From chemistry-request@server.ccl.net Wed May 15 03:49:18 2002 Received: from sun1.udg.es ([130.206.45.89]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4F7nHP02697 for ; Wed, 15 May 2002 03:49:17 -0400 Received: from iqc.udg.es (woodstock.udg.es [130.206.128.118]) by sun1.udg.es (8.9.3/8.9.3/otb) with ESMTP id JAA21081; Wed, 15 May 2002 09:46:28 +0100 (WET DST) Message-ID: <3CE22FED.2000401@iqc.udg.es> Date: Wed, 15 May 2002 11:52:45 +0200 From: Pedro Salvador Sedano User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: uccatvm CC: CCL , Tanja van Mourik Subject: Re: CCL:counterpoise with LMP2 References: <200205142159.g4ELxUC29583@socrates-a.ucl.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All I'd like to point out that the SCF-MI method is actually from A. Famulari, M. Raimondi, M. Sironi, E. Gianinetti (and recently has been reformulated by S. Iwata in a more compact fashion). With this method, the uncorrected and BSSE-corrected interaction energies do not approach asimptotically each other improving the basis set, since some physical delocalizations are removed from the SCf calculation Mayer's approach is the Chemical Hamiltonian Approach (CHA), which has been proved to be free of such pitfalls. (See for instance, "The Chemical Hamiltonian Approach for treating the BSSE problem of intermolecular interactions" I. Mayer Int. J. Q. Chem. 1998 70 41 ) Pedro uccatvm wrote: > Hi Gerd, > > Thank you for your answer. However, my question was more specifically how > to get the best orbital domain match for the dimer and monomer+ghost > calculations in local MP2, and not so much how to do counterpoise > calculations in general. > > The SCF-MI methods of Mayer and co-workers are a different approach to > deal with BSSE, and are not without problems. For example, with > SCF-MI/VB method and the aug-cc-pV5Z basis set, the De of He2 is 10.64 K > at 5.8 bohr - J. Mol. Struct. (Theochem) 549, 77, 2001. The FCI/aug-cc-pV5Z > estimate is 10.17 K at 5.6 a.u. (J. Chem. Phys. 111, 9248, 1999). I > think this shows that SCF-MI overestimates the interaction energy. > > Tanja > > >>maybe the work of Istvan Mayer et al. >> >> author = {I. Mayer and \'A. Vib\'ok and G. Hal\'asz and P. Valiron}, >> title = {A BSSE-Free SCF Algorithm for Intermolecular >> Interactions. III. Generarlization for Three-Body >> Systems and for Using Bond Functions}, >> journal = {Int. J. Quantum Chem.}, >> year = {1996}, >> volume = {57}, >> pages = {1049} >> >>(see also the references there) is useful for you. This approach is >>especially useful if you are going to use small basis sets. Here you >>also get a BSSE free wave function. Furthermore as far as I know you >>will find also a discussion how the classical Boys Bernardi Method >>should be applied - this should be sufficient if you just go for BSSE >>free energies. >> >>Gerd >> >> From: uccatvm >> Date: Mon, 13 May 2002 21:56:43 +0100 (BST) >> >> Hi all, >> >> I am wondering what the most correct way is to do counterpoise with local >> MP2. In the local MP2 method originally proposed by Pulay (Chem.Phys.Lett. >> 100, 151, 1983), to each localised MO a subset (orbital domain) of the >> virtual orbitals is assigned. To calculate the interaction energy of a >> weakly interacting system, the orbital domains of the subsystems are first >> determined at large distance, and used in subsequent dimer calculations at >> smaller intermolecular distances (as recommended in for example Schutz et al., >> J. Phys. Chem. 102, 5997, 1998). >> >> Now, I assume that (to keep a true counterpoise) it is best to use the >> orbital domains determined at large distance for the monomer+ghost >> calculation. For this, one would first have to determine the domains of the >> monomer+ghost with the ghost at large R, and use the thus obtained orbital >> domains in the monomer+ghost calculation at the smaller distance. What >> do people think? Would this be the correct way of doing it? >> >> Of course, the BSSE is strongly reduced in LMP2, and should in principle >> be negligible when using an appropriate basis set. However, when using >> small basis sets it may not be negligible, and I would like to know the >> best way of doing counterpoise for these cases. >> >> Thanks in advance, >> >> Tanja >> >> -- >> ===================================================================== >> Tanja van Mourik >> Royal Society University Research Fellow >> Chemistry Department >> University College London phone: +44 (0)20-7679-4663 >> 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk >> London WC1H 0AJ, UK home: tanja@netcomuk.co.uk >> >> http://www.chem.ucl.ac.uk/people/vanmourik/index.html >> ===================================================================== >> >> >> >> >> >> >> > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- -------------------------------------------------------------------- Pedro Salvador Sedano Ph.D. Student I'll stare the sundown, Institut de Quimica Computacional untill my eyes go blind. Universitat de Girona I won't change direction, Campus Montilivi 17071, Girona,Spain and I won't change my mind. iqc.udg.es/~perico -------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed May 15 07:26:01 2002 Received: from relay.unizar.es ([155.210.3.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FBPvP08304 for ; Wed, 15 May 2002 07:25:58 -0400 Received: from celes.unizar.es (celes.unizar.es [155.210.11.15]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id g4FBQ6h27370 for ; Wed, 15 May 2002 13:26:06 +0200 (MET DST) Received: from there (santiago@[155.210.93.83]) by celes.unizar.es (8.11.1/8.11.1) with SMTP id g4FCNWT14221 for ; Wed, 15 May 2002 14:23:32 +0200 (MET DST) Message-Id: <200205151223.g4FCNWT14221@celes.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: chemistry@ccl.net Subject: hbonds charmm Date: Wed, 15 May 2002 13:23:53 +0200 X-Mailer: KMail [version 1.3.2] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi everbody !! I'm trying to calculate hbonds time correlation series from MD trayectories with the academic version of charmm. After reading correctly trayectories, I've used: correl maxseries 12 maxtimesteps 50000 maxatom 80 - eps 1.0 cutnb @4 ctofnb @6 ctonnb @5 vswi - ewald pmewald kappa @kap fftx 32 ffty 32 fftz 32 order @ord - @7 @8 @9 - inbf 1 ihbf 1 imgf 1 enter phi1 dihe prot 24 C prot 25 N prot 25 CA prot 25 C geometry enter psi1 dihe prot 25 N prot 25 CA prot 25 C prot 26 N geometry enter phi2 dihe prot 28 C prot 29 N prot 29 CA prot 29 C geometry enter psi2 dihe prot 29 N prot 29 CA prot 29 C prot 30 N geometry enter phi1 time enter psi1 time enter phi2 time enter psi2 time ! (HBONDS) enter hbn1 hbond prot 31 N prot 16 OE2 DIST ! or ( enter hbn1 hbond prot 31 N prot 31 HN prot 16 OE2 DIST enter hbn1 time BUT I obtain this error: : No hydrogen bond parameters for 1 ( NH1 OH1 ) I'll be very grateful if someone could help me. Thanks in advance: Santiago Cuesta ------------------------------------- Santiago