From chemistry-request@ccl.net Wed Nov 10 07:42:30 2004 Received: from prserv.net (out1.prserv.net [32.97.166.31]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAACgTAd004041 for ; Wed, 10 Nov 2004 07:42:30 -0500 Message-Id: <200411101242.iAACgTAd004041*at*server.ccl.net> Received: from reg.prserv.net (reg.backbone.sch.us[10.254.181.241]) by attglobal.net (out1) with SMTP id <2004111012560020104a3s3be>; Wed, 10 Nov 2004 12:56:00 +0000 From: jmmckel*at*attglobal.net To: chemistry*at*ccl.net Subject: Semiempirical vibration frequencies Date: Wed, 10 Nov 2004 12:56:00 +0000 X-Priority: 3 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit CCLers, Could anyone point me to references comparing vibration frequencies from semiempirical methods with those fron ab initio or DFT? Many thanks! John McKelvey From chemistry-request@ccl.net Wed Nov 10 03:39:26 2004 Received: from nunki.cid.csic.es (nunki.cid.csic.es [161.111.220.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAA8dOcD004699 for ; Wed, 10 Nov 2004 03:39:24 -0500 Received: from iiqab.csic.es (localhost [127.0.0.1]) (authenticated) by nunki.cid.csic.es (8.11.6/8.11.6) with ESMTP id iAA8qmQ07132; Wed, 10 Nov 2004 09:52:48 +0100 Message-ID: <4191D6A3.10001~at~iiqab.csic.es> Date: Wed, 10 Nov 2004 09:51:47 +0100 From: Ramon Crehuet User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-GB; rv:1.4) Gecko/20030630 X-Accept-Language: en-us, en MIME-Version: 1.0 To: annek~at~chem.au.dk, CHEMISTRY~at~ccl.net Subject: Re: CCL:Transition state optimization References: <1100015930.4190e93ab619b~at~mail.chem.au.dk> In-Reply-To: <1100015930.4190e93ab619b~at~mail.chem.au.dk> X-Enigmail-Version: 0.76.1.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Anne, If you know reactant and product structures, the NEB method: http://www-theory.chem.washington.edu/~graeme/research/neb/neb.html http://www-theory.chem.washington.edu/~graeme/research/docs/review.pdf or the LUP method, by Elber's Group can be useful. They are implemented in some Molecular Dynamics software (i.e. CHARMM). Best regards, Ramon Crehuet annek~at~chem.au.dk wrote: >Does anyone have a suggestion to how I could perform a transition state >optimisation on a bimolecular system. I have tried the qst-method in Gaussian >with now succes. Propably because my optimized reagtants differs to much from >the structure of the products? To perform qst3 calculation I need an initial >guess for the transition struture. Is there any general /computational) way to >find such a structure?? > >Anne Kjaersgaard > >Denmark > > > > >-= 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, jlabanow~at~nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Wed Nov 10 02:28:09 2004 Received: from mailhub2.uq.edu.au (mailhub2.uq.edu.au [130.102.149.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAA7S7cD028763 for ; Wed, 10 Nov 2004 02:28:07 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub2.uq.edu.au (8.12.11/8.12.11) with ESMTP id iAA7fZVa064205 for ; Wed, 10 Nov 2004 17:41:35 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id iAA7fZ1U008308 for ; Wed, 10 Nov 2004 17:41:35 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Wed, 10 Nov 2004 17:41:35 +1000 From: Dr Seth OLSEN To: chemistry~at~ccl.net Message-ID: <930b4d931c63.931c63930b4d~at~uq.edu.au> Date: Wed, 10 Nov 2004 17:41:35 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: CCL: Changing SYSV parameters for parallel GAMESS X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=4.5 required=7.5 tests=IMPRONONCABLE_1,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Collegues, I recently installed and ran parallel GAMESS using DDI on a 2CPU Xeon machine with hyperthreading (4 virtual CPU's). I ran through the entire included test set using 4, 2 and 1 cpus and found interesting results for the timings. The time to run gamess seemed to be by