From borkent@caos.kun.nl Wed Jul 10 03:59:30 1996 Received: from cammsg1.caos.kun.nl for borkent@caos.kun.nl by www.ccl.net (8.7.5/950822.1) id DAA14907; Wed, 10 Jul 1996 03:31:24 -0400 (EDT) Received: from cammsg5 (cammsg5.caos.kun.nl [131.174.88.5]) by cammsg1.caos.kun.nl (8.7.1/8.7.1) with SMTP id JAA00532 for ; Wed, 10 Jul 1996 09:31:16 +0200 (MDT) From: Hens Borkent Message-Id: <199607100731.JAA00532@cammsg1.caos.kun.nl> Subject: M: negative freq's. To: chemistry@www.ccl.net Date: Wed, 10 Jul 1996 09:31:15 +0200 (MDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL-ers, I mis-sent my reaction last week, but I think it is still relevant, so I repeat it here: In case you want to get rid of spurious negative frequencies (which is often not necessary for the conclusions you draw >from a calculation) it helps if you visualize the movement involved (MOLDEN on unix machines, Re_view on PC's). I have had examples where these frequencies corresponded to small deviations from symmetry, and it helped to start with a perfectly symmetrical structure. E.g. I observed in an sp3-sp3 chain a motion corresponding to rotation around the central bond, with a negative frequency, after minimization. It disappeared after changing the dihedral angles from 179.5 to 179.9999. (and a full minimization of course, although you can do a step in between in which you fix the symmetry). Best regards, -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html From borkent@caos.kun.nl Wed Jul 10 04:13:07 1996 Received: from cammsg1.caos.kun.nl for borkent@caos.kun.nl by www.ccl.net (8.7.5/950822.1) id DAA14907; Wed, 10 Jul 1996 03:31:24 -0400 (EDT) Received: from cammsg5 (cammsg5.caos.kun.nl [131.174.88.5]) by cammsg1.caos.kun.nl (8.7.1/8.7.1) with SMTP id JAA00532 for ; Wed, 10 Jul 1996 09:31:16 +0200 (MDT) From: Hens Borkent Message-Id: <199607100731.JAA00532@cammsg1.caos.kun.nl> Subject: M: negative freq's. To: chemistry@www.ccl.net Date: Wed, 10 Jul 1996 09:31:15 +0200 (MDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL-ers, I mis-sent my reaction last week, but I think it is still relevant, so I repeat it here: In case you want to get rid of spurious negative frequencies (which is often not necessary for the conclusions you draw >from a calculation) it helps if you visualize the movement involved (MOLDEN on unix machines, Re_view on PC's). I have had examples where these frequencies corresponded to small deviations from symmetry, and it helped to start with a perfectly symmetrical structure. E.g. I observed in an sp3-sp3 chain a motion corresponding to rotation around the central bond, with a negative frequency, after minimization. It disappeared after changing the dihedral angles from 179.5 to 179.9999. (and a full minimization of course, although you can do a step in between in which you fix the symmetry). Best regards, -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html From ncapron@ccr.jussieu.fr Wed Jul 10 04:48:05 1996 Received: from shiva.jussieu.fr for ncapron@ccr.jussieu.fr by www.ccl.net (8.7.5/950822.1) id DAA14825; Wed, 10 Jul 1996 03:20:09 -0400 (EDT) Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id JAA15741 for ; Wed, 10 Jul 1996 09:20:04 +0200 (METDST) Received: from (ncapron@localhost) by moka.ccr.jussieu.fr (8.7.5/jtpda-5.2) id JAA130345 for chemistry@www.ccl.net; Wed, 10 Jul 1996 09:20:03 +0200 Date: Wed, 10 Jul 1996 09:20:03 +0200 From: ncapron@ccr.jussieu.fr (Nathalie CAPRON) Message-Id: <199607100720.JAA130345@moka.ccr.jussieu.fr> To: chemistry@www.ccl.net Subject: About bulk modulus Dear all, Few weeks ago I sent this following message I give you now answers I got : Thanks to these persons ! Good holidays ........... > Dear