From chemistry-request@ccl.net Wed Nov 5 09:14:30 2003 Received: from matrix.chem.yale.edu (matrix.chem.yale.edu [130.132.25.93]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5EDxVc032358 for ; Wed, 5 Nov 2003 09:13:59 -0500 Received: from matrix.chem.yale.edu (localhost [127.0.0.1]) by matrix.chem.yale.edu (8.12.10/8.12.10) with ESMTP id hA5EDxbk005609; Wed, 5 Nov 2003 14:13:59 GMT Received: (from julian@localhost) by matrix.chem.yale.edu (8.12.10/8.12.10/Submit) id hA5EDxxA005607; Wed, 5 Nov 2003 09:13:59 -0500 (EST) Message-Id: <200311051413.hA5EDxxA005607~at~matrix.chem.yale.edu> Date: Wed, 5 Nov 2003 09:13:58 -0500 (EST) To: d.dogaru~at~csuohio.edu Cc: chemistry~at~ccl.net Subject: Re: CCL:ESP charges From: Julian Tirado-Rives In-Reply-To: <608AF095-0EED-11D8-8DC2-000393C8EB28~at~csuohio.edu> X-Mailer: Ishmail 2.1.0-20020308-mips-sgi-irix6.3 MIME-Version: 1.0 Content-Type: text/plain X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Daniela: Actually, there is no problem ... most of the OPLS charges are not really ESP, although for many cases that is our typical "starting guess". We usually arrive to the final non-bonded parameters for a given type of molecule in an iterative fashion in which we try to reproduce through actual simulations as many experimentally (well-) determined thermodynamic parameters as we can find for one or more molecules of the same type, typically pure liquid densities, heats of vaporization, free energies of solvation, rdf's if available, etc. In the course of the iterations we may (but not always do) vary both the Lennard-Jones parameters and the charges while trying to balance the precision of the results with the generality, number of atomic types in the FF, etc. I hope this answer your question, but if you have further doubts feel free to email me. Good Luck! - Julian - Daniela Dogaru wrote: > Dear all, > I have a question regarding the ESP charges which are used in OPLS > parameters from MD programs like Gromacs . I got some discrepancies > between the OPLS charges I calculate with Gaussian and the ones that > are implemented in Gromacs force field , for Tyrosine residue. > What do you think will be the problem? > My best wishes! > Daniela > ---------------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives~at~yale.edu | | New Haven, CT 06520-8107 | | ---------------------------------------------------------------------- From chemistry-request@ccl.net Wed Nov 5 08:59:59 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 hA5DxQVd032075 for ; Wed, 5 Nov 2003 08:59:26 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2003110508592329608 for ; Wed, 05 Nov 2003 08:59:23 -0500 Received: from [198.110.101.2] (polik{at}hope.edu) by hope.edu; Wed, 5 Nov 2003 08:59:23 -0500 X-WM-Posted-At: hope.edu; Wed, 5 Nov 03 08:59:23 -0500 Message-Id: <5.2.0.9.2.20031105084820.0202bf98{at}webmail.hope.edu> X-Sender: polik{at}webmail.hope.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Wed, 05 Nov 2003 08:57:17 -0500 To: CHEMISTRY{at}ccl.net From: "William F. Polik" Subject: Re: CCL:Bond order in gaussian In-Reply-To: <200311050220.KAA14732{at}mx1.ustc.edu.cn> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_69803296==.ALT" X-Spam-Status: No, hits=-0.7 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_30_40,HTML_FONT_FACE_ODD, HTML_MESSAGE,IN_REP_TO,QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_69803296==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Ding, WebMO (www.webmo.net) is a very useful tool for learning how to construct input files to perform particular tasks. For example, to calculate bond order in Gaussian, build a test molecule, choose Gaussian, request a "Bond Orders" calculation, and choose to "Preview Input File". For H2O, this might result in: >#N HF/3-21G SP POP=NBOREAD > >H2O > >0 1 >O >H 1 B1 >H 1 B2 2 A1 > >A1 109.47122 >B1 1.0500000 >B2 1.0500000 > >$nbo bndidx $end > from which one learns that the important keywords are "POP=NBOREAD" followed by "$nbo bndidx $end". The resulting output includes >Wiberg bond index matrix in the NAO basis: > > Atom 1 2 3 > ---- ------ ------ ------ > 1. O 0.0000 0.8146 0.8146 > 2. H 0.8146 0.0000 0.0019 > 3. H 0.8146 0.0019 0.0000 What you have listed are the Natural Bonding Orbitals, which are "localized orbitals" that look very similar to "organic chemistry bonds", i.e., BD=Bond, CR=core, LP=lone pair, RY=Rydberg, *=excited/antibonding, etc. Will Polik At 09:21 PM 11/4/2003, Ding Xunlei wrote: >I am try to do a bond order analysis with G98. > Here is my test with O2 molecule. > >#B3LYP/6-31G opt pop=(NBO,Bonding) > >HF > >0 3 >O 0.00 0.00 0.000000 >O 0.00 0.00 1.200000 > >The last lines of the output file is below, and I don't think it is right. >How can I read the table correctly? And what the LP,RY* stand for? > > Thank you very much for your help!!!!!!!!!!!!!!!!! > > Natural Bond Orbitals (Summary): > > Principal > Delocalizations > NBO Occupancy Energy (geminal,vicinal,remote) > >=============================================================================== > Molecular unit 1 (O2) > 1. BD ( 1) O 1- O 2 1.00000 -1.03224 > 2. BD ( 2) O 1- O 2 1.00000 -0.45369 > 3. BD ( 3) O 1- O 2 1.00000 -0.45369 > 4. CR ( 1) O 1 0.99997 -19.14436 12(v) > 5. CR ( 1) O 2 0.99997 -19.14436 8(v) > 6. LP ( 1) O 1 0.99984 -0.87950 12(v) > 7. LP ( 1) O 2 0.99984 -0.87950 8(v) > 8. RY*( 1) O 1 0.00019 0.95747 > 9. RY*( 2) O 1 0.00000 0.88719 > 10. RY*( 3) O 1 0.00000 0.88719 > 11. RY*( 4) O 1 0.00000 1.07773 > 12. RY*( 1) O 2 0.00019 0.95747 > 13. RY*( 2) O 2 0.00000 0.88719 > 14. RY*( 3) O 2 0.00000 0.88719 > 15. RY*( 4) O 2 0.00000 1.07773 > 16. BD*( 1) O 1- O 2 0.00000 0.26370 > 17. BD*( 2) O 1- O 2 0.00000 -0.13403 > 18. BD*( 3) O 1- O 2 0.00000 -0.13403 > ------------------------------- > Total Lewis 6.99962 ( 99.9946) > Valence non-Lewis 0.00000 ( 0.0000) > Rydberg non-Lewis 0.00038 ( 0.0054) > ------------------------------- > Total unit 1 7.00000 (100.0000) > Charge unit 1 1.00000 > > > > >Ding Xunlei >2003-11-05 >______________________________________________ >Ding Xunlei, Ph.D. Candidate >Open Laboratory of Bond Selective Chemistry >University of Science & Technology of China >Hefei, Anhui 230026, P.R.China >Tel.: 0086-551-3603418 >Fax.: 0086-551-3602969 >E-mail: dxl{at}mail.ustc.edu.cn >Http://www.bsc.ustc.edu.cn/~dxl > --=====================_69803296==.ALT Content-Type: text/html; charset="us-ascii" Ding,

