American science, and once again must feel excluded without reason. Be then this mail a note of disappointment and protest. Best Regards, -- &/////////////////////////////////////////////////// &Juan Alexander Padrsn-Garcma &Researcher, PhD Student &Laboratory of Computational & Theoretical Chemistry, &Chemistry Faculty Havana University, Cuba &padrongj.-at-.fq.uh.cu, alex2473.-at-.yahoo.es &http://www.fq.uh.cu/investigacion/lqct ____________ ///////////////////////////////////////// -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Dec 4 13:01:10 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4I0cxp030916 for ; Thu, 4 Dec 2003 13:00:39 -0500 Expiry-Date: Fri, 27 Feb 2004 -1:-1:-1 +0000 Reply-To: training.-at-.accelrys.com To: CHEMISTRY.-at-.ccl.net Subject: CCL: Accelrys Customer Training Events for February MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Thu, 4 Dec 2003 10:00:36 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 12/04/2003 10:00:38, Serialize complete at 12/04/2003 10:00:38 Content-Type: text/plain; charset="US-ASCII" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Accelrys Inc. are holding the following training workshops at locations in the US and Europe during February. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. MACROMOLECULAR MODELING Introduction to DS Modeling 4-5 February in Burlington, MA Introduction to InsightII for Life Sciences 24-25 February in San Diego, CA Homology-Based protein Design 26-27 February in San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html CHEMINFORMATICS Accord Visual Objects 23 February in Cambridge, UK Accord SDK 24-25 February in Cambridge, UK Accord Chemistry Cartridge 26 February in Cambridge, UK Accord CombiChem Add-on 27 February in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html BIOINFORMATICS Introduction to Wisconsin Package and SeqLab 10-11 February in San Diego, CA Introduction to SeqWeb 12 February in San Diego, CA Introduction to DS Gene 13 February in San Diego, CA For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss.-at-.accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Thu Dec 4 15:12:39 2003 Received: from struggle.mr.itd.umich.edu (struggle.mr.itd.umich.edu [141.211.14.79]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4KC8xp001303 for ; Thu, 4 Dec 2003 15:12:08 -0500 Received: from Garfield (pcp05005614pcs.sanarb01.mi.comcast.net [68.40.225.128]) by struggle.mr.itd.umich.edu (smtp) with ESMTP id hB4KC5uo010125 for ; Thu, 4 Dec 2003 15:12:08 -0500 From: "Joslyn Kravitz" To: Subject: CCL:windows based orbital viewing Date: Thu, 4 Dec 2003 15:12:15 -0500 Message-ID: <002501c3baa2$ec1abf30$80e12844@Garfield> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0026_01C3BA79.0344B730" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_80_90,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0026_01C3BA79.0344B730 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello all, Does anyone know of viewing program that can display molecular orbitals > from Gaussian output? I am looking for something that runs on windows and preferably is free. Thanks, Joslyn Kravitz ------=_NextPart_000_0026_01C3BA79.0344B730 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello all,

 

Does anyone know of viewing program that can display molecular orbitals from Gaussian output? I = am looking for something that runs on windows and preferably is = free.

 

