From chemistry-request@server.ccl.net Mon Apr 14 02:10:20 2003 Received: from web15212.mail.bjs.yahoo.com ([202.3.77.142]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3E6AI302153 for ; Mon, 14 Apr 2003 02:10:19 -0400 Message-ID: <20030414061017.79127.qmail@web15212.mail.bjs.yahoo.com> Received: from [61.177.56.180] by web15212.mail.bjs.yahoo.com via HTTP; Mon, 14 Apr 2003 14:10:16 CST Date: Mon, 14 Apr 2003 14:10:16 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: Summary -- problems during GAMESS optimization To: CCL , Gamess MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, On 23 March 2003, I posted my first question on this list: ===== I have encountered difficulties during my GAMESS geometry optimization. The molecule that I hope to optimize is acetylcholine, which has one positive charge. After about one and half hour, I get the following message in the GAMESS outfile. How should I do in the next? Thank you very much in advance! ***** Failure to locate stationary point, too many steps taken ***** Updated Hessian, geometry, and vectors will be punched for restart **** The geometry search is not converged! **** ===== > From then, I receive many kind replies to this question. I can't paste all of this email here. However, I give a summary here: ===== The first and simple way is give a large NSTEP in $STATPT group like this: $STATPT NSTEP= 200 OPTTOL= 0.001 $END The second way is to extract the coordinates from the punch file (*.dat) or output file (*.log) with lowest energy, and insert this coordinates to input file and replace the original coordinates, and restart it normally. Please note, if in the $CONTROL group of the input file, COORD is not given as UNIQUE, change it to UNIQUE. The third way, it's useful for a big system, with a big basis and higher level, is to reuse the $VEC and/or $GRAD group in the punch file (*.dat). Change the $GUESS group to $GUESS GUESS= MOREAD NORB= 40 $END where NORB is the number of orbitals to be read in the $VEC group. Thus the input file like this: $CONTRL UNITS=ANGS COORD=CART RUNTYP=OPTIMIZE SCFTYP=RHF ICHARG= 1 MULT= 1 $END $GUESS GUESS= MOREAD NORB= 40 $END $SYSTEM MEMORY= 3000000 $END $BASIS GBASIS=STO NGAUSS=3 POLAR=POPLE $END $STATPT NSTEP= 50 OPTTOL= 0.001 $END $DATA ... $END $VEC ... $END $GRAD ... $END Please note that the $GRAD group is read automatically if it is presented. So it also could be reused in the first two way. And Molden, a software recommended by Carlos Silva López is useful to visualize the output of GAMESS. Here is the URL: http://www.cmbi.kun.nl/~schaft/molden/molden.html Any comments and/or suggestions to this summary will be greatly appreciated. At last, I wish to express my honest appreciation to Markus Dittrich, Carlos Silva López, Ernst Schumacher, Eike Huebner, Rudolf Herrmann, Henrik Nilsson. Thank you very much for your patience and kindly help. Best regards Jinsong Zhao ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong@yahoo.com.cn _________________________________________________________ Do You Yahoo!? 雅虎通网络KTV, 随时随地免费卡拉OK~~ http://rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com//chat/index.html From chemistry-request@server.ccl.net Sun Apr 13 22:55:44 2003 Received: from smtp03.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3E2te300564 for ; Sun, 13 Apr 2003 22:55:43 -0400 Received: from lq (unknown [202.127.145.3]) by smtp03.sohu.com (Postfix) with ESMTP id A6E265693 for ; Mon, 14 Apr 2003 10:55:24 +0800 (CST) From: "Li Qiang" To: "cHEMISTRY@ccl.net" Subject: about hyperchem' script X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====002_Dragon475003402371_=====" Date: Mon, 14 Apr 2003 10:55:4 +0800 Message-Id: <20030414025524.A6E265693@smtp03.sohu.com> This is a multi-part message in MIME format. --=====002_Dragon475003402371_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLers, How to use HyperChem's Script to input sugar, Can you help me? There are "add-nucleic-acid" and "add-amino-acid", but no "add-sugar". I don't want to click the Saccharides by menu. Thank you in advance! Li Qiang Key Labortary of Computer Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences No.354 Road FengLin ShangHai, 200032, China Phone: 08621-64163300-2753 E-mail: chem_liqiang@sohu.com --=====002_Dragon475003402371_===== Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: 7bit

Dear CCLers,

    How to use HyperChem's Script to input sugar, Can you help me? There are "add-nucleic-acid" and "add-amino-acid", but no "add-sugar". I don't want to click the Saccharides by menu. 