Cuesta Predoctoral student Dep. Física de la Materia Condensada. Universidad de Zaragoza. (Spain) From chemistry-request@server.ccl.net Tue May 14 23:37:44 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4F3biC26155 for ; Tue, 14 May 2002 23:37:44 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g4F3biF29420 for ; Tue, 14 May 2002 23:37:44 -0400 (EDT) Date: Tue, 14 May 2002 23:37:43 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net Subject: 02.11.17 Int. Conference on Heavy Organics Deposition: HOD-2002 in Puerto Vallarta, Mexico (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT ---------- Forwarded message ---------- Return-Path: From: "Yosadara Ruiz-Morales" To: jkl@ccl.net Date: Tue, 14 May 2002 15:13:31 -0600 Subject: 02.11.17 Int. Conference on Heavy Organics Deposition: HOD-2002 in Puerto Vallarta, Mexico Reply-to: yruiz@www.imp.mx Subject: 02.11.17 Int. Conference on Heavy Organics Deposition: HOD-2002 in Puerto Vallarta, Mexico Dear Colleagues: This is to invite you to contribute with an oral or poster presentation in the "2002 International Conference on Heavy Organics Deposition" (HOD 2002), which will be held on November 17-21, 2002 in Puerto Vallarta, Jalisco, Mexico. HOD 2002 is a scientific forum to discuss on the various physicochemical phenomena associated to the study of heavy organics depositions (Wax, Asphaltene, resin, etc.) from petroleum, which greatly affect the economy of the oil industry. HOD 2002 will feature a number of Invited Lectures and Technical Sessions on the following topics: Asphaltene Structural Studies, Asphaltene and Wax Characterization, Asphaltenes in Oil Reservoirs, Modeling Asphaltene and Wax Precipitation, Flow Assurance, Molecular Computations, Field-Related Applications and more!. The beautiful beaches of sunny Puerto Vallarta, will additionally provide all attendants to HOD 2002 with a pleasant place to stay, from which fruitful discussions and a closer interaction will be favored. To submit your or your colleagues´ Abstract, an on-line internet submission facility has been enabled at the Conference Internet Site: www.hod2002.com, where submission deadlines, registration costs and all related information on this event can be found. In the conference there will be several sessions (please check the web site), in particular there will be a session on Molecular Computations. If you are interested in participating in this session please contact Dr. Yosadara Ruiz-Morales (yruiz@imp.mx) who is the chair of this session. Looking forward with pleasure to see you in Puerto Vallarta in November, Truly yours, C. Lira-Galeana HOD 2002 Conference Chairman Mexican Inst. of Petroleum Mexico City From chemistry-request@server.ccl.net Wed May 15 09:52:00 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FDq0s12520 for ; Wed, 15 May 2002 09:52:00 -0400 Received: from onco_irmb.health.nb.ca ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with ESMTP id ca for ; Wed, 15 May 2002 10:51:54 -0300 Message-Id: <5.1.0.14.0.20020515104457.009eb910@mailhub.health.nb.ca> X-Sender: miroslavac@mailhub.health.nb.ca X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 15 May 2002 10:54:55 -0300 To: CCL From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) Subject: MOE question Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, Can anybody tell me how to replace a residue in DNA molecule using MOE software while keeping position of other residues in the DNA molecule constant. This should be simple (but finding out how-to from help files isn't) and I apologize for bothering everybody with such a daft question. Thanks a lot for your help, Miroslava Miroslava Cuperlovic-Culf Ph.D. Beausejour Medical Research Institute 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 e-mail: miroslavac@health.nb.ca From chemistry-request@server.ccl.net Wed May 15 11:20:59 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FFKxs14612 for ; Wed, 15 May 2002 11:20:59 -0400 Received: from psu.edu (amoeba.chem.psu.edu [128.118.172.90]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id LAA391178 for ; Wed, 15 May 2002 11:20:59 -0400 Message-ID: <3CE27CDC.12A26EC0@psu.edu> Date: Wed, 15 May 2002 11:20:59 -0400 From: Ed Brothers Reply-To: enb108@psu.edu Organization: PSU Merz Group X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: DIIS SCF in UHF and UDFT Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I am currently implementing DIIS to accelerate SCF convergence as per Pulay, J. Comp. Chem., V 3, #4, 556-60, 1982. In the RHF case the construction of the error vectors is fairly straight forward: e(i) = F(i) D(i) S - S D(i) F(i) Where i is the step index, F is the operator matrix, D is the total density matrix, and S is the overlap matrix. I am a bit unsure how to proceed with the unrestricted case. I have implemented e(i) = Fa(i) Da(i) S - S Da(i) Fa(i) + Fb(i) Db(i) S - S Db(i) Fb(i) Where the a and b are the alpha and beta electron versions of the matrix. This causes the generation of of a single B matrix and thus a single set of coefficients from the linear equation. Is this the right way to set up the error matrix for step i in UHF and UDFT? If it isn't, what is? Dose anyone know a reference where this is discussed? Thanks for your time. Ed Bothers. Merz Goup, Penn State enb108@psu.edu From chemistry-request@server.ccl.net Wed May 15 12:35:08 2002 Received: from estrella.pasteur-lille.fr ([194.254.237.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FGZ7s16246 for ; Wed, 15 May 2002 12:35:08 -0400 Received: from adelaide.pasteur-lille.fr (adelaide.pasteur-lille.fr [193.49.178.2]) by estrella.pasteur-lille.fr (8.12.1/jtpda-5.4) with ESMTP id g4FGLTlJ002059 for ; Wed, 15 May 2002 18:21:29 +0200 Received: from pasteur-lille.fr (pax-197.pasteur-lille.fr [194.254.248.197]) by adelaide.pasteur-lille.fr (8.11.6/8.11.6/SuSE Linux 0.5) with ESMTP id g4FGYh308256 for ; Wed, 15 May 2002 18:34:43 +0200 Sender: Julien.Michel@pasteur-lille.fr Message-ID: <3CE28E04.C5D47CE4@pasteur-lille.fr> Date: Wed, 15 May 2002 18:34:12 +0200 From: Julien Michel Organization: IBL UMR8525 Institut Pasteur de Lille X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Efficiency of LIE method References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean Dear all, I am trying to apply the Linear Interaction Energy method to a set of peptides. Unfortunately the method is not very successfull, I have trouble obtaining convergence of the Electrostatic potential. I believe this is because a few residues are charged. I have the impression that increasing the length of the simulation won't help solve the problem. So I'd like to know if there are ways to solve this problem within the context of the LIE method or if the method is not adapted for simulating charged ligands. Julien Michel From chemistry-request@server.ccl.net Wed May 15 13:08:32 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FH8Vs17001 for ; Wed, 15 May 2002 