Thanks,

Joslyn Kravitz

------=_NextPart_000_0026_01C3BA79.0344B730-- From chemistry-request@ccl.net Thu Dec 4 14:22:40 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4JM9xp000313 for ; Thu, 4 Dec 2003 14:22:09 -0500 Received: from santiago.ks.uiuc.edu (santiago.ks.uiuc.edu [130.126.120.99]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hB4JM9u5026280; Thu, 4 Dec 2003 13:22:09 -0600 (CST) Received: from localhost (jim@localhost) by santiago.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id hB4JM9i18080; Thu, 4 Dec 2003 13:22:09 -0600 X-Authentication-Warning: santiago.ks.uiuc.edu: jim owned process doing -bs Date: Thu, 4 Dec 2003 13:22:09 -0600 (CST) From: Jim Phillips To: Juan Alexander Padron cc: CCL Subject: Re: CCL:A note of disappointment In-Reply-To: <3FCF52BA.8774BB80:at:fq.uh.cu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,MAILTO_TO_SPAM_ADDR, QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, While I understand your reaction to being excluded from ACS journals, I would suggest that you should avoid ACS publications anyway due to their restrictive copyright policy that prevents authors from posting their own publications on their own websites. The APS is much more liberal, as is the completely free http://www.plos.org/ effort. -Jim On Thu, 4 Dec 2003, Juan Alexander Padron wrote: > Dear CCL list: > > I am reluctant to use this list for any reason that differs from > scientific exchange, but I feel that all my colleagues must be aware of > the recent news regarding to my country. > > It have came to me the horrendous information that the ACS, compelled by > the US government, has forbidden to authors of (by this precise order) > Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > > from my point of view, is the ultimate violation of the rights of the > people that devote their life to the development of science. No > political reasons are valid to exclude anyone from the scientific > community, mostly if those are from third developed countries who are > the ones who required all the help that they can get. In the case of my > country they are no reason to declare such blockade, cause we are not a > thread to anyone: instead of this they are thousands of Cubans in a lot > of countries helping in fields like health care, agriculture, education > and many others that are vital. My country is also the place of birth of > lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. > Finlay, Pedro Kourm, and many others that have make serious advances in > different fields of knowledge. This is a dark precedent to the new > generation of researches in my country, that sincerely appreciate the > tremendous scientific capacities of the American science, and once again > must feel excluded without reason. Be then this mail a note of > disappointment and protest. > > Best Regards, > -- > &/////////////////////////////////////////////////// > &Juan Alexander Padrsn-Garcma > &Researcher, PhD Student > &Laboratory of Computational & Theoretical Chemistry, > &Chemistry Faculty Havana University, Cuba > &padrongj:at:fq.uh.cu, alex2473:at:yahoo.es > &http://www.fq.uh.cu/investigacion/lqct ____________ > ///////////////////////////////////////// > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Dec 4 14:43:38 2003 Received: from pantheon-po03.its.yale.edu (pantheon-po03.its.yale.edu [130.132.50.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4Jh7xp000647 for ; Thu, 4 Dec 2003 14:43:07 -0500 Received: from yale.edu (aneth.chem.yale.edu [130.132.25.204]) by pantheon-po03.its.yale.edu (8.11.6p2-20030917/8.11.6) with ESMTP id hB4Jh7006988 for ; Thu, 4 Dec 2003 14:43:07 -0500 (EST) Message-ID: <3FCF8E4B.7030907:at:yale.edu> Date: Thu, 04 Dec 2003 14:43:07 -0500 From: Ivan Tubert-Brohman User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry Subject: Re: CCL:A note of disappointment References: In-Reply-To: X-Enigmail-Version: 0.76.7.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-YaleITSMailFilter: Version 1.1d (attachment(s) not renamed) X-Spam-Status: No, hits=-2.1 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > List: > > Pardon my doubting Thomas nature. Can anyone confirm this. I have no > doubt that the current gov't of the US might pull something like this > and, unfortunately, I can figure out the reasons why the ACS might bow > to the demand. However, this would truly be a black mark against ACS. > > Thanks. > > Pete Gannett This was published November 24 in Chemical and Engineering News: ---- ACS imposes moratorium on some foreign papers The American Chemical Society has imposed a moratorium on publishing journal articles that are written by authors in Cuba, Iran, Iraq, Libya, or Sudan. Robert D. Bovenschulte, president of the society's Publications Division, writes in a memorandum to ACS journal editors that "this action, which I hope will be temporary," has been taken "with great reluctance." The moratorium follows a ruling by the Treasury Department, whose Office of Foreign Assets Control (OFAC) "advised that papers from these nations may be published but only if no editorial services are provided," Bovenschulte writes. Such services could be deemed to violate U.S. trade sanctions against the countries. The Treasury Department ruling was prompted by actions of the Institute of Electrical & Electronics Engineers (IEEE), which is attempting to obtain a license from OFAC that will allow IEEE to edit articles by authors in the affected countries. If IEEE, which Bovenschulte notes has "taken the lead with the government on this problem," can obtain such a license, "ACS can then use that precedent to make the same case to OFAC and so obtain our own license." ---- Ivan From chemistry-request@ccl.net Thu Dec 4 15:02:59 2003 Received: from ccserver1.chemcodes.com (66-152-40-106.ded.btitelecom.net [66.152.40.