WebMO (www.webmo.net) is a very useful tool for learning how to construct input files to perform particular tasks.

For example, to calculate bond order in Gaussian, build a test molecule, choose Gaussian, request a "Bond Orders" calculation, and choose to "Preview Input File".  For H2O, this might result in:

#N HF/3-21G SP POP=NBOREAD

H2O

0 1
O
H 1 B1
H 1 B2 2 A1

A1 109.47122
B1 1.0500000
B2 1.0500000

$nbo bndidx $end
from which one learns that the important keywords are "POP=NBOREAD" followed by "$nbo bndidx $end".  The resulting output includes

Wiberg bond index matrix in
the NAO
basis:                                    

     Atom   
1      
2       3
     ---- ------  ------  ------
   1.  O  0.0000  0.8146  0.8146
   2.  H  0.8146  0.0000  0.0019
   3.  H  0.8146  0.0019  0.0000

What you have listed are the Natural Bonding Orbitals, which are "localized orbitals" that look very similar to "organic chemistry bonds", i.e., BD=Bond, CR=core, LP=lone pair, RY=Rydberg, *=excited/antibonding, etc.

Will Polik

At 09:21 PM 11/4/2003, Ding Xunlei wrote:

I am try to do a bond order analysis with G98.
        Here is my test with O2 molecule. 

#B3LYP/6-31G opt pop=(NBO,Bonding)

HF

0 3
O   0.00 0.00 0.000000
O   0.00 0.00 1.200000

The last lines of the output file is below, and I don't think it is right.
How can I read the table correctly?     And what the LP,RY* stand for?

    Thank you very much for your help!!!!!!!!!!!!!!!!!  
                