all, > I should need for my study a complete > ( or near ) list of the calculations carried out on silicon > which give the theoritical values for the elastic constants > and especially bulk modulus > I have already some papers but I am affraid to miss some > important information. > Could someone give me the references of these papers ? > Thank you in advance > Nathalie Capron Laboratoire de Chimie Physique Matiere et Rayonnement 11, rue Pierre et Marie Curie 75231 Paris Cedex 01 ncapron@ccr.jussieu.fr ----------------------------------------------------------------------------------- Hi Nathalie, see for instance: O.H. Nielsen and R.M. Martin, Phys.Rev. B 32, 3792(1985) D.J. Chadi and R.M.Martin, Sol.State.Comm. 19, 643(1976) and references therein. Bye, -- Leonardo De Maria SISSA | Universita di Trieste Scuola Internazionale | Dipartimento di Fisica Teorica Superiore di Studi Avanzati | Strada Costiera 11 via Beirut 2-4, Grignano | Miramare-Grignano I-34014 - Trieste | I-34014 - Trieste tel: +39 40 3787506 | tel: +39 40 224265 fax: 3787528 | fax: 224601 e-mail:demaria@neumann.sissa.it | e-mail : demaria@vstst0.ts.infn.it ------------------------------------------------------------------------------------ Hello Nathalie; Here are some references about Si calculations. I think they contain info about the bulk modulus and also other elastic constants: E. R. Cowley, Phys. Rev. Lett. 60 (1988) 2379 B. W. Dodson, Phys. Rev. B 35 (1987) 2795 M. T. Yin and M. L. Cohen, Phys. Rev. B 24 (1981) 2303 M. T. Yin and M. L. Cohen, Phys. Rev. B 26 (1982) 5668 M. T. Yin and M. L. Cohen, Phys. Rev. B 29 (1984) 6996 Regards, Rene Fournier fournier@physics.unlv.edu ------------------------------------------------------------------------------------- Tres chere Nathalie, J'ai entre les mains un excellent article concernqnt l'oxyde de Ti. C'est quelque peu different de ton systeme d'etude, mais toute la procedure de calcul de bulk modulus et autre snt reportes dans cet article. Cela peut t'aider. "Structural and electronic properties of titanium dioxide", K. M. Glassford et J. R. Chelikowsky, Physical Review B, vol 46, N 3, p.1284-1298, 1992. Frederic Bouyer -- __________________________________________________________________________ Frederic Bouyer Groupe Chimie Corrosion - RNE-EMA EDF-DER Les Renardieres Tel: (33) 1-60-73-69-65 Route de Sens, Ecuelles, BP1 Fax: (33) 1-60-73-68-89 77250 MORET-SUR-LOING - FRANCE Email: Frederic.Bouyer@der.edfgdf.fr __________________________________________________________________________ -------------------------------------------------------------------------------------- From wieland@btm2d1.mat.uni-bayreuth.de Wed Jul 10 06:13:06 1996 Received: from btm2d1.mat.uni-bayreuth.de for wieland@btm2d1.mat.uni-bayreuth.de by www.ccl.net (8.7.5/950822.1) id FAA00929; Wed, 10 Jul 1996 05:25:05 -0400 (EDT) From: Received: by btm2d1.mat.uni-bayreuth.de (IBM OS/2 SENDMAIL VERSION 1.3.14/2.12um) id AA0800; Wed, 10 Jul 96 11:24:55 +0200 Message-Id: <9607100924.AA0800@btm2d1.mat.uni-bayreuth.de> Mime-Version: 1.0 Date: Wed, 10 Jul 96 10:04:43 +0200 To: MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemistry@www.ccl.net Subject: Summary: Toplogical indices and active sites X-Mailer: Ultimedia Mail/2 Lite, IBM T. J. Watson Research Center Content-Id: <246_96_1_837007483> Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear netters, last week I posted a question about the connections between topological indices, similarity, screening and drug design. There were 9 summarizable replies most of which were rather lengthy. In order to avoid filling your mail boxes with too much trash, this is just an announcement about the