13:08:31 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id UAA23653 for ; Wed, 15 May 2002 20:08:31 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 15 May 2002 20:08:30 +0300 (EET DST) From: Mikael Johansson X-Sender: To: Subject: Proper B3LYP reference? In-Reply-To: <3CE27CDC.12A26EC0@psu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! What's the "proper" B3LYP reference to use? Usually Becke's paper [1] is cited, and sometimes additionally the paper by Stephens et al. [2]. Paper [1] does not contain the B3LYP-functional, altough it defines the 3 parameters for the different types of contribution. Paper [2] explicitly explains the alterations to Becke's original formulation, but I find at least one earlier paper [3] mentioning/using B3LYP. > From the articles, I assume B3LYP was something introduced by the Gaussian program package, am I right? Furthermore, does anyone know of an even earlier B3LYP reference than [3]? [1] A.D. Becke, J.Chem.Phys. 98 (1993) 5648-5652 [2] P.J. Stephens, F.J. Devlin, C.F. Chabalowski, M.J Frisch, J.Phys.Chem. 98 (1994) 11623-11627 [3] K. Kim, K.D. Jordan, J.Phys.Chem. 98 (1994) 10089-10094 Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@server.ccl.net Wed May 15 13:12:20 2002 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FHCKs17103 for ; Wed, 15 May 2002 13:12:20 -0400 Received: from there (ice.chem.rochester.edu [128.151.195.5]) by mail.rochester.edu (8.12.1/8.12.1) with SMTP id g4FHBTsT14989221; Wed, 15 May 2002 13:11:29 -0400 (EDT) Message-Id: <200205151711.g4FHBTsT14989221@mail.rochester.edu> Content-Type: text/plain; charset="us-ascii" From: weizhuang Reply-To: weiz@mail.rochester.edu To: CHEMISTRY@ccl.net Subject: help on parellel computing Date: Wed, 15 May 2002 13:13:11 -0400 X-Mailer: KMail [version 1.3.1] Cc: cpmd-list@cpmd.org MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Filter-Version: 1.7 (mail1) Hi, friends: I was running CPMD program on a linux cluster, I set the restart file to be saved every 5 steps. however, every time when the machine is going to save the restart file. the job is crashed. and following is the information. could anybody give me some clue about what is wrong here and any suggestion of how to solve it. thanks a lot. wei zhuang ----------------- MPI_Recv: process in local group is dead (rank 4, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 1, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 8, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 2, MPI_COMM_WORLD) Rank (1, MPI_COMM_WORLD): Call stack within LAM: Rank (1, MPI_COMM_WORLD): - MPI_Recv() Rank (1, MPI_COMM_WORLD): - MPI_Barrier() Rank (1, MPI_COMM_WORLD): - main() Rank (2, MPI_COMM_WORLD): Call stack within LAM: Rank (2, MPI_COMM_WORLD): - MPI_Recv() Rank (2, MPI_COMM_WORLD): - MPI_Barrier() Rank (2, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 5, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 9, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 10, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 3, MPI_COMM_WORLD) Rank (4, MPI_COMM_WORLD): Call stack within LAM: Rank (4, MPI_COMM_WORLD): - MPI_Recv() Rank (4, MPI_COMM_WORLD): - MPI_Barrier() Rank (4, MPI_COMM_WORLD): - main() Rank (3, MPI_COMM_WORLD): Call stack within LAM: Rank (3, MPI_COMM_WORLD): - MPI_Recv() Rank (3, MPI_COMM_WORLD): - MPI_Barrier() Rank (3, MPI_COMM_WORLD): - main() Rank (5, MPI_COMM_WORLD): Call stack within LAM: Rank (5, MPI_COMM_WORLD): - MPI_Recv() Rank (5, MPI_COMM_WORLD): - MPI_Barrier() Rank (5, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 6, MPI_COMM_WORLD) Rank (6, MPI_COMM_WORLD): Call stack within LAM: Rank (6, MPI_COMM_WORLD): - MPI_Recv() Rank (6, MPI_COMM_WORLD): - MPI_Barrier() Rank (6, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 11, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 12, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 13, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 14, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 7, MPI_COMM_WORLD) Rank (9, MPI_COMM_WORLD): Call stack within LAM: Rank (9, MPI_COMM_WORLD): - MPI_Recv() Rank (9, MPI_COMM_WORLD): - MPI_Barrier() Rank (9, MPI_COMM_WORLD): - main() Rank (7, MPI_COMM_WORLD): Call stack within LAM: Rank (7, MPI_COMM_WORLD): - MPI_Recv() Rank (7, MPI_COMM_WORLD): - MPI_Barrier() Rank (7, MPI_COMM_WORLD): - main() Rank (8, MPI_COMM_WORLD): Call stack within LAM: Rank (8, MPI_COMM_WORLD): - MPI_Recv() Rank (8, MPI_COMM_WORLD): - MPI_Barrier() Rank (8, MPI_COMM_WORLD): - main() Rank (10, MPI_COMM_WORLD): Call stack within LAM: Rank (10, MPI_COMM_WORLD): - MPI_Recv() Rank (10, MPI_COMM_WORLD): - MPI_Barrier() Rank (10, MPI_COMM_WORLD): - main() Rank (12, MPI_COMM_WORLD): Call stack within LAM: Rank (12, MPI_COMM_WORLD): - MPI_Recv() Rank (12, MPI_COMM_WORLD): - MPI_Barrier() Rank (12, MPI_COMM_WORLD): - main() Rank (11, MPI_COMM_WORLD): Call stack within LAM: Rank (11, MPI_COMM_WORLD): - MPI_Recv() Rank (11, MPI_COMM_WORLD): - MPI_Barrier() Rank (11, MPI_COMM_WORLD): - main() Rank (14, MPI_COMM_WORLD): Call stack within LAM: Rank (14, MPI_COMM_WORLD): - MPI_Recv() Rank (14, MPI_COMM_WORLD): - MPI_Barrier() Rank (14, MPI_COMM_WORLD): - main() Rank (13, MPI_COMM_WORLD): Call stack within LAM: Rank (13, MPI_COMM_WORLD): - MPI_Recv() Rank (13, MPI_COMM_WORLD): - MPI_Barrier() Rank (13, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 15, MPI_COMM_WORLD) Rank (15, MPI_COMM_WORLD): Call stack within LAM: Rank (15, MPI_COMM_WORLD): - MPI_Recv() Rank (15, MPI_COMM_WORLD): - MPI_Barrier() Rank (15, MPI_COMM_WORLD): - main() From chemistry-request@server.ccl.net Wed May 15 13:53:40 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FHres17903 for ; Wed, 15 May 2002 13:53:40 -0400 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id g4FHrcI273430; Wed, 15 May 2002 10:53:39 -0700 Date: Wed, 15 May 2002 10:53:38 -0700 (PDT) From: Roy Jensen To: chemistry@ccl.net Subject: MRCI in Gaussian? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Is it possible to do a multireference CI calculation using Gaussian 98? If so, could someone provide a typical input file. Roy Jensen I will summarize to the List. From chemistry-request@server.ccl.net Wed May 15 14:05:21 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FI5Ls18157 for ; Wed, 15 May 2002 14:05:21 -0400 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id g4FI5JI65362; Wed, 15 May 2002 11:05:20 -0700 Date: Wed, 15 May 2002 11:05:19 -0700 (PDT) From: Roy Jensen To: chemistry@ccl.net Subject: Hybridization... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Students leave first-year chemistry with the belief that hybridization is the gospel wrt bonding. So much so that bonding in diatomics, HCl, Cl2, etc., is sometimes taught as occuring through hybridized orbitals: experiment, symmetry, and ab-initio calcs indicate otherwise. Is there an article that discusses this at the non-specialist (graduate/ undergraduate) level? I vaguely recall a website that details this for HCl. Can anyone point me to the website again? Roy Jensen I will summarize to the List. From chemistry-request@server.ccl.net Wed May 15 15:23:18 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FJNIs20492 for ; Wed, 15 May 2002 15:23:18 -0400 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id g4FJNGI73890; Wed, 15 May 2002 12:23:16 -0700 Date: Wed, 15 May 2002 12:23:16 -0700 (PDT) From: Roy Jensen To: chemistry@ccl.net Subject: Maximum in PES scans... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII PES scans often show a maximum along the dissociation coordinate. What is the physical interpretation of this maximum? Roy Jensen I will summarize to the List. From chemistry-request@server.ccl.net Wed May 15 17:21:55 2002 Received: from aspx-smtp.netaspx.com ([137.66.136.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4FLLts23929 for ; Wed, 15 May 2002 17:21:55 -0400 Received: from aspx-mail.netaspx.com ([137.66.136.3]) by aspx-smtp.netaspx.com (Lotus Domino Release 5.0.9) with SMTP id 2002051516214640:154981 ; Wed, 15 May 2002 16:21:46 -0500 To: chemistry@ccl.net Subject: Summary: Loacting a transition state X-Mailer: Lotus Notes Release 5.0.4a July 24, 2000 From: Genzo.Tanaka@netaspx.com Message-ID: Date: Wed, 15 May 2002 16:21:47 -0500 MIME-Version: 1.0 X-MIMETrack: Serialize by Router on ASPX-Mail/netASPx(Release 5.0.6a |January 17, 2001) at 05/15/2002 04:21:48 PM, Itemize by SMTP Server on ASPX-SMTP/netASPx(Release 5.0.9 |November 16, 2001) at 05/15/2002 04:21:46 PM, Serialize by Router on ASPX-SMTP/netASPx(Release 5.0.9 |November 16, 2001) at 05/15/2002 04:21:52 PM Content-Type: multipart/mixed; boundary="=_mixed 0075789C85256BBA_=" --=_mixed 0075789C85256BBA_= Content-Type: multipart/alternative; boundary="=_alternative 0075789C85256BBA_=" --=_alternative 0075789C85256BBA_= Content-Type: text/plain; charset="us-ascii" Hi all, I would like to thank those who responded my questions on locating a transition state. All of them are quite instructive for me. Special thanks go to David Gallagher and James J.P. Stewart who actually located the transition state for my system (See below). I could also locate a transition state. Responses exhibited wide spectra of perception of the transition state search: |---- Easy David Gallagher, James J.P. Stewart, David Close | |---- Accurate methods Valentine Ananikov, Alexander Martins | |---- Difficult Irene Newhouse, Bin Shan | |---- Black art Markus Dittrich | |----More than one TS Stephen Bowlus | |---- Existence of TS David Shobe David Gallagher did find the transition state for the hydrolysis reaction of acetylcholine with water using PM5 method in CAChe version of MOPAC 2002. Using PM3 in MOPAC, James Stewart proved that the structure derived > from the above PM5 method has only one negative frequency. I used the PM5 TS structure with PM3 in Gaussin98 [#P RHF/PM3 opt=(TS,CalcFC)], however, the job stopped yielding two negative frequencies (Optimization stopped. -- Wrong number of Negative eigenvalues: Desired= 1 Actual= 2 ). The suggestion by Valentine Ananikov, Alexander Martins and Bin Shan [opt=(modredundant,TS,noeigen)] solved this problem. In the above, we assume that there is a transition state for a given reaction. David Shobe raised a question whether or not the transition structure exists, pointing out a no barrier reaction for TiCl4 + H2O --> TiCl4(H2O). The existence of a TS may be considered from the free energies for the reactants and the products. If the products are higher in free energy than the reactants, there must be a barrier. However, for the opposite case, there is no grantee that the barrier exists. Are anyone aware of any criteria for the existence of the transition state? Regards, Genzo My posting was Hi, I am trying to locate a transition state for a system about 30 atoms using an empirical method. So far I haven't had any success. I would appreciate if you could give me any suggestions. I am interested in a hydrolysis reaction pathway, using PM3 in Gaussian 98: R-C-O-C-R' + H*-O'H ---> R-C-O-H* + H-O'-C-R' I have done the following: 1) opt=Ts ; This always failed due to incorrect number of negative frequencies. 2) Scan ; I have not tried much. 3) opt=ModRedundant: Scanning succeeded, but the population analysis after the scanning seemed failed. The output did not indicate why it failed, but the heading of population analysis appeared, followed by signal 11 error. 4) opt=qst2; There is (are) one or two statement(s) "stationary point was found" (the distances were the same for all, but the angles and torsions were slightly different in the two stationary points) in the output, but the optimization (?) kept going and failed; Optimization aborted --- No acceptable step or Inconsistency: ModMin= 2. I optimized two reactant molecules individually and moved them close to make a reaction. The products were also optimized. The order of the atoms are exactly the same. Thanks, Genzo Tanaka Here are the responses for my questions *** This should be easy, but what exactly is R-C-O-C-R meant to be? An ether (R-CH2-0-CH2-R) or an anhydride (R-CO-O-CO-R) or what? If you send me the exact structures, I'll try and run it for you. David Gallagher *** Although, the old MOPAC PM3 hamiltonian seems to have difficulty in locating a transition state for your reaction, the latest PM5 method in MOPAC 2002 nailed it first go with a saddle calculation. The attached Zip file includes pictures and the MOPAC output of the gas phase transition state for your hydrolysis reaction. In the picture, the bond thickness indicates the relative bond order and the numbers are the atom distances in Angstroms. The force calculation shows a single negative vibration and the IRCs verify that this is the only transition state along this particular reaction path for the concerted reaction. The new PM5 method has been re-parameterized for higher accuracy and MOPAC 2002 includes new algorithms. It seems to be much faster and more reliable for finding transition states than the older MOPAC methods such as PM3 and AM1. Also, I was able to model the transition state with the COSMO water solvent field. As expected, the energy was much lower. Although, the old PM3 seems to work fine for a simple ester hydrolysis, the charged quaternary ammonium group seems to confuse it. The best transition state structure I got out of PM3 had a second negative vibration due to a methyl rotation. However, the bond orders, atom distances and negative vibration all indicated a proton transfer only (not the C-O bond break), so I don't think that this was the correct transition state for the reaction. If you need more information about MOPAC 2002 you can view the manual at http://www.cachesoftware.com/techsupport/mopac/ The pictures and calculations were done with the CAChe version of MOPAC 2002. I hope this helps Regards David Gallagher, Fujitsu *** Attached are two MOPAC data sets. In the