far lowest with 1cpu, and 2,4 cpus scaled about linearly against each other. However, running on 2 or 4 nodes resulted in very, very low cpu usage (<10%) and longer cpu and wall times. At this point I extended the sysV shared memory from 33MB to 1GB, thinking that this was why there was no improvement in time with parallel use. What I found after this was that 1) the computer was significantly slowed down for everything, even mundane tasks 2) the cpu usage was marginally improved for 2 & 4 node use, but was reduced for 1 node use 3) the wall time was made longer in all cases and had no obvious correlation with the number of nodes used. Can any of the discussion group member shed light on these observations? Should I have increased the SYSV shared memory? Should I increase the number of semaphores as well? What kind of improvements should I expect using parallel GAMESS? Cheers, Seth Olsen ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1~at~uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From chemistry-request@ccl.net Tue Nov 9 19:10:52 2004 Received: from smtp.seznam.cz (smtp.seznam.cz [212.80.76.43]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAA0AmcD017374 for ; Tue, 9 Nov 2004 19:10:49 -0500 Received: (qmail 5821 invoked from network); 10 Nov 2004 00:24:15 -0000 Received: from unknown (HELO ?127.0.0.1?) (jaroslav.burda@143.132.1.1) by smtp.seznam.cz with SMTP; 10 Nov 2004 00:24:15 -0000 Message-ID: <4190FD29.2060709|at|karlov.mff.cuni.cz> Date: Tue, 09 Nov 2004 18:23:53 +0100 From: Jaroslav Burda User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: Workshop in Prague Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.0 required=7.5 tests=DATE_IN_PAST_06_12 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear colleagues, I would like to post our workshop at your CCL list of conferences. Its name is "Modeling Interaction in Biomolecules" and it will be held in Prague in 5.-9. 9. 2005 Details are available on the address: http://physics.mff.cuni.cz/kchfo/workshop/ With best regards, Jaroslav Burda -- ================================================== Dr. Jaroslav Burda Charles University in Prague Faculty of Mathematics and Physics Department of Chemical Physics and Optics Ke Karlovu 3 121 16 Prague 2 Czech Republic Tel.: (00-420)-2-2191-1246 FAX: (00-420)-2-2191-1249 Email: burda|at|karlov.mff.cuni.cz http://physics.mff.cuni.cz/kchfo/burda ================================================= From chemistry-request@ccl.net Wed Nov 10 00:23:31 2004 Received: from smtp3.vsnl.net (smtp3.vsnl.net [203.200.235.233]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAA5NTcD015043 for ; Wed, 10 Nov 2004 00:23:30 -0500 Received: from kalpana ([127.0.0.1]) by smtp3.vsnl.net (vsnl mail server) with ESMTPA id <0I6Y000KW7MYTX|at|smtp3.vsnl.net> for chemistry|at|ccl.net; Wed, 10 Nov 2004 11:07:53 +0530 (IST) Received: from ([61.11.58.76]) by smtp3.vsnl.net (InterScan E-Mail VirusWall Unix); Wed, 10 Nov 2004 11:07:53 +0530 (IST) Date: Wed, 10 Nov 2004 11:04:05 +0530 From: Kalpana Krishnaswami Subject: RE: Transition state optimization In-reply-to: <1100015930.4190e93ab619b|at|mail.chem.au.dk> To: annek|at|chem.au.dk, chemistry|at|ccl.net Message-id: <000001c4c6e6$e5fd0a80$4c3a0b3d@kalpana> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Mailer: Microsoft Outlook, Build 10.0.2616 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net In the past I have used SPARTAN to generate a guess Transition State and optimized it with MOPAC. If my memory serves me right I think you can do it directly in MOPAC too. Hope this helps. Regards Kalpana Krishnaswami Seascape Learning -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request|at|ccl.net] On Behalf Of annek|at|chem.au.dk Sent: Tuesday, November 09, 2004 9:29 PM To: chemistry|at|ccl.net Subject: CCL:Transition state optimization Does anyone have