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4K2Sxp001073 for ; Thu, 4 Dec 2003 15:02:28 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: A note of disappointment Date: Thu, 4 Dec 2003 15:02:28 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: A note of disappointment thread-index: AcO6mQJo6wCwpauYRAGyCHfr5XjQKAAB78UQ From: "Ihlenfeldt, Wolf D." To: "Peter Gannett" Cc: X-Spam-Status: No, hits=-0.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hB4K2xxp001083 This information is correct. Actually, it does not only affect ACS, but *ALL* US scientific societies with a publishing branch. ACS is not the first to suffer - it all started with the IEEE: http://www.spectrum.ieee.org/WEBONLY/wonews/oct03/1003ofac.html -----Original Message----- From: Peter Gannett [mailto:pgannett/at/hsc.wvu.edu] Sent: Thursday, December 04, 2003 1:47 PM To: chemistry/at/ccl.net; padrongj/at/fq.uh.cu Subject: CCL:A note of disappointment List: Pardon my doubting Thomas nature. Can anyone confirm this. I have no doubt that the current gov't of the US might pull something like this and, unfortunately, I can figure out the reasons why the ACS might bow to the demand. However, this would truly be a black mark against ACS. Thanks. Pete Gannett >>> Juan Alexander Padron 12/04/03 10:28AM >>> Dear CCL list: I am reluctant to use this list for any reason that differs from scientific exchange, but I feel that all my colleagues must be aware of the recent news regarding to my country. It have came to me the horrendous information that the ACS, compelled by the US government, has forbidden to authors of (by this precise order) Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > from my point of view, is the ultimate violation of the rights of the people that devote their life to the development of science. No political reasons are valid to exclude anyone from the scientific community, mostly if those are from third developed countries who are the ones who required all the help that they can get. In the case of my country they are no reason to declare such blockade, cause we are not a thread to anyone: instead of this they are thousands of Cubans in a lot of countries helping in fields like health care, agriculture, education and many others that are vital. My country is also the place of birth of lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. Finlay, Pedro Kourm, and many others that have make serious advances in different fields of knowledge. This is a dark precedent to the new generation of researches in my country, that sincerely appreciate the tremendous scientific capacities of the American science, and once again must feel excluded without reason. Be then this mail a note of disappointment and protest. Best Regards, -- &/////////////////////////////////////////////////// &Juan Alexander Padrsn-Garcma &Researcher, PhD Student &Laboratory of Computational & Theoretical Chemistry, &Chemistry Faculty Havana University, Cuba &padrongj/at/fq.uh.cu, alex2473/at/yahoo.es &http://www.fq.uh.cu/investigacion/lqct ____________ ///////////////////////////////////////// -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net If your mail is bouncing from CCL.NET domain send it to the maintainer: -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Dec 4 14:44:48 2003 Received: from fep05-svc.swip.net (fep05.swip.net [130.244.199.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4JiGxp000700 for ; Thu, 4 Dec 2003 14:44:17 -0500 Received: from avdemo.tiscalinet.ch ([213.103.132.150]) by fep05-svc.swip.net with ESMTP id <20031204194336.PEON2070.fep05-svc.swip.net/at/avdemo.tiscalinet.ch>; Thu, 4 Dec 2003 20:43:36 +0100 Message-Id: <5.0.2.1.0.20031204202954.02b83440/at/mail.tiscalinet.ch> X-Sender: barry.hardy/at/mail.tiscalinet.ch X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Thu, 04 Dec 2003 20:34:53 +0100 To: Juan Alexander Padron , CCL From: Barry Hardy Subject: Re: CCL:A note of disappointment In-Reply-To: <3FCF52BA.8774BB80/at/fq.uh.cu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=-1.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,MAILTO_TO_SPAM_ADDR, QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Can you verify an official source/reference/link for this news? If it is true, I think it is absolutely disgraceful and totally misguided. Although repeating the obvious probably, scientific publication should be based on merit, quality and originality alone. And such a measure, surely is counter-productive even from a political point of view: Today's world will progress only by supporting knowledge leaders and cultivators in these countries. Are am I missing something here? Barry Hardy Douglas Connect www.douglasconnect.com At 09:28 04/12/03 -0600, Juan Alexander Padron wrote: >Dear CCL list: > >I am reluctant to use this list for any reason that differs from >scientific exchange, but I feel that all my colleagues must be aware of >the recent news regarding to my country. > >It have came to me the horrendous information that the ACS, compelled by >the US government, has forbidden to authors of (by this precise order) > Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > > from my point of view, is the ultimate violation of the rights of the >people that devote their life to the development of science. No >political reasons are valid to exclude anyone from the scientific >community, mostly if those are from third developed countries who are >the ones who required all the help that they can get. In the case of my >country they are no reason to declare such blockade, cause