    Thank you in advance!

 

Li Qiang

Key Labortary of Computer Chemistry
Shanghai Institute of Organic Chemistry
Chinese Academy of Sciences

No.354 Road FengLin
ShangHai, 200032, China
Phone: 08621-64163300-2753
E-mail: chem_liqiang@sohu.com


--=====002_Dragon475003402371_=====-- From chemistry-request@server.ccl.net Mon Apr 14 04:35:59 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3E8Zx317878 for ; Mon, 14 Apr 2003 04:35:59 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id EA4BEABA84A; Mon, 14 Apr 2003 10:35:57 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id D348DABA847; Mon, 14 Apr 2003 10:35:56 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 14 Apr 03 10:35:56 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 14 Apr 03 10:35:54 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Jane-Jane Ou Date: Mon, 14 Apr 2003 10:35:42 +0100 Subject: Re: CCL:Transition Dipole Moments from Gaussian98 Reply-To: spanget@ruc.dk Cc: CHEMISTRY@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <224450145E7@virgil.ruc.dk> X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Jane Ou: > Are predicted Transition Dipole Moments > from Gaussian 98 in good agreement with > experimental values? Are there publications > about this? Thank you very much. Are you interested in vibrational or electronic transition moments? In any case, I think you should distinguish between situations where the transition moment direction is determined by the molecular symmetry, and those situations where it is not. The paper by Radziszewski and coworkers may be of interest to you: J. G. Ranziszewski et al., "How Predictable Are IR Transition Moments? Vibrational Transitions in Propene and Deuterated Propenes?", J. Am. Chem. Soc. 118, 10275-10284 (1996) Jens >--< ---> NB! I am out of town April 23 - May 2, 2003 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Apr 14 11:02:07 2003 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3EF26324632 for ; Mon, 14 Apr 2003 11:02:07 -0400 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id PAA32338 for ; Mon, 14 Apr 2003 15:26:38 +0200 (MET DST) Date: Mon, 14 Apr 2003 15:26:38 +0200 (MET DST) Message-Id: <200304141326.PAA32338@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Summary Question on resonance structures Hi, I would like to thank the people who responded on my question. What I learn from the reactions is that the "resonance" concept is irrelevant in solid state systems like the infinite all-trans-poly-acetyleen molecule. The two distinct electronic structures lay at the same energy, and are connected through a transition state. This bond alternation picture (symmetry breaking) arises due to correlation energy, and is imposed by the Jahn-Teller effect (or the one-dimensional Peierls distortion). Is this correct ? Thanks Serge Hello, Serge. I believe "resonance" concept is irrelevant in systems with strong electron-lattice coupling, like Peierls transitions or Jahn-Teller phenomena. It is a pure electronic concept and should not include symmetry-breaking nuclear displacements. Don't you think so? In order to treat electronic and nuclear motions at the same time, you should go to vibronic state, a linear combination of products of electronic and nuclear wavefunctions. Motohiro NAKANO ---------------------------------------------------- I think you are talking about the *acyclic* molecule H2C=CH-CH=CH-CH=CH-.... I know that 1,3-butadiene is well-described by just *one* resonance structure, and 1,3,5-hexatriene by one resonance structure too. I would not be surprised if this is not true for polyacetylene too, although Zi realize that the pi-MO levels are squeezed together (causing near-degeneracy?) for a big, polymeric C=C-C type molecule. E. Lewars ---------------------------------------------------- The original question was: > As you know, poly-acetylene has a doubly degenerate ground state structure, > because of the Peierls distortion. The skelet structures can be seen in terms > of bond alternations as struct1 = (=-=-=)n and struct2 = (-=-=-)n. They both > consist of a linear combination of partial wavefunctions describing > wave1 = (=-=-=)n and wave2 = (-=-=-)n (in VB theory). > > If I'm not mistaken wave1 and wave2 are resonance (canonics ?) structures and > should therefore be written as wave1 <--> wave2. On the other hand, struct1 > and struct2 are different molecular structures and they should therefore be > written as struct1 <==> (i.e. as a chemical equilibrium). I believe these > structures are called bondisomers. > > Each of these structures can thus be given by A*wave1+B*wave2. > > I would like your opinion on this and would like to get advise on the accurate > nomenclature of structs and waves. ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/TheoChem ___________________________________________________