first, bug.mop, I used David's geometry from his PM5 result. I changed PM5 to PM3, and ran the TS. This runs without problem. From the ARC file, I made bug1.mop. This runs the FORCE calculation and confirms that there is exactly 1 imaginary frequency. So, in summary, both PM3 and PM5 (and, I assume, all the other methods) give more-or-less the same transition state. As far as the system being difficult, my apologies, but what was difficult? (I use MOPAC as stand alone, because I'm more comfortable with that.) Best wishes, Jimmy *** I'm not really an expert on TS optimizations, although I was willing to help someone who was even further back on the learning curve than I was. And I've never had much luck with opt=qst2. You've checked that the atoms correspond properly between reactant and product, which is good. I think sometimes opt=qst2 has trouble if the path from reactants to products is indirect: opt=qst2 will try to find a path that takes the reagent *through* the other molecule, instead of going *around* it. I don't even know what signal 11 error is. It sounds like a Unix message. Two possibilities that come to mind are that there was a time limit for the job which ran out, or that the system administrator "killed" it for some reason. Given what you've told me, I would try the opt=modredundant again, after I found out what Signal 11 error means and had done whatever was necessary to avoid it. Oh, and you may want to send your question to the CCL list, since someone else may have a better idea! --Dave S. *** I think of these as being multi-step reactions. Maybe you're trying to find a TS that doesn't exist, because you skipped a step? > I am interested in a hydrolysis reaction pathway, using PM3 in > Gaussian 98: > > R-C-O-C-R' + H*-O'H ---> R-C-O-H* + H-O'-C-R' > It turns out that in one of the examples that poisoned my mind against opt=qst2, the transition state was not found for an equally good reason: the reaction was an association reaction TiCl4 + H2O --> TiCl4(H2O), and as it turns out the energy is monotonic from reactants to product: there is no activation barrier. Anyway, I wish you luck in solving your transition state puzzles. --David Shobe *** Transition states are always a difficult problem. You will have to be pretty close to the actual state to get it to optimize. Yes, that's as circular as it sounds! I would strongly urge you to search the literature for similar transition states & use those structures to guide you in your initial guess. Irene Newhouse *** The results of the first step are very common. But this is not a problem. You must look at the output with software that will show the vibration frequencies. Only one of them will involve motion along the coordinates of the reaction path you are trying to follow. Look at the other negative frequencies. You will see that they have nothing to do with your reaction coordinates. It may be some low frequency involving the wagging of an exo-cyclic group. Find the atoms involved in the unwanted motion. Go to the Standard Orientation near the end of the output and disturb these coordinates a little (maybe change them 0.1 A). Run the OPT (TS) again with these new coordinates. You will quickly come down off the local minimia you are stuck on and be at the true TS. Regards, Dave Close. *** First, I would further research whether the (apparently) four center reaction that is being done here is really feasible (or is that the question you are trying to answer?) I would guess there are two TS that are encountered in this reaction. For example, addition of water to form RCO- ... +H2O'CR' (tight) ion pair, followed by hydrogen transfer to form the two neutral species. Regardless of the mechanism, I would use something like SADDLE in Mopac or CHAIN in Ampac to get an estimate of the possible TS, then refine the TS using eigenvector following or some gentle gradient reduction method. The general idea is to come up with an approximate starting geometry that is somewhere on the reaction coordinate (not just two molecules in space; this is where some inference about the probable mechanism is needed); a final product geometry that is on the other side of the hump, and then work both ends against the middle to find an approximate TS. Then refine. Then do IRC calculations to assure that you are actually doing the chemistry you think. There is a section in the Mopac manual about all this, and it is included in an early JCAMD (around 1996, I think). Sorry if this is redundant to what you know ... Stephen Bowlus *** I can't tell you much concrete. Finding transition states aka looking for saddle point is a black art. I am currently doing something similar for a 20 atom system using ab initio methods and don't have much experience with semi-empirical ones. In general you have to start as close as possible to the true transitions state when starting a saddle point search. Otherwise you won't be able to get it. You could make an educated guess or first constrain some degrees of freedom you think are important while looking for saddle points. Comparing the energies can give you a hint in which direction you have to go. Just moving two optimized molecules close to each other won't do in 99.9% of the cases. Your transition state will be 'something inbetween'. Maybe a partial transfer of your groups, partial bond formation... You will have to play around. If you have a good guess about a possible reaction coordinate contrain you system such that you mimick the reaction, monitoring the energies. That should allow you to position your system as close to the transition state as possible. In any case. Once you think you found the transition state you have to make sure that you have found a saddle point by recalculating your hessian matrix which has to have one and only one imaginary frequency. Otherwise you're back to where you were before. Good luck, Markus Dittrich *** opt(TS, noeigentest) should help. I suggest you HF/3-21G instead of PM3 for preliminary calculations and B3LYP/6-31G* for more accurate data. regards, Valentin Ananikov. *** Hi, First of all, it's a good idea use DFT methods instead of semiempirical ones. The results ara more reliable. You can use the keyword OPT=(TS, NoEigenTest) with a good guess for the geometry. Futhermore, the keyword OPT=QST3 it's a good option too. Don't forget use a good basis set, like 6-31G. Try these sugestions. Good luck, Alexander Martins. *** Hi, Genzo,try something like this # opt(modredundant,TS,noeigen,CalcFC) rb3lyp/6-31g(d) nosymm CalcFC calculates the initial force constants be computed at the first point and helps to determine which direction the atoms are to to move.The keyword noeigen and nosymm are also important. And it is also extremely important to specify a good initial guess.Finding transition state is by no means an easy task...according to my experience. Good luck. Bin Shan *** --=_alternative 0075789C85256BBA_= Content-Type: text/html; charset="us-ascii"
Hi all,