we are not a >thread to anyone: instead of this they are thousands of Cubans in a lot >of countries helping in fields like health care, agriculture, education >and many others that are vital. My country is also the place of birth of >lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. >Finlay, Pedro Kourm, and many others that have make serious advances in >different fields of knowledge. This is a dark precedent to the new >generation of researches in my country, that sincerely appreciate the >tremendous scientific capacities of the American science, and once again >must feel excluded without reason. Be then this mail a note of >disappointment and protest. > >Best Regards, >-- >&/////////////////////////////////////////////////// >&Juan Alexander Padrsn-Garcma >&Researcher, PhD Student >&Laboratory of Computational & Theoretical Chemistry, >&Chemistry Faculty Havana University, Cuba >&padrongj/at/fq.uh.cu, alex2473/at/yahoo.es >&http://www.fq.uh.cu/investigacion/lqct ____________ >///////////////////////////////////////// > > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY/at/ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Barry Hardy, PhD +41 61 851 0170 (office) +41 79 755 2340 (mobile) Email: barry.hardy/at/tiscalinet.ch From chemistry-request@ccl.net Thu Dec 4 14:47:53 2003 Received: from smtpgw.sud-chemieinc.com ([208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4JlMxp000816 for ; Thu, 4 Dec 2003 14:47:22 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id B2A1E4867A for ; Thu, 4 Dec 2003 14:43:09 -0500 (EST) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 24310-09 for ; Thu, 4 Dec 2003 14:43:08 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 3155E4824B for ; Thu, 4 Dec 2003 14:43:08 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Thu, 4 Dec 2003 14:47:21 -0500 Subject: RE: A note of disappointment MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 4 Dec 2003 14:47:19 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0047FC74/at/srvkyem1.unitedcatalysts.com> X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: A note of disappointment Thread-Index: AcO6nVhFnRN2LeagTYWCt7AmLTNXWgAAC1xQ From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 04 Dec 2003 19:47:21.0118 (UTC) FILETIME=[6E64EBE0:01C3BA9F] X-Spam-Status: No, hits=-0.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hB4Jlrxp000843 *********************** Your mail has been scanned for SPAM by SpamAssassin and for Virus by InterScan MSS. Questions about SpamAssassin and Interscan MSS should be directed to postmaster/at/sud-chemieinc.com *********************** If the U.S. State Department decides that this is the law, the American Chemical Society has no choice, other than to disobey and have everyone there sent to jail (or Guantanamo? ;-), or to pull up stakes and move to another country and hire only non-US-citizens. So, don't blame the ACS. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On Behalf Of Peter Gannett Sent: Thursday, December 04, 2003 1:47 PM To: chemistry/at/ccl.net; padrongj/at/fq.uh.cu Subject: CCL:A note of disappointment *********************** Your mail has been scanned for SPAM by SpamAssassin and for Virus by InterScan MSS. Questions about SpamAssassin and Interscan MSS should be directed to postmaster/at/sud-chemieinc.com *********************** List: Pardon my doubting Thomas nature. Can anyone confirm this. I have no doubt that the current gov't of the US might pull something like this and, unfortunately, I can figure out the reasons why the ACS might bow to the demand. However, this would truly be a black mark against ACS. Thanks. Pete Gannett >>> Juan Alexander Padron 12/04/03 10:28AM >>> Dear CCL list: I am reluctant to use this list for any reason that differs from scientific exchange, but I feel that all my colleagues must be aware of the recent news regarding to my country. It have came to me the horrendous information that the ACS, compelled by the US government, has forbidden to authors of (by this precise order) Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > from my point of view, is the ultimate violation of the rights of the people that devote their life to the development of science. No political reasons are valid to exclude anyone from the scientific community, mostly if those are from third developed countries who are the ones who required all the help that they can get. In the case of my country they are no reason to declare such blockade, cause we are not a thread to anyone: instead of this they are thousands of Cubans in a lot of countries helping in fields like health care, agriculture, education and many others that are vital. My country is also the place of birth of lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. Finlay, Pedro Kourm, and many others that have make serious advances in different fields of knowledge. This is a dark precedent to the new generation of researches in my country, that sincerely appreciate the tremendous scientific capacities of the American science, and once again must feel excluded without reason. Be then this mail a note of disappointment and protest. Best Regards, -- &/////////////////////////////////////////////////// &Juan Alexander Padrsn-Garcma &Researcher, PhD Student &Laboratory of Computational & Theoretical Chemistry, &Chemistry Faculty Havana University, Cuba &padrongj/at/fq.uh.cu, alex2473/at/yahoo.es &http://www.fq.uh.cu/investigacion/lqct ____________ ///////////////////////////////////////// -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net If your mail is bouncing from CCL.NET domain send it to the maintainer: -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Dec 4 14:45:55 