a suggestion to how I could perform a transition state optimisation on a bimolecular system. I have tried the qst-method in Gaussian with now succes. Propably because my optimized reagtants differs to much > from the structure of the products? To perform qst3 calculation I need an initial guess for the transition struture. Is there any general /computational) way to find such a structure?? Anne Kjaersgaard Denmark -= 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, jlabanow|at|nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Nov 10 10:58:02 2004 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAAFw10l031413 for ; Wed, 10 Nov 2004 10:58:01 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 1001) id 4DF28238289; Wed, 10 Nov 2004 17:11:31 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 8FFA2238295; Wed, 10 Nov 2004 17:11:10 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 10 Nov 04 17:11:10 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 10 Nov 04 17:11:09 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: jmmckel-.at.-attglobal.net, chemistry-.at.-ccl.net Date: Wed, 10 Nov 2004 17:11:02 +0100 Subject: Re: CCL:Semiempirical vibration frequencies Reply-To: spanget-.at.-ruc.dk Message-ID: <41924BA7.20418.185BF06@localhost> Priority: normal In-reply-to: <200411101242.iAACgTAd004041-.at.-server.ccl.net> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Status: No, hits=0.2 required=7.5 tests=BAD_X_HEADERS autolearn=no version=2.61 X-Spam-Level: John, A.P. Scott & L. Radom, J. Phys. Chem. 1996, 100, 16502-16513, compare the vibrational frequencies predicted by AM1 and PM3 with those obtained with a variety of HF, MP2, QCISD, and DFT procedures. Jens >--< > CCLers, > > Could anyone point me to references comparing vibration frequencies from > semiempirical methods with those fron ab initio or DFT? > > Many thanks! > > John McKelvey =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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-.at.-ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed Nov 10 11:22:58 2004 Received: from mb1i1.ns.pitt.edu (mb1i1.ns.pitt.edu [136.142.11.139]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAAGMw0l002604 for ; Wed, 10 Nov 2004 11:22:58 -0500 Received: from Drude ([136.142.60.48]) by pitt.edu (PMDF V6.2-X27 #30902) with SMTP id <01LH2GHD5JN0002CTM(at)mb1i1.ns.pitt.edu> for chemistry(at)ccl.net; Wed, 10 Nov 2004 11:36:18 -0500 (EST) Date: Wed, 10 Nov 2004 11:36:20 -0500 From: Brad Tsai Subject: CCL: Stuttgart's one electron pseudopotential for Au To: chemistry(at)ccl.net Message-id: <001701c4c743$68a422a0$303c8e88@Drude> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Mailer: Microsoft Outlook Express 6.00.2900.2180 Content-type: multipart/alternative; boundary="----=_NextPart_000_0014_01C4C719.7FC36C40" X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=4.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C4C719.7FC36C40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers,=20 Could anyone point out the corresponding valence basis set of Au for = Stuttgart's ECP78SHF? I can find the basis set on their website for the = 78 core-electron, but cannot find any basis set for the last valence = electron. Should I use other valence electron basis set, like ECP60MHF? = or I just simply miss something=20 Really appreciate if anyone who has experience can provide some = information. Best regards, -Brad Tsai ------=_NextPart_000_0014_01C4C719.7FC36C40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
Could anyone point out the = corresponding valence=20 basis set of Au for Stuttgart's ECP78SHF? I can find the basis set on = their=20 website for the 78 core-electron, but cannot find any basis=20 set for the last valence electron. Should I use other valence = electron=20 basis set, like ECP60MHF? or I just simply miss something
 