I would like to thank those who responded my questions on locating a transition state.  All of them are quite instructive for me. Special thanks go to  David Gallagher and James J.P. Stewart who actually located the transition state for my system (See below). I could also locate a transition state.

Responses exhibited wide spectra of perception of the transition state search:

|---- Easy                                              David Gallagher, James J.P. Stewart, David Close
|
|---- Accurate methods                    Valentine Ananikov, Alexander Martins
|
|---- Difficult                                          Irene Newhouse, Bin Shan
|
|---- Black art                                      Markus Dittrich
|
|----More than one TS                     Stephen Bowlus
|
|---- Existence of TS                        David Shobe

 David Gallagher did find the transition state for the hydrolysis reaction of acetylcholine with water using PM5 method in CAChe version of MOPAC 2002. Using PM3 in MOPAC, James Stewart proved that the structure derived from the above PM5 method has only one negative frequency. I used the PM5 TS structure with PM3 in Gaussin98 [#P RHF/PM3 opt=(TS,CalcFC)], however, the job stopped yielding two negative frequencies (Optimization stopped.   -- Wrong number of Negative eigenvalues: Desired=  1 Actual=  2 ). The suggestion by Valentine Ananikov, Alexander Martins and Bin Shan  [opt=(modredundant,TS,noeigen)] solved this problem.