2003 Received: from bureau14.utcc.utoronto.ca (bureau14.utcc.utoronto.ca [128.100.132.42]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4JjOxp000761 for ; Thu, 4 Dec 2003 14:45:24 -0500 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1506]) by bureau14.utcc.utoronto.ca with SMTP id <890181-10728>; Thu, 4 Dec 2003 14:45:19 -0500 From: "William Wei" To: "CCLers" Subject: Summary:Gaussian: Error on Z-matrix card number Date: Thu, 4 Dec 2003 14:48:47 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Importance: Normal X-Spam-Status: No, hits=-0.9 required=7.0 tests=IN_REP_TO,MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) About ten days ago, I posted a question about dealing with the Error on Z-matrix Card number. I got a lot of valuable replies. Thanks for all the helps. Original Q: If I run relaxed Potential Energy Surface (PES) scan under Gaussian 98, the Z-Matrix card error always comes to me. ...... Error on Z-matrix card number 11 angle Alpha is outside the valid range of 0 to 180. Conversion from Z-matrix to cartesian coordinates failed: ...... I explored on this issue. There are two possible situations related to this. One is the Z-Matrix definition on ring system. The other is the torsional angle reaching 0 degree. (Please let me know if I am wrong.) Replies: >>>>>>>>>> This happens to me all the time. Check the angle on atom 11. It's probably either greater than 180 degrees, or negative. If that's not it, check the torsion for that atom. It doesn't matter if the torsion is big or negative, but it the middle angle of the torsion is out of bounds, it will cause an error (so if it's defined A-B-C-D, both A-B-C and B-C-D have to be between 0 and 180 degrees, but A-B-C-D can be anything. Joslyn Kravitz >>>>>>>>>>> Generally this problem is solved by adding a dummy atom. Example if I have a triatomic molecule ABC and I want to see how the energy changes as I change the angle ABC from 90 degree's through 180 degree's inclusive every thing works fine until the angle hits 180 degree's. Then the program crashes with the error message you describe. The solution is to make up a new molecule X ABC where the angle ABX=90 degree's and X is bonded to B. if you then scan a new angle XBC from 0 to 90 degree's then no problem will be encountered. For more complicated situations you'l have to be a little more inventive, but in general the principle is the same. Hope this helps, All the best Laurence Cuffe >>>>>>>>>> Funny, I have just been wrestling with the same problem myself! I suspect the second option you mentioned, namely: The Z-matrix only accepts angles between 0 and 180 degrees, so of course one first has to make sure there are no 0 or 180 angles in the initial molecule specification. However, this is sometimes not enough, since it can happen that an initial structure with an angle close to the cutoff values gets optimized to a structure where the angle does indeed "overstep the bounds", causing Gaussian to crash! The solution would be to redefine the problem atoms in terms of less "dangerous" angles (i.e. angles which could potentially become less than 0 or more than 180 in the course of the optimization), using dummy atoms if neccessary, or simply adding a ModRedundant section and doing the PES scan in redundant internal coordinates. Good luck! Heidi >>>>>>>>>> In my experience, g98 only allows Z-matrix angles to be between 0 and 180 degees. Some other programs, e.g., mopac, permit them to be between 0 and 360 degrees. The solution is to redefine your z-matrix. If you are using WebMO Pro, there is a z-matrix editor that does exactly that! Will Polik ------------------ I hope this can help to build our problem-soving database. William From chemistry-request@ccl.net Thu Dec 4 19:45:07 2003 Received: from visual1.chem.pitt.edu (visual1.chem.pitt.edu [136.142.153.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB50iYxp007081 for ; Thu, 4 Dec 2003 19:44:35 -0500 Received: from darth (ararat.chem.pitt.edu [136.142.109.25]) by visual1.chem.pitt.edu (8.12.6-20030917/8.12.6) with SMTP id hB50eARP019107; Thu, 4 Dec 2003 19:40:12 -0500 Message-ID: <03de01c3bac8$f0246b50$196d8e88@darth> From: "Kadir Diri" To: "Joslyn Kravitz" , References: <002501c3baa2$ec1abf30$80e12844@Garfield> Subject: Re: CCL:windows based orbital viewing Date: Thu, 4 Dec 2003 19:44:27 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_03DB_01C3BA9F.072E5830" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.1 required=7.0 tests=HTML_70_80,HTML_MESSAGE,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_03DB_01C3BA9F.072E5830 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Joslyn, Molden can display molecular orbitals generated by Gaussian, Molpro and = probably the other popular programs. However even the windows version of = Molden requires an x server. There should be some trial versions of free = x servers. Alternatively, Cygwin is free and has an x server. Gopenmol should also be able to plot orbitals. The program that I like for Gaussian outputs is Gausview, however it is = not free. You can check the web sites for these packages for the details. There = might be many other programs as well, these are the ones I know. Regards, Kadir ----- Original Message -----=20 From: Joslyn Kravitz=20 To: chemistry.-at-.ccl.net=20 Sent: Thursday, December 04, 2003 3:12 PM Subject: CCL:windows based orbital viewing Hello all, =20 Does anyone know of viewing program that can display molecular = orbitals from Gaussian output? I am looking for something that runs on = windows and preferably is free. =20 Thanks, Joslyn Kravitz ------=_NextPart_000_03DB_01C3BA9F.072E5830 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Joslyn,
 