Really appreciate if anyone who has = experience can=20 provide some information.
 
Best regards,
-Brad Tsai
 
------=_NextPart_000_0014_01C4C719.7FC36C40-- From chemistry-request@ccl.net Wed Nov 10 10:35:24 2004 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 iAAFZK0l028755 for ; Wed, 10 Nov 2004 10:35:21 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2655.55) id ; Wed, 10 Nov 2004 13:47:32 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C5894*at*correio.cetem.gov.br> From: Ian Hovell To: "'chemistry'" Subject: CCL: Integration grid defaulting to unpruned value Date: Wed, 10 Nov 2004 13:47:24 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4C744.F46D3DC0" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_FONTCOLOR_UNKNOWN, HTML_MESSAGE,LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4C744.F46D3DC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Dear CCLers, =20 I am calculating the heats of reactions containing organo-mercury = compounds. I am using G03 and DFT methods. The program, when mercury is involved, defaults to an unpruned integration grid for this atom. The manual = states that one should use the same grid when comparing energies. Does this = mean that I should be defining an unpruned grid for all of my calculations = i.e. the compounds without mercury in the isodesmic reaction? If so how do I define an unpruned grid the same as the one being used by gaussian when mercury is involved. The manual does not talk about unpruned grids. I = have enclosed the relevant output section below.=20 =20 TIA Ian Hovell - Ph.D.=20 NUCLEO DE MODELAGEM MOLECULAR-NMM=20 Centro de Tecnologia Mineral - CETEM=20 Ministerio da Ci=EAncia e da Tecnologia- MCT=20 Avenida Ip=EA, No 900 - Cidade Universitaria=20 Ilha do Fund=E3o Rio de Janeiro RJ Brasil=20 CEP 21941-590=20 tel 00 55 (xx) 3865 7344 ou 3865 - 7216=20 Fax 00 55 (xx) 22602837 ou 2290-4286=20 e-mail hovell*at*cetem.gov.br =20 =20 NPDir=3D0 NMtPBC=3D 1 NCelOv=3D 1 NCel=3D 1 NClECP=3D = 1 NCelD=3D 1 NCelK=3D 1 NCelE2=3D 1 NClLst=3D 1 CellRange=3D = 0.0. One-electron integrals computed using PRISM. One-electron integral symmetry used in STVInt 6 Symmetry operations used in ECPInt. ECPInt: NShTT=3D 1653 NPrTT=3D 3635 LenC2=3D 1654 LenP2D=3D = 3491. LDataN: DoStor=3DF MaxTD1=3D 8 Len=3D 415 LDataN: DoStor=3DT MaxTD1=3D 8 Len=3D 415 NBasis=3D 178 RedAO=3D T NBF=3D 114 64 NBsUse=3D 178 1.00D-06 NBFU=3D 114 64 Precomputing XC quadrature grid using IXCGrd=3D 2 IRadAn=3D 0 IRanWt=3D -1 IRanGd=3D = 0. Defaulting to unpruned grid for atomic number 80. NRdTot=3D 316 NPtTot=3D 50504 NUsed=3D 51937 NTot=3D = 51953 NSgBfM=3D 178 178 178 178. =20 =20 ------_=_NextPart_001_01C4C744.F46D3DC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

 

=

<= span class=3DEstiloDeCorreioEletrnico18><= span style=3D"mso-spacerun: yes"> Dear = CCLers,

 

I am calculating the heats of reactions = containing organo-mercury compounds. I am using G03 and DFT methods. The program, = when mercury is involved, defaults to an unpruned integration grid for this = atom. The manual states that one should use the same grid when comparing = energies. Does this mean that I should be defining an unpruned grid for all of my calculations i.e. the compounds without mercury in the isodesmic = reaction? If so how do I define an unpruned grid the same as the one being used by = gaussian when mercury is involved. The manual does not talk about unpruned = grids. I have enclosed the relevant output section below. =

 

TIA

Ian Hovell - Ph.D. = =

NUCLEO = DE MODELAGEM MOLECULAR-NMM

Centro de Tecnologia Mineral - CETEM

Ministerio da Ci=EAncia e da Tecnologia- MCT

Avenida Ip=EA, No 900 - Cidade Universitaria

Ilha do Fund=E3o 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 <= o:p>

e-mail hovell*at*cetem.gov.br

 

 

NPDir=3D0 NMtPBC=3D     1 NCelOv=3D     1 NCel=3D       1 NClECP=3D     1 = NCelD=3D      = 1=

         = NCelK=3D      1 NCelE2=3D     1 NClLst=3D     1 CellRange=3D     0.0.

=

 One-electron integrals computed using PRISM.

 One-electron integral symmetry used in STVInt

   6 = Symmetry operations used in ECPInt.