 Natural Bond Orbitals (Summary):

                                                     Principal Delocalizations
           NBO              Occupancy    Energy      (geminal,vicinal,remote)
 ===============================================================================
        Molecular unit  1  (O2)
   1. BD ( 1) O 1- O 2       1.00000    -1.03224
   2. BD ( 2) O 1- O 2       1.00000    -0.45369
   3. BD ( 3) O 1- O 2       1.00000    -0.45369
   4. CR ( 1) O 1            0.99997   -19.14436    12(v)
   5. CR ( 1) O 2            0.99997   -19.14436    8(v)
   6. LP ( 1) O 1            0.99984    -0.87950    12(v)
   7. LP ( 1) O 2            0.99984    -0.87950    8(v)
   8. RY*( 1) O 1            0.00019     0.95747
   9. RY*( 2) O 1            0.00000     0.88719
  10. RY*( 3) O 1            0.00000     0.88719
  11. RY*( 4) O 1            0.00000     1.07773
  12. RY*( 1) O 2            0.00019     0.95747
  13. RY*( 2) O 2            0.00000     0.88719
  14. RY*( 3) O 2            0.00000     0.88719
  15. RY*( 4) O 2            0.00000     1.07773
  16. BD*( 1) O 1- O 2       0.00000     0.26370
  17. BD*( 2) O 1- O 2       0.00000    -0.13403
  18. BD*( 3) O 1- O 2       0.00000    -0.13403
       -------------------------------
              Total Lewis    6.99962  ( 99.9946)
        Valence non-Lewis    0.00000  (  0.0000)
        Rydberg non-Lewis    0.00038  (  0.0054)
       -------------------------------
            Total unit  1    7.00000  (100.0000)
           Charge unit  1    1.00000
        
        

                                
Ding Xunlei
2003-11-05
______________________________________________
Ding Xunlei, Ph.D. Candidate
Open Laboratory of Bond Selective Chemistry
University of Science & Technology of China
Hefei, Anhui 230026, P.R.China
Tel.: 0086-551-3603418
Fax.: 0086-551-3602969
E-mail: dxl{at}mail.ustc.edu.cn
Http://www.bsc.ustc.edu.cn/~dxl