availability of the summary. You can get it from: http://www.mathe2.uni-bayreuth.de/thomas/summary.html or I send it to you as e-mail on your request. My deep thanks go to all who responded. I think we should keep the track on this issue. Best regards, Thomas Wieland From guillem@gauss.uib.es Wed Jul 10 06:17:41 1996 Received: from gauss.uib.es for guillem@gauss.uib.es by www.ccl.net (8.7.5/950822.1) id FAA00964; Wed, 10 Jul 1996 05:33:05 -0400 (EDT) Received: by gauss.uib.es; id AA17705; Wed, 10 Jul 1996 11:31:23 +0100 Sender: guillem@gauss.uib.es Message-Id: <31E3867B.1372@gauss.uib.es> Date: Wed, 10 Jul 1996 11:31:23 +0100 From: "Guillem A. Sunyer" Organization: Departament de Quimica, Universitat de les Illes Balears X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.2 alpha) Mime-Version: 1.0 To: Computational Chemistry List Subject: unit cell generation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I post the following query on behalf of my colleague Dr. Pablo Ballester: Dear CCL members, I will like to know if someone is aware of a program able to generate a unit cell from X-ray data (internal coordinates, a b c values, angles , number of molecules per unit cell etc.) that is, drawing a box representing the cell and also the molecules inside it. I will summarize to the net if there is interest. Please e-mail me directly. Pablo Ballester +++++++++++++++++++++++++++++++++++++++++ + Pablo Ballester, Associate Professor + + Universitat de les Illes Balears + + Departamento de Quimica + + 07071-Palma de Mallorca, SPAIN + + phone: 34 71 173265 + + fax: 34 71 173426 + + E-mail: dqupbb0@ps.uib.es + +++++++++++++++++++++++++++++++++++++++++ -- Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS E-07071-Palma de Mallorca, SPAIN. E-mail: guillem@gauss.uib.es Tel: + 34 71 173498 Fax: + 34 71 173426 WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html From tmmec@fcindy5.NCIFCRF.GOV Wed Jul 10 06:19:48 1996 Received: from fcindy5.NCIFCRF.GOV for tmmec@fcindy5.NCIFCRF.GOV by www.ccl.net (8.7.5/950822.1) id GAA01092; Wed, 10 Jul 1996 06:07:37 -0400 (EDT) Received: by fcindy5.NCIFCRF.GOV (940816.SGI.8.6.9/930416.SGI.AUTO) id GAA23705; Wed, 10 Jul 1996 06:10:46 -0700 From: "tmmec" Message-Id: <9607100610.ZM23703@fcindy5.NCIFCRF.GOV> Date: Wed, 10 Jul 1996 06:10:42 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: cachau@fcindy5.NCIFCRF.GOV Subject: TMMeC: Call for Papers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii TMMeC CALL FOR PAPERS A final agreement has been reached between TMMeC and Elsevier Publishers for the joint publication of articles in TMMeC and THEOCHEM. The text of the agreement can be found in the WWW pages of TMMeC and THEOCHEM. We believe that this mechanism of publication will greatly reduce the lag between referees acceptance and the public access of a paper. An open discussion will follow the publication of a paper, thus bringing together the advantages of a traditional journal and those of an electronic conference. Please read the Publication Policy in TMMeC for more details on this mechanism of publication. TMMeC is a non-commercial Web publication developed by the Montevideo Theoretical Chemistry Lab, Universidad de la Republica, Montevideo, Uruguay. TMMeC is a distributed resource. Please choose the mirror nearest to your place to access TMMeC pages. TMMeC Mirrors: http://bilbo.edu.uy/agora/Mirrors.html http://uqbar.ncifcrf.gov/agora/Mirrors.html THEOCHEM: http://www.elsevier.nl/section/chemical/theochem/ ---------------- From wallenborn@phys.chem.ethz.ch Wed Jul 10 06:21:58 1996 Received: from bernina.ethz.ch for wallenborn@phys.chem.ethz.ch by www.ccl.net (8.7.5/950822.1) id FAA01022; Wed, 