 ECPInt:  NShTT=3D    1653 NPrTT=3D    3635 LenC2=3D    1654 LenP2D=3D    3491.

 LDataN:  DoStor=3DF MaxTD1=3D 8 = Len=3D  415

=

 LDataN:  DoStor=3DT MaxTD1=3D 8 = Len=3D  415

=

 NBasis=3D   178 RedAO=3D T  NBF=3D   114    64

 NBsUse=3D   178 1.00D-06 = NBFU=3D   114    64

 Precomputing XC quadrature grid using

 IXCGrd=3D 2 IRadAn=3D           = 0 IRanWt=3D          -1 IRanGd=3D           = 0.

=

 Defaulting = to unpruned grid for atomic number  80.

 NRdTot=3D     316 = NPtTot=3D       = 50504 NUsed=3D       51937 NTot=3D       = 51953

=

 NSgBfM=3D   178   178   178   = 178.=

 

 =

------_=_NextPart_001_01C4C744.F46D3DC0-- From chemistry-request@ccl.net Wed Nov 10 10:26:26 2004 Received: from fujitsu2.fujitsu.com (fujitsu2.fujitsu.com [192.240.0.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAAFQO0l027608 for ; Wed, 10 Nov 2004 10:26:24 -0500 Received: from fujitsu2.fujitsu.com (localhost [127.0.0.1]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id iAAFdrNo021526 for ; Wed, 10 Nov 2004 07:39:53 -0800 (PST) Received: from fnanic.fujitsu.com ([133.164.253.2]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id iAAFdr2K021476; Wed, 10 Nov 2004 07:39:53 -0800 (PST) Received: from cachemail.fnanic.fujitsu.com (localhost [127.0.0.1]) by fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id iAAFdlmA004020; Wed, 10 Nov 2004 07:39:47 -0800 (PST) Received: from Dave-Lifebook02.cachesoftware.com (localhost [127.0.0.1]) by cachemail.fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id iAAFfHE3022322; Wed, 10 Nov 2004 07:41:23 -0800 (PST) Message-Id: <6.1.2.0.0.20041110072132.01e72ec0@133.164.253.31> X-Sender: dgallagher@133.164.253.31 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Wed, 10 Nov 2004 07:39:37 -0800 To: annek*at*chem.au.dk, chemistry*at*ccl.net From: David Gallagher Subject: Re: CCL:Transition state optimization In-Reply-To: <1100015930.4190e93ab619b*at*mail.chem.au.dk> References: <1100015930.4190e93ab619b*at*mail.chem.au.dk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Anne, It may be easier to start by locating a semiempirical TS that can be used as a starting guess for a higher level method. If you send me details of your reaction off-line (i.e. reactants, products, expected T-S geometry, solvent, phase, catalyst, etc.), I'll see if it can be done with CAChe for you. CAChe has several different methods for finding difficult transition states with multiple molecules and, it employs various quantum methods including MOPAC AM1, PM3, PM5, DGauss and Gaussian. Regards, David Gallagher Fujitsu At 07:58 AM 11/9/2004, annek*at*chem.au.dk wrote: >Does anyone have a suggestion to how I could perform a transition state >optimisation on a bimolecular system. I have tried the qst-method in Gaussian >with now succes. Propably because my optimized reagtants differs to much from >the structure of the products? To perform qst3 calculation I need an initial >guess for the transition struture. Is there any general /computational) way to >find such a structure?? > >Anne Kjaersgaard > >Denmark > > > > >-= 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, jlabanow*at*nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Nov 10 13:35:33 2004 Received: from mx4.trentu.ca (mx4.trentu.ca [192.75.12.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAAIZUAQ014584 for ; Wed, 10 Nov 2004 13:35:30 -0500 Received: (qmail 30556 invoked by uid 510); 10 Nov 2004 18:48:59 -0000 Received: from 209.42.102.117 by mx4.trentu.ca (envelope-from , uid 501) with qmail-scanner-1.23 (f-prot: 4.4.1/3.14.11. fsecure: 4.52/2461/libra database 2004-11-04/orion database 2004-11-09/avp(2004-11-09). spamassassin: 3.0.0. Clear:RC:1(209.42.102.117):. Processed in 0.147469 secs); 10 Nov 2004 18:48:59 -0000 X-Qmail-Scanner-Mail-From: elewars:at:trentu.ca via mx4.trentu.ca X-Qmail-Scanner: 1.23 (Clear:RC:1(209.42.102.117):. Processed in 0.147469 secs) Received: from unknown (HELO trentu.ca) (209.42.102.117) by mx4.trentu.ca with SMTP; 10 Nov 2004 18:48:58 -0000 Message-ID: <4192631A.3020908:at:trentu.ca> Date: Wed, 10 Nov 2004 13:51:06 -0500 From: errol lewars User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Ramon Crehuet , chemistry:at:ccl.net Subject: Re: CCL:Transition state optimization References: <1100015930.4190e93ab619b:at:mail.chem.au.dk> <4191D6A3.10001:at:iiqab.csic.es> In-Reply-To: <4191D6A3.10001:at:iiqab.csic.es> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net hello, In many cases a guess structure based on chemical intuition will optimize smoothly to a TS, especially at the AM1 or PM3 level. This semiempirical TS structure then usually serves as a good input for a higher-level job (initiating the TS opt with a semiempirical hessian). What is the reaction whose TS you want? EL ==== Ramon Crehuet wrote: > Dear Anne, > If you know reactant and product structures, the NEB method: > http://www-theory.chem.washington.edu/~graeme/research/neb/neb.html > http://www-theory.chem.washington.edu/~graeme/research/docs/review.pdf > or the LUP method, by Elber's Group can be useful. > They are implemented in some Molecular Dynamics software (i.e. CHARMM). > Best regards, > > Ramon Crehuet > > > > annek:at:chem.au.dk wrote: > >> Does anyone have a suggestion to how I could perform a transition state >> optimisation on a bimolecular system. I have tried the qst-method in >> Gaussian >> with now succes. Propably because my optimized reagtants differs to >> much from >> the structure of the products? To perform qst3 calculation I need an >> initial >> guess for the transition struture. Is there any general >> /computational) way to >> find such a structure?? >> >> Anne Kjaersgaard >> >> Denmark >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > > > -= 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, jlabanow:at:nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Nov 10 11:45:55 2004 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAAGjr0l004214 for ; Wed, 10 Nov 2004 11:45:53 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id iAAFq9702273 for ; Wed, 10 Nov 2004 08:52:09 -0700 Message-ID: <419248E5.9060501/at/eyesopen.com> Date: Wed, 10 Nov 2004 09:59:17 -0700 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry/at/ccl.net Subject: FRED 2.0 released - extremely fast, exhaustive ligand docking in a protein active site Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net OpenEye has released FRED 2.0, an accurate and extremely fast docking program. For every ligand, FRED exhaustively searches all possible poses within a protein active site, filtering for shape complementarity and optional pharmacaphoric features before being evaluated by several scoring functions (ChemScore, PLP, ScreenScore, ChemGauss, PBSA). Whereas most docking codes use stochastic methods to find binding modes, FRED uses a systematic search algorithm, accurately predicting binding modes in a reproducible manner. Furthermore, FRED allows the scientist to take advantage of known structure activity relationships; they may perform directed docking wherein certain pharmacaphoric features are guaranteed to be in specific regions of the active site. Despite being exhaustive, FRED is extremely fast; distributed processing via PVM docks even the largest libraries in reasonable time frames. With equivalent resolution settings, FRED will out-perform all competitive methods. FRED 2.0 has two new, more accurate, scoring functions: ChemGauss adds chemical perception to the original shape-based function; PBSA provides Poisson-Boltzman electrostatic binding energies. FRED 2.0 is capable of refining docked structures in the context of the active site using the high-quality Merck Molecular Force Field (MMFF). For consensus scoring, FRED 2.0 supports multiple simultaneous scoring functions and hit lists. To eliminate promiscuous binders, FRED 2.0 can scale scoring results based upon Multiple Active Site Corrections. For further information, please visit www.eyesopen.com or contact business/at/eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software