--=====================_69803296==.ALT-- From chemistry-request@ccl.net Wed Nov 5 06:10:01 2003 Received: from mail.szote.u-szeged.hu (mail.szote.u-szeged.hu [160.114.96.63]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5B9SVc026898 for ; Wed, 5 Nov 2003 06:09:29 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr{at}ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id MAA32226 for ; Wed, 5 Nov 2003 12:09:27 +0100 Received: (qmail 2431 invoked by uid 525); 5 Nov 2003 11:09:27 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 5 Nov 2003 11:09:27 -0000 Date: Wed, 5 Nov 2003 12:09:27 +0100 (CET) From: "Dr. Csaba Hetenyi" To: Alex Sutcliffe cc: chemistry{at}ccl.net Subject: Re: CCL:blind docking of large protein molecules In-Reply-To: <20031104140524.GA27892@alex> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Blind docking of peptides and short peptide fragment of p24 protein of HIV to cypA (on the cover) was investigated in our paper: Hetenyi, C. and van der Spoel, D. Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Science, 2002 11: 1729-1737 Best wishes, Csaba From chemistry-request@ccl.net Wed Nov 5 10:58:07 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5FvYVc003346 for ; Wed, 5 Nov 2003 10:57:34 -0500 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.2-X17 #30546) id <01L2OHKKBC5S000FLY{at}cuces.unisi.it> for chemistry{at}ccl.net; Wed, 05 Nov 2003 16:57:33 +0100 (MET) Received: from unisi.it (sgio2.ctf.unisi.it [172.16.52.81]) by cuces.unisi.it (PMDF V6.2-X17 #30546) with ESMTPA id <01L2OHKGBSBC000L8Q{at}cuces.unisi.it> for chemistry{at}ccl.net; Wed, 05 Nov 2003 16:57:33 +0100 (MET) Date: Wed, 05 Nov 2003 16:54:47 +0100 From: Stefano Forli Subject: AutoDock Tools Sender: stefano{at}student.unisi.it To: chemistry{at}ccl.net Message-id: <3FA91D47.27994498{at}unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7bit X-Accept-Language: en X-Spam-Status: No, hits=-0.3 required=7.0 tests=SIGNATURE_LONG_DENSE,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, when I try to use ADT (on a SGI workstation), somethimes I get some error messages in the Python shell, but programm always do his job correctly. But when I tried to analyze the output of an LGA, the shell report the following error, and nothing happens. Traceback (innermost last): File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/ViewerFramework/VF.py", line 598, in tryto result = apply( command, args, kw ) File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/AutoDockTools/autoanalyzeCommands.py", line 1275, in doit d.readDlg(dlgFile) File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/AutoDockTools/Docking.py", line 64, in readDlg dlo = DockingLogObject(self, dlgFile) File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/AutoDockTools/Docking.py", line 164, in __init__ self.dpo = self._buildDpo(parser.dpfLines) File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/AutoDockTools/Docking.py", line 180, in _buildDpo dpo._parse(lines) File "/disk2/autodock/ADT/rel.1.1/share/lib/python1.5/site-packages/AutoDockTools/DockingParameters.py", line 454, in _parse if p=='fld': NameError: p What's going on? Thanks, Stefano -- *********************************** Forli Stefano PhD Student Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@ccl.net Wed Nov 5 11:11:17 2003 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5GAjVc003726 for ; Wed, 5 Nov 2003 11:10:46 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hA5GAkjm010333; Wed, 5 Nov 2003 11:10:46 -0500 Date: Wed, 5 Nov 2003 11:10:46 -0500 (EST) From: Jan Labanowski To: chemistry_at_ccl.net cc: Barry Hardy Subject: Launch of Cheminformatics Hub and eCheminformatics 2003 virtual conference [forward] Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) The Cheminformatics Hub launches next Monday 10th November with the eCheminformatics 2003 virtual conference, Applications of Cheminformatics to Drug Discovery Please visit http://conferences.metalayer.net/echeminfo/ for updated information on the Hub and event. As a special introductory membership offer we are offering access to the eCheminformatics 2003 virtual conference including all its recorded talks, posters and discussions for one month for only $100. Last minute registrants may pay securely online by Visa or Mastercard. You can also visit the Hub and conference Exhibition for free and try it out. Introduction Sessions An Introduction to the Cheminformatics Hub and eCheminformatics 2003 conference, delivered by Conference Chair, Barry Hardy Thursday 6th November 9.00 EST, 15.00 CET and 11.00 EST, 17.00 CET Friday 7th November 9.00 EST, 15.00 CET and 11.00 EST, 17.00 CET (EST = US East Coast time, CET = Central European time) Program The final Speaker program with abstracts and bios can be viewed at: http://conferences.metalayer.net/echeminfo/design/conference/html/speakerinformation.htm The list of Posters received so far can be viewed at: http://conferences.metalayer.net/echeminfo/design/conference/html/posters.htm