In the above, we assume that there is a transition state for a given reaction. David Shobe raised a question whether or not the transition structure exists, pointing out a no barrier reaction for TiCl4 + H2O --> TiCl4(H2O). The existence of a TS may be considered from the free energies for the reactants and the products. If the products are higher in free energy than the reactants, there must be a barrier. However, for the opposite case, there is no grantee that the barrier exists. Are anyone aware of any criteria for the existence of the transition state?

Regards,


Genzo



My posting was

Hi,

I am trying to locate a transition state for a system about 30 atoms using an empirical
method. So far I haven't had any success. I would appreciate if you could
give me any suggestions.

I am interested in a hydrolysis reaction pathway, using PM3 in Gaussian 98:

R-C-O-C-R' + H*-O'H ---> R-C-O-H*  + H-O'-C-R'

I have done the following:
1) opt=Ts ; This always failed due to incorrect number of negative
frequencies.
2) Scan  ; I have not tried much.
3) opt=ModRedundant: Scanning succeeded, but the population analysis after
the scanning seemed failed. The output did not indicate why it failed, but
the heading of population analysis appeared, followed by signal 11 error.
4) opt=qst2; There is (are) one or two statement(s) "stationary point was
found" (the distances were the same for all, but the angles and torsions were slightly different in the two stationary points) in the output, but the optimization (?) kept going and failed; Optimization aborted
--- No acceptable step or Inconsistency: ModMin=   2.

I optimized two reactant molecules individually and moved them close to make
a reaction. The products were also optimized. The order of the atoms are
exactly the same.


Thanks,

Genzo Tanaka


Here are the responses for my questions

***
This should be easy, but what exactly is R-C-O-C-R meant to be?

An ether (R-CH2-0-CH2-R) or an anhydride (R-CO-O-CO-R) or what?

If you send me the exact structures, I'll try and run it for you.

David Gallagher   <dgallagher@cachesoftware.com>
***

Although, the old MOPAC PM3 hamiltonian seems to have difficulty in locating a transition state for your reaction, the latest PM5 method in MOPAC 2002 nailed it first go with a saddle calculation.

The attached Zip file includes pictures and the MOPAC output of the gas phase transition state for your hydrolysis reaction. In the picture, the bond thickness indicates the relative bond order and the numbers are the atom distances in Angstroms. The force calculation shows a single negative vibration and the IRCs verify that this is the only transition state along this particular reaction path for the concerted reaction. The new PM5 method has been re-parameterized for higher accuracy and MOPAC 2002 includes new algorithms. It seems to be much faster and more reliable for finding transition states than the older MOPAC methods such as PM3 and AM1. Also, I was able to model the transition state with the COSMO water solvent field. As expected, the energy was much lower.

Although, the old PM3 seems to work fine for a simple ester hydrolysis, the charged quaternary ammonium group seems to confuse it. The best transition state structure I got out of PM3 had a second negative vibration due to a methyl rotation. However, the bond orders, atom distances and negative vibration all indicated a proton transfer only (not the C-O bond break), so I don't think that this was the correct transition state for the reaction.

If you need more information about MOPAC 2002 you can view the manual at http://www.cachesoftware.com/techsupport/mopac/ The pictures and calculations were done with the CAChe version of MOPAC 2002.

I hope this helps
Regards
David Gallagher, Fujitsu   <dgallagher@cachesoftware.com>
***
Attached are two MOPAC data sets.  In the first, bug.mop, I used David's
geometry from his PM5 result.  I changed PM5 to PM3, and ran the TS.  This
runs without problem.

From the ARC file, I made bug1.mop.  This runs the FORCE calculation and
confirms that there is exactly 1 imaginary frequency.

So, in summary, both PM3 and PM5 (and, I assume, all the other methods)
give more-or-less the same transition state.

As far as the system being difficult, my apologies, but what was difficult?

(I use MOPAC as stand alone, because I'm more comfortable with that.)

Best wishes,

Jimmy   <jstewart@fujitsu.com>
***

I'm not really an expert on TS optimizations, although I was willing to help
someone who was even further back on the learning curve than I was.  And
I've never had much luck with opt=qst2.  You've checked that the atoms
correspond properly between reactant and product, which is good.  I think
sometimes opt=qst2 has trouble if the path from reactants to products is
indirect: opt=qst2 will try to find a path that takes the reagent *through*
the other molecule, instead of going *around* it.