10 Jul 1996 05:49:37 -0400 (EDT) Received: from helios (actually helios-chem.ethz.ch) by bernina.ethz.ch with SMTP inbound; Wed, 10 Jul 1996 11:49:15 +0200 Received: from jetson by helios.ethz.ch id AA09738; Wed, 10 Jul 1996 11:49:13 +0200 Sender: wall@phys.chem.ethz.ch Message-Id: <31E37C98.3CCE@phys.chem.ethz.ch> Date: Wed, 10 Jul 1996 11:49:12 +0200 From: Ernst Wallenborn Organization: ETH Zuerich X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: [Q] MOLCAS (SLAPAF) question X-Url: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, I have a problem with the slapaf input (molcas 3.0). It's the following: I'm trying to do a casscf geometry optimization in molcas (i don't feel like doing it in g94 with a different basis set and transferring the resulting geometry to molcas, although this would be my last resort). My dummy problem is formaldehyde, the route seward-scf-alaska-slapaf (as in the scfgrad script. I left out the rasscf because the problem is not connected with it). Input files are: -----seward.input----- &SEWARD &END Title formaldehyde Square Symmetry x y Basis set C.ANO-S...3s2p1d. C .0000000000 .0000000000 -1.0143690059 End of basis Basis set O.ANO-S...3s2p1d. O .00000000 .0000000000 1.2925328919 End of basis Basis set H.ANO-S...2s1p. H .0000000000 1.7657335076 -2.1270245501 End of basis End of input -----scf.input----- &SCF &END Title formaldehyde Occupied 5 1 2 0 Ivo End of input -----alaska.input----- &ALASKA &END End of Input -----slapaf.input----- &SLAPAF &END Internal coordinates r1 = Bond C O r2 = Bond C H r3 = Bond C H(y) a1 = Angle O C H a2 = Angle O C H(y) d1 = Dihedral H O C H(y) Vary r1 r2 r3 a1 a2 d1 End of internal Iterations 20 Print 1 111 99 End of Input -----end----- the Iterations and Print statements are taken from the worked example in the Molcas documentation (which works, actually). They shouldn't be a problem. Everything works fine until slapaf. It exits with the output -----slapaf.output----- [snip] ******************************************** * Values of primitive internal coordinates * ******************************************** R1 : Bond Length= 2.3069/ bohr R2 : Bond Length= 2.0871/ bohr R3 : Bond Length= 2.0871/ bohr A1 : Angle= 122.2166/degree, 2.1331/rad A2 : Angle= 122.2166/degree, 2.1331/rad Warning: dihedral angle close to end of range D1 : Dihedral Angle= 180.0000/degree, 3.1416/rad ********************************************* * Value of internal coordinates / au or rad * ********************************************* R1 2.3069 R2 2.0871 R3 2.0871 A1 2.1331 A2 2.1331 D1 3.1416 ESV2105S DGEICD FACTORIZATION FAILED DUE TO NEAR ZERO PIVOT NUMBER (4). EXECUTION TERMINATING DUE TO ERROR COUNT FOR ERROR NUMBER 2105 MESSAGE SUMMARY: MESSAGE NUMBER - COUNT 2103 1 2105 1 -----end of slapaf.output----- I have no idea what causes this behaviour. I thought that the near 180 deg dihedral was responsible, and substituted a third angle for it. Also i tried to avoid using symmetry in the input, as in the manual's worked example (enediyne), where no two internal coordinates are connected to each other by a symmetry operation. The result was the same. NEAR ZERO PIVOT NUMBER. The molcas homepage (garm.teokem.lu.se) has not been reachable since yesterday, so i can't get information from there. Er, help? -- -ernst wallenborn. i'm not a bug. i'm an undocumented feature. From tp@elptrs7.rug.ac.be Wed Jul 10 06:24:11 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id GAA01088; Wed, 10 Jul 1996 06:06:32 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA16230; Wed, 10 Jul 1996 12:07:01 +0200 Date: Wed, 10 Jul 1996 12:07:01 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: Searching transition