Molden can display = molecular=20 orbitals generated by Gaussian, Molpro and probably the other popular = programs.=20 However even the windows version of Molden requires an x server. There = should be=20 some trial versions of free x servers. Alternatively, Cygwin is free and = has an=20 x server.
Gopenmol should also be = able to plot=20 orbitals.
The program that I like = for Gaussian=20 outputs is Gausview, however it is not free.
You can check the web = sites for=20 these packages for the details. There might be many other programs as = well,=20 these are the ones I know.
Regards,
 
Kadir
 
 
----- Original Message -----
From:=20 Joslyn=20 Kravitz
Sent: Thursday, December 04, = 2003 3:12=20 PM
Subject: CCL:windows based = orbital=20 viewing

Hello=20 all,

 

Does anyone know of = viewing=20 program that can display molecular orbitals from=20 Gaussian output? I am looking for something that runs on windows and=20 preferably is free.

 

Thanks,

Joslyn=20 Kravitz

------=_NextPart_000_03DB_01C3BA9F.072E5830-- From chemistry-request@ccl.net Thu Dec 4 16:36:13 2003 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.120]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4LZgxp003403 for ; Thu, 4 Dec 2003 16:35:42 -0500 Received: from alphahelix (alphahelix.Stanford.EDU [171.64.126.26]) by smtp1.Stanford.EDU (8.12.10/8.12.10) with ESMTP id hB4LZbJv003192; Thu, 4 Dec 2003 13:35:37 -0800 Reply-To: From: "Joseph Han" To: "'Joslyn Kravitz'" , Subject: RE: windows based orbital viewing Date: Thu, 4 Dec 2003 13:35:48 -0800 Keywords: NoHTML Message-ID: <004001c3baae$94f3fe40$1a7e40ab@alphahelix> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4927.1200 In-Reply-To: <002501c3baa2$ec1abf30$80e12844@Garfield> Importance: Normal X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) In our work, we mainly use Molden. It is free. It is available on many platforms (including Windows). Additionally, not only can it display orbitals, but Molden can also export orbitals into POV-Ray, VRML, or it's own OpenGL viewer. To use it on Windows, you will need an X-Windows Server for Windows. http://www.cmbi.kun.nl/~schaft/molden/molden.html I have also heard that Chem3D can display orbitals from a Gaussian formatted checkpoint file, though I have never done so myself. Joseph Han Department of Chemical Engineering Stanford University 650-723-0420 FAX: 650-725-7294 > > Hello all, > > Does anyone know of viewing program that can display > molecular orbitals > from Gaussian output? I am looking for something that runs on windows > and preferably is free. > > > Thanks, > Joslyn Kravitz > > From chemistry-request@ccl.net Thu Dec 4 17:51:57 2003 Received: from smtp4.server.rpi.edu (smtp4.server.rpi.edu [128.113.2.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4MpQxp005076 for ; Thu, 4 Dec 2003 17:51:26 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp4.server.rpi.edu (8.12.10/8.12.9) with ESMTP id hB4MpQto017516; Thu, 4 Dec 2003 17:51:27 -0500 Message-Id: <200312042251.hB4MpQto017516[at]smtp4.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: dshobe[at]sud-chemieinc.com From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry[at]ccl.net X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Thu, 04 Dec 2003 17:51:25 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:A note of disappointment X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Thu, 4 Dec 2003 14:47:19 -0500 "Shobe, David" wrote: > > > If the U.S. State Department decides that this is the law, the American > Chemical Society has no choice, other than to disobey and have everyone > there sent to jail (or Guantanamo? ;-), or to pull up stakes and move to > another country and hire only non-US-citizens. > > So, don't blame the ACS. > But WE have a choice as to whether we want to continue being part of a racist organization (however "reluctant") and a discriminatory regime. Sukumar From chemistry-request@ccl.net Thu Dec 4 16:22:12 2003 Received: from life.ai.mit.edu (life.ai.mit.edu [128.52.32.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB4LLdxp003134 for ; Thu, 4 Dec 2003 16:21:40 -0500 Received: from horsepower.ai.mit.edu (horsepower [128.52.37.26]) by life.ai.mit.edu (8.12.10/8.12.9/BASENAME(ai.master.life-8.12.9.mc,.mc):RCS_REVISION(Revision: 1.23)) with ESMTP id hB4LLevn007068; Thu, 4 Dec 2003 16:21:40 -0500 (EST) Received: from localhost (dfgreen@localhost) by horsepower.ai.mit.edu (8.9.1/8.8.4AI/ai.client:1.5) with ESMTP id QAA27087; Thu, 4 Dec 2003 16:21:39 -0500 (EST) X-Authentication-Warning: horsepower.ai.mit.edu: dfgreen owned process doing -bs Date: Thu, 4 Dec 2003 16:21:39 -0500 (EST) From: "David F. Green" X-Sender: dfgreen@horsepower To: Barry Hardy cc: Juan Alexander Padron , CCL Subject: Re: CCL:A note of disappointment In-Reply-To: <5.0.2.1.0.20031204202954.02b83440[at]mail.tiscalinet.