I don't even know what signal 11 error is.  It sounds like a Unix message.
Two possibilities that come to mind are that there was a time limit for the
job which ran out, or that the system administrator "killed" it for some
reason.

Given what you've told me, I would try the opt=modredundant again, after I
found out what Signal 11 error means and had done whatever was necessary to
avoid it.  Oh, and you may want to send your question to the CCL list, since
someone else may have a better idea!

--Dave S.   <dshobe@sud-chemieinc.com>
***
I think of these as being multi-step reactions.  Maybe you're trying to find
a TS that doesn't exist, because you skipped a step?  

> I am interested in a hydrolysis reaction pathway, using PM3 in
> Gaussian 98:
>
> R-C-O-C-R' + H*-O'H ---> R-C-O-H* + H-O'-C-R'
>

It turns out that in one of the examples that poisoned my mind against
opt=qst2, the transition state was not found for an equally good reason: the
reaction was an association reaction TiCl4 + H2O --> TiCl4(H2O), and as it
turns out the energy is monotonic from reactants to product: there is no
activation barrier.

Anyway, I wish you luck in solving your transition state puzzles.

--David Shobe   <dshobe@sud-chemieinc.com>
***
Transition states are always a difficult problem.  You will have to be
pretty close to the actual state to get it to optimize.  Yes, that's as
circular as it sounds!

I would strongly urge you to search the literature for similar transition
states & use those structures to guide you in your initial guess.

Irene Newhouse   <einew@hotmail.com>
***
The results of the first step are very common.  But this is not a problem.
You must look at the output with software that will show the vibration
frequencies.  Only one of them will involve motion along the coordinates
of the reaction path you are trying to follow.  Look at the other negative
frequencies.  You will see that they have nothing to do with your reaction
coordinates.  It may be some low frequency involving the wagging of an
exo-cyclic group.  Find the atoms involved in the unwanted motion.  Go to
the Standard Orientation near the end of the output and disturb these
coordinates a little (maybe change them 0.1 A).  Run the OPT (TS) again
with these new coordinates.  You will quickly come down off the local
minimia you are stuck on and be at the true TS.
 Regards, Dave Close.   <closed@ACCESS.ETSU.EDU>
***

First, I would further research whether the (apparently) four center reaction that is being done here is really feasible (or is that the question you are trying to answer?)  I would guess there are two TS that are encountered in this reaction.  For example, addition of water to form RCO-  ... +H2O'CR' (tight) ion pair, followed by hydrogen transfer to form the two neutral species.
 
Regardless of the mechanism, I would use something like SADDLE in Mopac or CHAIN in Ampac to get an estimate of the possible TS, then refine the TS using eigenvector following or some gentle gradient reduction method.  The general idea is to come up with an approximate starting geometry that is somewhere on the reaction coordinate (not just two molecules in space; this is where some inference about the probable mechanism is needed); a final product geometry that is on the other side of the hump, and then work both ends against the middle to find an approximate TS.  Then refine.  Then do IRC calculations to assure that you are actually doing the chemistry you think.  There is a section in the Mopac manual about all this, and it is included in an early JCAMD (around 1996, I think).
 
Sorry if this is redundant to what you know ...
 
Stephen Bowlus    <stephen.bowlus@lionbioscience.com>
***
I can't tell you much concrete. Finding transition states aka
looking for saddle point is a black art. I am currently
doing something similar for a 20 atom system using ab initio methods and
don't have much experience with semi-empirical ones.

In general you have to start as close as possible to the true
transitions state when starting a saddle point search. Otherwise
you won't be able to get it. You could make an educated guess or
first constrain some degrees of freedom you think are important
while looking for saddle points. Comparing the energies can give
you a hint in which direction you have to go.
Just moving two optimized molecules close to each other won't
do in 99.9% of the cases. Your transition state will be
'something inbetween'. Maybe a partial transfer of your groups,
partial bond formation... You will have to play around.
If you have a good guess about a possible reaction coordinate
contrain you system such that you mimick the reaction, monitoring
the energies. That should allow you to position your system as
close to the transition state as possible.

In any case. Once you think you found the transition state you
have to make sure that you have found a saddle point
by recalculating your hessian matrix which has to have one and
only one imaginary frequency. Otherwise you're back to where
you were before.


Good luck,
Markus Dittrich   <markus@ks.uiuc.edu>
***
opt(TS, noeigentest) should help.

I suggest you HF/3-21G instead of PM3 for preliminary calculations
and B3LYP/6-31G* for more accurate data.

regards, Valentin Ananikov.   <val@cacr.ioc.ac.ru>
***
Hi,

       First of all, it's a good idea use DFT methods instead of
semiempirical ones. The results ara more reliable.

       You can use the keyword OPT=(TS, NoEigenTest) with a good guess
for the geometry. Futhermore, the keyword OPT=QST3 it's a good option
too. Don't forget use a good basis set, like 6-31G.

       Try these sugestions.

       Good luck,

       Alexander Martins.   <alex.msilva@uol.com.br>
***
Hi,
   Genzo,try something like this

# opt(modredundant,TS,noeigen,CalcFC) rb3lyp/6-31g(d) nosymm

CalcFC calculates the initial force constants be computed at the first point
and helps to determine which direction the atoms are to to move.The keyword
noeigen and nosymm are also important.
  And it is also extremely important to specify a good initial
guess.Finding transition state is by no means an easy task...according to my
experience.
  Good luck.

Bin Shan   <philipbshan@hotmail.com>
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