To submit a Poster please visit the Web site, sign-up via the registration form and use the Upload facilities available from the first page after login to submit an abstract and poster. All accepted Posters will be eligible for the eCheminformatics 2003 Best Poster Award, as judged by our Speaker panel. Young academic researchers (under 35 years of age) will be considered for a limited number of sponsored Bursaries allowing them a waiver of the registration fee. We wish to acknowledge the generous support of Bio-Rad Laboratories, Inc., towards our Young Investigator Sponsorship program. Companies presenting or exhibiting at eCheminformatics 2003 include Serono, ID Business Solutions Ltd, Bio-Rad Laboratories, Cresset BioMolecular Discovery Ltd, Leadscope , Lion Bioscience, SimBioSys, Inc, Merck, Chemaxon, Omniviz, De Novo Pharmaceuticals, ACD/Labs, Premier Conferencing, BioSolve Information Technology GmbH, Metalayer and Umetrics AB Sincerely, Dr. Barry Hardy Conference Secretariat Douglas Connect http://www.douglasconnect.com/ barry.hardy_at_tiscalinet.ch +41 61 851 0170 From chemistry-request@ccl.net Wed Nov 5 11:00:20 2003 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5FxnVc003414 for ; Wed, 5 Nov 2003 10:59:49 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id hA5FwRbt029636; Wed, 5 Nov 2003 10:59:43 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.1.32) with SMTP id M2003110510594304758 ; Wed, 05 Nov 2003 10:59:43 -0500 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id hA5Fxh0h000533; Wed, 5 Nov 2003 10:59:43 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id hA5FxgE9006097; Wed, 5 Nov 2003 10:59:43 -0500 (EST) Date: Wed, 5 Nov 2003 10:59:42 -0500 (EST) From: Yong Liang Yang To: David Gallagher cc: chemistry_at_ccl.net Subject: Re: CCL:Tips on how to locate TS structures In-Reply-To: <5.2.1.1.0.20031104051716.0265a490_at_wheresmymailserver.com> Message-ID: References: <5.2.1.1.0.20031104051716.0265a490_at_wheresmymailserver.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) hi, Dr. Gallagher: Thanks a lot for the help on calculating TS for us. But I think I did not make myself clear. The two methyl amine are supposed to simulate the "general" acid/base catalyzed epoxide ring open reactions, which means, the epoxide oxygen can not be protonated first hand as acid catalyzed epoxide ring open reaction. Strong hydrogen bonding is expected to stabilize the TS structure and in our case, one of the methyl amine which act as " gerneral" base is expected to play a much important role. By the way, at last we need the position information of the two methyl amine to design an enzyme to catalyze epoxide ring open reaction. K.N.Houk has a few publications which discussed about the "theozyme" catalyzed epoxide ring open reaction. One of them is : JACS, 1996, 118, 9204-9205 Thanks again for your kind help. Cheers Yong L. Y. On Tue, 4 Nov 2003, David Gallagher wrote: > Hi Yong, > > I have been able generate transition states and complete reaction paths for > the first two probable steps for acid catalyzed epoxide ring opening > (protonation by the methylammonium+ ion, followed by epoxide ring opening) > from the files you sent me. I shall attach the two transition state > structures to you in a separate email. > > All calculations were done with PM3 gas phase (for speed), using CAChe > MOPAC 2002. However, a COSMO solvent calculation would probably be more > realistic if you are trying to simulate the reaction in solution. The > transition states were confirmed by a single negative vibration (FORCE > calculation), followed by intrinsic reaction coordinates (IRCs) to confirm > no other intermediates. We have a complete tutorial for reaction modelling > with CAChe available, let me know if you need a copy. > > The next step would be to explore the subsequent reaction steps in a > simplified form and, finally, combine them all into one system. At that > point you could test if the reaction is concerted or stepwise, by running > IRCs from the transition states. > > These kinds of calculations are very easy to do from CAChe's graphical > interface (about 1 hour to sketch and calculate all the reactants, > products, transition states, and reaction paths for these two steps on a > Windows laptop PC), but usually more difficult to do with a stand-alone > quantum chemistry package. I hope this helps. > > Let me know if you need any further information. > > Regards, > David Gallagher > CAChe Group, Fujitsu > > > >----- Original Message Follows ----- > > > Hi Yong, > > > > > > When protonated, some epoxides can ring open with very little > > > activation energy. However, the automated tools in CAChe MOPAC 2002 > > > are usually quite good at finding transition states. If you send me > > > the complete reactant and product structures (sketch or 3D files) > > > we'll try and locate the TS geometry for you. Is it in gas phase or a > > > solvent? Then, if you wish, you could use it as