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,MAILTO_TO_SPAM_ADDR, QUOTED_EMAIL_TEXT,RCVD_IN_NJABL,RCVD_IN_UNCONFIRMED_DSBL, REPLY_WITH_QUOTES,USER_AGENT_PINE,X_AUTH_WARNING, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) It's right here: C&E News, November 24, 2003. Page 25. David +--------------------------------------------------------------------+ | David F. Green | | | Postdoctoral Associate | Phone: 617-253-5438 | | Division of Bioengineering and Computer | Mobile: 617-953-3922 | | Science & Artificial Intelligence Lab | Fax: 617-258-8682 | | Massachusetts Institute of Technology | | | 200 Technology Sq., NE43-739 | E-mail: dfgreen[at]mit.edu | | Cambridge, MA 02139 | | +--------------------------------------------------------------------+ On Thu, 4 Dec 2003, Barry Hardy wrote: > > Can you verify an official source/reference/link for this news? If it is > true, I think it is absolutely disgraceful and totally misguided. Although > repeating the obvious probably, scientific publication should be based on > merit, quality and originality alone. And such a measure, surely is > counter-productive even from a political point of view: Today's world will > progress only by supporting knowledge leaders and cultivators in these > countries. Are am I missing something here? > > Barry Hardy > Douglas Connect > www.douglasconnect.com > > > > At 09:28 04/12/03 -0600, Juan Alexander Padron wrote: > >Dear CCL list: > > > >I am reluctant to use this list for any reason that differs from > >scientific exchange, but I feel that all my colleagues must be aware of > >the recent news regarding to my country. > > > >It have came to me the horrendous information that the ACS, compelled by > >the US government, has forbidden to authors of (by this precise order) > > Cuba, Iran, Iraq, Libya, or Sudan to publish on their journals. This, > > > from my point of view, is the ultimate violation of the rights of the > >people that devote their life to the development of science. No > >political reasons are valid to exclude anyone from the scientific > >community, mostly if those are from third developed countries who are > >the ones who required all the help that they can get. In the case of my > >country they are no reason to declare such blockade, cause we are not a > >thread to anyone: instead of this they are thousands of Cubans in a lot > >of countries helping in fields like health care, agriculture, education > >and many others that are vital. My country is also the place of birth of > >lots of prestigious scientist like Tomas Romaig, Felipe Poey, Carlos J. > >Finlay, Pedro Kourm, and many others that have make serious advances in > >different fields of knowledge. This is a dark precedent to the new > >generation of researches in my country, that sincerely appreciate the > >tremendous scientific capacities of the American science, and once again > >must feel excluded without reason. Be then this mail a note of > >disappointment and protest. > > > >Best Regards, > >-- > >&/////////////////////////////////////////////////// > >&Juan Alexander Padrsn-Garcma > >&Researcher, PhD Student > >&Laboratory of Computational & Theoretical Chemistry, > >&Chemistry Faculty Havana University, Cuba > >&padrongj[at]fq.uh.cu, alex2473[at]yahoo.es > >&http://www.fq.uh.cu/investigacion/lqct ____________ > >///////////////////////////////////////// > > > > > > > > > > > > > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > Barry Hardy, PhD > +41 61 851 0170 (office) > +41 79 755 2340 (mobile) > Email: barry.hardy[at]tiscalinet.ch > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl[at]ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Dec 4 19:57:42 2003 Received: from visual1.chem.pitt.edu (visual1.chem.pitt.edu [136.142.153.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB50vBxp007399 for ; Thu, 4 Dec 2003 19:57:11 -0500 Received: from darth (ararat.chem.pitt.edu [136.142.109.25]) by visual1.chem.pitt.edu (8.12.6-20030917/8.12.6) with SMTP id hB50qlRP019196 for ; Thu, 4 Dec 2003 19:52:48 -0500 Message-ID: <042701c3baca$b31f29f0$196d8e88@darth> From: "Kadir Diri" To: "Computational Chemistry List" References: Subject: casscf with gaussian Date: Thu, 4 Dec 2003 19:57:04 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0424_01C3BAA0.CA33C530" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.5 required=7.0 tests=HTML_30_40,HTML_MESSAGE,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0424_01C3BAA0.CA33C530 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all! Has anyone done casscf calculations with Gaussian 03 or 98? I want to = compare my Molpro and Molcas results with Gaussian, however when I have = large number of configurations, Gaussian does not print them (even the = most important ones!), although it does print them if the number of = configs is small. Has anyone else encountered this problem, and if yes, = is there a solution?=20 Thanks in advance! Kadir ------=_NextPart_000_0424_01C3BAA0.CA33C530 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all!
 