a starting structure > > > for refinement with an alternative method. There is a brief guide to > > > locating TS structures with CAChe MOPAC at > > > http://www.cachesoftware.com/pdfs/CACheGuideTransitionStateModel.pdf > > > > > > Regards, > > > David Gallagher > > > CAChe Group, Fujitsu > > > > > > > > > At 09:50 AM 10/31/2003 -0500, Yong Liang Yang wrote: > > > > > > >hi, CCL users: > > > > > > > >I am now trying to locate a TS struture of an epoxide > > > >ring open reaction. But I failed many times using > > > >QST2 and QST3 method to locate it. I even failed to > > > >optimize a "guess" structure which is supposed to be > > > >a saddle point on potential energy surface to TS structure. > > > >Could anyone give me some tips on how to locate a TS structure > > > >effectively? Is there any general procedure to do that? > > > >(e.g. do I need a PES scan ? ) Any suggestions would be > > > >highly appreciated! Have a good day. > > > > > > > > > > > >Cheers > > > > > > > >Yong L. Y. > > > > > > > > > > > > > > > > > > > >-= 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 Wed Nov 5 07:15:13 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5CEeVc028809 for ; Wed, 5 Nov 2003 07:14:41 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 5 Nov 2003 10:15:11 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF36B0E6_at_correio.cetem.gov.br> From: Ian Hovell To: "'dxl_at_mail.ustc.edu.cn'" , chemistry_at_ccl.net Subject: CCL:Bond order in gaussian Date: Wed, 5 Nov 2003 10:15:10 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=QUOTED_EMAIL_TEXT,RCVD_IN_UNCONFIRMED_DSBL 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 hA5CFDVc028840 Ding, Try the following site http://www.chem.wisc.edu/~nbo5/index.htm Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell_at_cetem.gov.br > ----- Mensagem original ----- > De: dxl_at_mail.ustc.edu.cn [SMTP:dxl_at_mail.ustc.edu.cn] > Enviada em: quarta-feira, 5 de novembro de 2003 00:22 > Para: chemistry_at_ccl.net > Assunto: CCL:Bond order in gaussian > > > Dear All > > I am try to do a bond order analysis with G98. > Here is my test with O2 molecule. > > #B3LYP/6-31G opt pop=(NBO,Bonding) > > HF > > 0 3 > O 0.00 0.00 0.000000 > O 0.00 0.00 1.200000 > > The last lines of the output file is below, and I don't think it is right. > How can I read the table correctly? And what the LP,RY* stand for? > > Thank you very much for your help!!!!!!!!!!!!!!!!! > > Natural Bond Orbitals (Summary): > > Principal > Delocalizations > NBO Occupancy Energy > (geminal,vicinal,remote) > > ========================================================================== > ===== > Molecular unit 1 (O2) > 1. BD ( 1) O 1- O 2 1.00000 -1.03224 > 2. BD ( 2) O 1- O 2 1.00000 -0.45369 > 3. BD ( 3) O 1- O 2 1.00000 -0.45369 > 4. CR ( 1) O 1 0.99997 -19.14436 12(v) > 5. CR ( 1) O 2 0.99997 -19.14436 8(v) > 6. LP ( 1) O 1 0.99984 -0.87950 12(v) > 7. LP ( 1) O 2 0.99984 -0.87950 8(v) > 8. RY*( 1) O 1 0.00019 0.95747 > 9. RY*( 2) O 1 0.00000 0.88719 > 10. RY*( 3) O 1 0.00000 0.88719 > 11. RY*( 4) O 1 0.00000 1.07773 > 12. RY*( 1) O 2 0.00019 0.95747 > 13. RY*( 2) O 2 0.00000 0.88719 > 14. RY*( 3) O 2 0.00000 0.88719 > 15. RY*( 4) O 2 0.00000 1.07773 > 16. BD*( 1) O 1- O 2 0.00000 0.26370 > 17. BD*( 2) O 1- O 2 0.00000 -0.13403 > 18. BD*( 3) O 1- O 2 0.00000 -0.13403 > ------------------------------- > Total Lewis 6.99962 ( 99.9946) > Valence non-Lewis 0.00000 ( 0.0000) > Rydberg non-Lewis 0.00038 ( 0.0054) > ------------------------------- > Total unit 1 7.00000 (100.0000) > Charge unit 1 1.00000 > > > > > Ding Xunlei > 2003-11-05 > ______________________________________________ > Ding Xunlei, Ph.D. Candidate > Open Laboratory of Bond Selective Chemistry > University of Science & Technology of China > Hefei, Anhui 230026, P.R.China > Tel.: 0086-551-3603418 > Fax.: 0086-551-3602969 > E-mail: dxl_at_mail.ustc.edu.cn > Http://www.bsc.ustc.edu.cn/~dxl > > = = = = = = = = = = = = = = = = = = = = > > -= 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 Wed Nov 5 05:26:57 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5AQPVc025274 for ; Wed, 5 Nov 2003 05:26:25 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AHKro-000NIaC; Wed, 5 Nov 2003 11:26 +0100 Message-ID: <3FA8D110.2020201{at}chem.vu.nl> Date: Wed, 05 Nov 2003 11:29:36 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Alex Sutcliffe CC: chemistry{at}ccl.net Subject: Re: CCL:blind docking of large protein molecules References: <20031104140524.GA27892@alex> In-Reply-To: <20031104140524.GA27892@alex> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,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) Alex Sutcliffe wrote: > Hi, > > I am interested in investigating potential dockings between protein molecules > and only have pretty limited ideas about potential binding sites. [...] > Does anyone have any experience or tips from similar efforts or know of > any papers etc detailing any efforts or methodologies that I might find > useful? I know there is a program designed specifically to dock proteins onto each other, called HADDOCK. You'd probably find it using e.g. google. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra{at}chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From jkl@ccl.net Wed Nov 5 05:28:47 2003 -0500 Return-Path: Message-Id: <200311051025.SAA09392.-at-.mx1.ustc.edu.cn> Date: Wed, 5 Nov 2003 18:26:36 +0800 From: Reply-To: dxl.-at-.mail.ustc.edu.cn To: chemistry.-at-.ccl.net Subject: Fw: Re: CCL:Bond order in gaussian Dear Harm#: Thank you very much But it is known that the ground state of O2 molecule is triplet and it has a bond order as 2.5 . The same job is done with N2 molecule which has the singlet ground state and hte bond order is 3.0. The output file is below. We can see here that there are 14 electrons in this molecule. There are 3 BD occupied with two electrons each, and the BD* have no electrons. So we can conclude that the bond order is 3 here. So I think only for singlet , G98 's results is write. ________________________________________________________________ Natural Bond Orbitals (Summary): (For N2 molecule) Principal Delocalizations NBO Occupancy Energy (geminal,vicinal,remote) ============================================================================= Molecular unit 1 (N2) 1. BD ( 1) N 1- N 2 2.00000 -1.26412 2. BD ( 2) N 1- N 2 2.00000 -0.47168 3. BD ( 3) N 1- N 2 2.00000 -0.47168 4. CR ( 1) N 1 1.99970 -14.25668 12(v) 5. CR ( 1) N 2 1.99970 -14.25668 8(v) 6. LP ( 1) N 1 1.99494 -0.63323 12(v) 7. LP ( 1) N 2 1.99494 -0.63323 8(v) 8. RY*( 1) N 1 0.00535 0.70631 9. RY*( 2) N 1 0.00000 0.66563 10. RY*( 3) N 1 0.00000 0.66563 11. RY*( 4) N 1 0.00001 0.79968 12. RY*( 1) N 2 0.00535 0.70631 13. RY*( 2) N 2 0.00000 0.66563 14. RY*( 3) N 2 0.00000 0.66563 15. RY*( 4) N 2 0.00001 0.79968 16. BD*( 1) N 1- N 2 0.00000 0.82329 17. BD*( 2) N 1- N 2 0.00000 -0.01517 18. BD*( 3) N 1- N 2 0.00000 -0.01517 ------------------------------- Total Lewis 13.98928 ( 99.9235) Valence non-Lewis 0.00000 ( 0.0000) Rydberg non-Lewis 0.01071 ( 0.0765) ------------------------------- Total unit 1 14.00000 (100.0000) Charge unit 1 0.00000 Ding Xunlei 2003-11-05 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl.-at-.mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl = = = = = = = = = = = = = = = = = = = = From chemistry-request@ccl.net Wed Nov 5 12:49:10 2003 Received: from mta3.appstate.edu (mta3.appstate.edu [152.10.1.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5HmcVc006987 for ; Wed, 5 Nov 2003 12:48:38 -0500 Received: from ws2.appstate.edu (ws2.appstate.edu [152.10.1.41]) by mta3.appstate.edu (8.12.8/8.12.8) with ESMTP id hA5Hf7Mj011282 for ; Wed, 5 Nov 2003 12:41:07 -0500 Received: from kohn.appstate.edu (cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.2-X17 #30685) with ESMTP id <01L2O8LOBRFOA5UQ8U..at..appstate.edu> for CHEMISTRY..at..ccl.net; Wed, 05 Nov 2003 12:40:23 -0400 (EDT) Date: Wed, 05 Nov 2003 12:41:02 -0500 From: Steve Williams Subject: CCL: fractional nuclear charge X-Sender: willsd..at..imap.appstate.edu To: CHEMISTRY..at..ccl.net Message-id: <5.1.0.14.0.20031105122817.02717938..at..imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii X-MailScanner-Information: Please contact the Helpdesk @ 6266 for more information X-MailScanner-ASU-mta3: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=0, required 7) 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) I have a colleague who would like to some quantum chemistry calculations on the following system: R-OH+ --> R-NH, that is, a smooth transition from an open shell alcohol radical cation to a neutral radical amide. Is there a way to do this? We discussed several options, based on what we have here: 1) Is there and IOP in G98 that would allow a particular nucleus to have a fractional charge so that a series of calculations he could gradually go > from Z=7 to Z=8? 2) If not, how hard would this be to do with a program where we can play with the source code, like GAMESS or perhaps NWCHEM? 3) Is there existing code out there that already does this? Thanks, Steve Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 From chemistry-request@ccl.net Wed Nov 5 11:50:42 2003 Received: from myrtle.rtpnc.epa.gov (myrtle.rtpnc.epa.gov [134.67.208.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5GoAVc005275 for ; Wed, 5 Nov 2003 11:50:10 -0500 Received: from epahub12.rtp.epa.gov (epahub12.rtp.epa.gov [134.67.213.53]) by epamail.epa.gov (PMDF V5.2-32 #42055) with ESMTP id <0HNW00ENG0XYHW|at|epamail.epa.gov> for chemistry|at|ccl.net; Wed, 5 Nov 2003 11:39:34 -0500 (EST) Date: Wed, 05 Nov 2003 11:39:31 -0500 From: Moudgal.Chandrika|at|epamail.epa.gov Subject: Re:need input on some QSAR descriptors To: chemistry|at|ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Content-type: text/plain; charset=US-ASCII X-MIMETrack: Serialize by Router on EPAHUB12/USEPA/US(Release 6.0.2CF1|June 9, 2003) at 11/05/2003 11:39:34 AM X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello All, Can someone please help us define/describe the following descriptors? 