Has anyone done casscf calculations = with Gaussian=20 03 or 98? I want to compare my Molpro and Molcas results with = Gaussian,=20 however when I have large number of configurations, Gaussian does not = print them=20 (even the most important ones!), although it does print them if the = number of=20 configs is small. Has anyone else encountered this problem, and if = yes, is=20 there a solution?
Thanks in advance!
 
Kadir
------=_NextPart_000_0424_01C3BAA0.CA33C530-- From jkl@ccl.net Thu Dec 4 21:13:35 2003 -0500 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry(at)ccl.net Cc: "Mark Thompson" Subject: CCL: windows based orbital viewing Date: Thu, 4 Dec 2003 18:11:17 -0800 Message-ID: <000d01c3bad5$10f66750$0200a8c0@planaria> Dear Joslyn, ArgusLab 4.0 (currently in beta release) integrates well with Gaussain 98 and Gaussian 03. You can easily view surfaces from cube files generated with Gaussian. ArgusLab is free for single-user academic faculty, staff, and students. You can download it at http://www.arguslab.com Mark *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark(at)arguslab.com http://www.arguslab.com *************************** ----- Original Message ----- From: Joslyn Kravitz To: chemistry(at)ccl.net Sent: Thursday, December 04, 2003 3:12 PM Subject: CCL:windows based orbital viewing Hello all, Does anyone know of viewing program that can display molecular orbitals from Gaussian output? I am looking for something that runs on windows and preferably is free. Thanks, Joslyn Kravitz From chemistry-request@ccl.net Thu Dec 4 21:23:56 2003 Received: from brass.metals.hope.edu (brass.metals.hope.edu [198.110.98.36]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hB52NPxq009238 for ; Thu, 4 Dec 2003 21:23:25 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2003120421221030487 ; Thu, 04 Dec 2003 21:22:10 -0500 Received: from [198.110.101.2] (polik:at:hope.edu) by hope.edu; Thu, 4 Dec 2003 21:22:36 -0500 X-WM-Posted-At: hope.edu; Thu, 4 Dec 03 21:22:36 -0500 Message-Id: <5.2.0.9.2.20031204202939.018e2888:at:webmail.hope.edu> X-Sender: polik:at:webmail.hope.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Thu, 04 Dec 2003 20:35:50 -0500 To: CHEMISTRY:at:ccl.net From: "William F. Polik" Subject: Re: CCL:windows based orbital viewing Cc: "Joslyn Kravitz" In-Reply-To: <002501c3baa2$ec1abf30$80e12844@Garfield> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_103727125==.ALT" X-Spam-Status: No, hits=0.3 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_20_30,HTML_MESSAGE,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_103727125==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Joslyn, At 03:12 PM 12/4/2003, "Joslyn Kravitz" wrote: >Does anyone know of viewing program that can display molecular orbitals >from Gaussian output? I am looking for something that runs on windows and >preferably is free. WebMO is a free web-based interface to several computational chemistry programs: Gaussian, Mopac, Gamess, and Molpro. The professional version, WebMO Pro, has a windows-based molecular orbital viewer, MOViewer, that allows you to view MO's that were calculated by any of the supported programs. MOViewer also displays isosurfaces, electrostatic potentials, and electrophilic/nucleophilic frontier surfaces. For general information, see the WebMO homepage at www.webmo.net A working demo (no download or installation required, since WebMO is web-based) is available at www.webmo.net/demo Color brochures are at http://www.webmo.net/download/WebMO_Brochure.pdf http://www.webmo.net/download/WebMOPro_Brochure.pdf Will Polik --=====================_103727125==.ALT Content-Type: text/html; charset="us-ascii" Joslyn,

At 03:12 PM 12/4/2003, "Joslyn Kravitz" <jyudenfr:at:umich.edu> wrote:
Does anyone know of viewing program that can display molecular orbitals from Gaussian output? I am looking for something that runs on windows and preferably is free.

WebMO is a free web-based interface to several computational chemistry programs:  Gaussian, Mopac, Gamess, and Molpro.  The professional version, WebMO Pro, has a windows-based molecular orbital viewer, MOViewer, that allows you to view MO's that were calculated by any of the supported programs.  MOViewer also displays isosurfaces, electrostatic potentials, and electrophilic/nucleophilic frontier surfaces.

For general information, see the WebMO homepage at
     www.webmo.net
A working demo (no download or installation required, since WebMO is web-based) is available at
     www.webmo.net/demo
Color brochures are at
     http://www.webmo.net/download/WebMO_Brochure.pdf
     http://www.webmo.net/download/WebMOPro_Brochure.pdf

Will Polik
--=====================_103727125==.ALT--