1) Average information content (x order)-based on Shannon's Index 2) total point charge and hybridization components of the molecular dipole Thank you in advance for your help. Chandrika J. Moudgal National Center for Environmental Assessment, US EPA 26 W. Martin Luther King Dr., MS 117 Cincinnati, OH 45268 Phone: 513-569-7078 Fax: 513-569-7475 e-mail: moudgal.chandrika|at|epa.gov From chemistry-request@ccl.net Wed Nov 5 11:45:51 2003 Received: from sunchem.chem.uga.edu (sunchem.chem.uga.edu [128.192.5.2]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hA5GjIVc004939 for ; Wed, 5 Nov 2003 11:45:19 -0500 Received: (qmail 1915 invoked by uid 728); 5 Nov 2003 16:40:54 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 5 Nov 2003 16:40:54 -0000 Date: Wed, 5 Nov 2003 11:40:54 -0500 (EST) From: Zhi-Xiang Wang To: chemistry|at|ccl.net Subject: gaussian in Opteron Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, everybody I tried to install g03 on computers with AMD Opteron. I was sucessful to compile it, but when I run a test jobs, it just went this far Entering Gaussian System, Link 0=/tmp/zxwang/g03/g03 Initial command: /tmp/zxwang/g03/l1.exe /tmp/h2odir/Gau-30345.inp -scrdir=/tmp/h2odir/ I would appreciate any suggestions to make the gaussian works in the Opteron. Thanks ZX From chemistry-request@ccl.net Wed Nov 5 13:10:26 2003 Received: from real.cyf-kr.edu.pl (real.cyf-kr.edu.pl [149.156.2.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5I9sVc007588 for ; Wed, 5 Nov 2003 13:09:55 -0500 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by real.cyf-kr.edu.pl (8.11.6/8.11.6) with ESMTP id hA5I28g27190; Wed, 5 Nov 2003 19:02:08 +0100 X-RAV-AntiVirus: This e-mail has been scanned for viruses on host: real.cyf-kr.edu.pl Received: (from mynowak@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id TAA07227; Wed, 5 Nov 2003 19:02:06 +0100 (MET) Date: Wed, 5 Nov 2003 19:02:04 +0100 (MET) From: Mateusz Nowak To: chemistry{at}ccl.net cc: a_sutcliffe{at}iprimus.com.au Subject: Re: CCL:blind docking of large protein molecules In-Reply-To: <3FA8D110.2020201{at}chem.vu.nl> Message-ID: References: <20031104140524.GA27892@alex> <3FA8D110.2020201{at}chem.vu.nl> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hallo! Here's another protein-protein docking software: http://reco3.ams.sunysb.edu/gramm/ ::regards =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | Mateusz Nowak M.Sc. | | Institute of Pharmacology | | Polish Academy of Sciences | | ul. Smetna 12 | | 31-343 Krakow | | POLAND | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= On Wed, 5 Nov 2003, Anton Feenstra wrote: > Alex Sutcliffe wrote: > > > Hi, > > > > I am interested in investigating potential dockings between protein molecules > > and only have pretty limited ideas about potential binding sites. > [...] > > Does anyone have any experience or tips from similar efforts or know of > > any papers etc detailing any efforts or methodologies that I might find > > useful? > > I know there is a program designed specifically to dock proteins onto each > other, called HADDOCK. You'd probably find it using e.g. google. > > > -- > Groetjes, > > Anton > _____________ _______________________________________________________ > | | | > | _ _ ___,| K. Anton Feenstra | > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | > |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | > | | Feenstra{at}chem.vu.nl - www.chem.vu.nl/~feenstra/ | > | | "If You See Me Getting High, Knock Me Down" | > | | (Red Hot Chili Peppers) | > |_____________|_______________________________________________________| > > > > -= 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 Wed Nov 5 14:55:06 2003 Received: from pilot06.cl.msu.edu (pilot06.cl.msu.edu [35.9.5.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5JsZVc010802 for ; Wed, 5 Nov 2003 14:54:35 -0500 Received: from [35.12.16.82] (pm846-03.dialip.mich.net [35.12.24.205]) by pilot06.cl.msu.edu (8.11.6p2/8.10.2) with ESMTP id hA5JsX0123370 for ; Wed, 5 Nov 2003 14:54:33 -0500 Mime-Version: 1.0 X-Sender: chieny/at/pilot.msu.edu Message-Id: Date: Wed, 5 Nov 2003 14:54:29 -0500 To: chemistry/at/ccl.net From: Yao-Ying Chien Subject: CCL: A Theory of Everything? 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) Hi, Anyone interested in String Theory might want to check this out. "Elegant Universe (String Theory -- A Theory of Everything?)" at PBS. Here is the link at PBS where you can *watch* it, http://www.pbs.org/wgbh/nova/elegant/program.html More at http://www.pbs.org/wgbh/nova/elegant/ Opinions are welcome regarding if it is too good to be true, or if it's a science fiction. -- Regards, Yao-Ying Chien Department of Crop and Soil Sciences Michigan State University Plant and Soil Sciences Building, Rm A526 East Lansing, MI 48824-1325 Office: (517)355-9284 Fax: (517)355-0270 email: chieny/at/pilot.msu.edu