state with MOPAC; part2 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I've received a lot of helpful messages from many CCLers, concerning my earlier questions on how to get the structure of transition state of the reaction, H H H H H H | \ / | | | H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) | / \ | | | H H H H H H gas-phase gas-phase methyl ethylene primary propyl carbenium ion carbenium ion Thanks a lot! I greatly appreciate all the messages concerning this problem. Most of the messages pointed out that I made a mistake to prepare the input file for SADDLE calculation; all the atom should be in the same order between reactants and product z-matrix field. I made second try with a corrected input file as follows; ************************************************************** SADDLE DENSITY GRAPH XYZ CHARGE=1 PRECISE Me--->p methylation activated complex C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 8.471619 1 0.000000 0 0.000000 0 1 0 0 C 1.325912 1 162.328125 1 0.000000 0 2 1 0 H 1.108597 1 65.592545 1 -150.347214 1 1 2 3 H 1.113968 1 120.001495 1 -151.401566 1 1 4 2 H 1.108612 1 119.996246 1 -179.367538 1 1 4 5 H 1.098282 1 122.722214 1 57.159393 1 2 3 1 H 1.098328 1 122.715210 1 179.999634 1 2 3 7 H 1.098267 1 122.715210 1 -0.316483 1 3 2 7 H 1.098206 1 122.715210 1 -179.684021 1 3 2 7 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 C .000000 0 .000000 0 .000000 0 0 0 0 C 1.506600 1 .000000 0 .000000 0 1 0 0 C 1.418947 1 116.688263 1 .000000 0 2 1 0 H 1.118077 1 111.116249 1 -59.952415 1 1 2 3 H 1.119762 1 109.783371 1 -179.449097 1 1 2 3 H 1.118210 1 111.069687 1 61.123405 1 1 2 3 H 1.150598 1 110.672989 1 174.990601 1 2 1 4 H 1.150955 1 110.650314 1 64.874481 1 2 1 4 H 1.109621 1 121.247902 1 -179.729874 1 3 2 1 H 1.110257 1 121.556961 1 .300391 1 3 2 1 0 .000000 0 .000000 0 .000000 0 0 0 0 ************************************************************** This time MOPAC produced a structure of transition state which is almost the same as that of reactants, that is, there was almost no change between reactants and transition state. I've tried to refine the transition state with the key words, "TS", "SIGMA", and "NLLSQ" separately, which gives no change either. Why is the result like this? Could anyone PLEASE tell me how can I go further to obtain a reliable structure of the transition state?? Thank you VERY MUCH in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From MEDVEN@olimp.irb.hr Wed Jul 10 09:13:10 1996 Received: from faust.irb.hr for MEDVEN@olimp.irb.hr by www.ccl.net (8.7.5/950822.1) id IAA02040; Wed, 10 Jul 1996 08:41:17 -0400 (EDT) Received: from olimp.irb.hr by faust.irb.hr with SMTP (1.37.109.16/16.2) id AA041412443; Wed, 10 Jul 1996 14:40:43 +0200 Date: Wed, 10 Jul 1996 14:40:41 +0200 (IST) From: ZELJKA MEDVEN Subject: QM calculations on hydrogen bonds To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Is any of you aware of semiempirical or ab initio calculations on hydrogen bonds involving nucleic acid bases or any other nitrogen containing aromatics? I would appreciate any reference. Sincerely, Zeljka ****************************************************************************** M.Sc. Zeljka Medven Area code: 385-1 Department of Chemistry Phone: 456-1089 Rugjer Boskovic Institute Fax: 272-648 POB 1016, HR-10001 Zagreb, Croatia e-mail: medven@olimp.irb.hr ****************************************************************************** From Frederic.Bouyer@der.edfgdf.fr Wed Jul 10 12:13:10 1996 Received: from cf01 for Frederic.Bouyer@der.edfgdf.fr by www.ccl.net (8.7.5/950822.1) id LAA03375; Wed, 10 Jul 1996 11:29:56 -0400 (EDT) Received: from clserv02.edf.fr (clserv02.edf.fr [130.98.118.118]) by cf01 (8.6.12/8.6.12) with ESMTP id RAA07778 for ; Wed, 10 Jul 1996 17:33:50 +0200 Received: from ret45ab.der.edf.fr (ret45ab.der.edf.fr [192.196.125.12]) by clserv02.edf.fr (8.6.12/8.6.12) with ESMTP id RAA21058 for <@mailhost.der.edf.fr:chemistry@www.ccl.net>; Wed, 10 Jul 1996 17:29:37 +0200 Received: by ret45ab.der.edf.fr (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id RAA01690; Wed, 10 Jul 1996 17:26:45 +0200 From: "Frederic Bouyer" Message-Id: <9607101726.ZM1688@ret45ab.der.edf.fr> Date: Wed, 10 Jul 1996 17:26:43 -0600 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: Semi-empirical codes for solids ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, I search a software (a semi-empirical one) that can treat solid phase and compute frequencies. I saw that MOSOL can deal with solids (special thanks to Ratty), but there is only H, Be, B, C, N, O, F, Al, Si, P, S, Cl, Ge, Br, Sn, and I. But I would like to have Li, Fe, Sn, Cr, O, Zr elements. Is it possible to have MOSOL with these elements included, or are there other packages that offer such capabilities ? Frederic Bouyer From KANTERS@urvax.urich.edu Wed Jul 10 12:18:18 1996 Received: from urvax.urich.edu for KANTERS@urvax.urich.edu by www.ccl.net (8.7.5/950822.1) id MAA03626; Wed, 10 Jul 1996 12:07:28 -0400 (EDT) Received: from urvax.urich.edu by urvax.urich.edu (PMDF V5.0-7 #11964) id <01I6WO4W7BU80019L6@urvax.urich.edu> for CHEMISTRY@www.ccl.net; Wed, 10 Jul 1996 12:05:29 -0400 (EDT) Date: Wed, 10 Jul 1996 12:05:29 -0400 (EDT) From: "Rene P.F. Kanters" Subject: XMol on SGI IRIS 6.2 To: CHEMISTRY@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCL'er: We just upgraded our SGI's from IRIS 5.3 to 6.2 and XMol can not run anymore (since it relies on COFF files that are not supported anymore). Does anybody know about a free-ware SGI IRIS 6.2 compatible application that can animate multistep XYZ files? Rene Kanters Chemistry Project Specialist Chemistry Department University of Richmond, VA 23173 phone (804) 287-6873 email kanters@urvax.urich.edu www http://www.science.urich.edu/~kanters From janr@tiger.chem.uw.edu.pl Wed Jul 10 13:13:16 1996 Received: from tiger.chem.uw.edu.pl for janr@tiger.chem.uw.edu.pl by www.ccl.net (8.7.5/950822.1) id MAA03868; Wed, 10 Jul 1996 12:56:54 -0400 (EDT) Received: by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA11448; Wed, 10 Jul 1996 18:53:46 +0200 Date: Wed, 10 Jul 1996 18:53:46 +0200 From: janr@tiger.chem.uw.edu.pl (Jan Radomski) Message-Id: <9607101653.AA11448@tiger.chem.uw.edu.pl> To: CHEMISTRY@www.ccl.net Subject: Q: 3D --> IsisDraw 2D mol_file conversion? Cc: janr@tiger.chem.uw.edu.pl Dear Netters, is there any utility allowing conversion from 3D structural data of molecule to the MDL's IsisDraw 2D molfile format? Or am I missing something obvious? Best regards, Jan Radomski From vangreve@univ-orleans.fr Wed Jul 10 13:20:54 1996 Received: from centre.univ-orleans.fr for vangreve@univ-orleans.fr by www.ccl.net (8.7.5/950822.1) id NAA03932; Wed, 10 Jul 1996 13:08:17 -0400 (EDT) Received: from TOURMALET.univ-orleans.fr (tourmalet.univ-orleans.fr [193.49.95.21]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id TAA10971 for ; Wed, 10 Jul 1996 19:09:08 +0200 Message-ID: <31E3E2D4.397D@univ-orleans.fr> Date: Wed, 10 Jul 1996 19:05:24 +0200 From: Eric VANGREVELINGHE Organization: ICOA X-Mailer: Mozilla 3.0b4Gold (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Software to calculate ionic mobility Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I am looking for a program which can compute the mobility of ionic compound. I don't know if it's exist but any help will be appreciated. Thanks in advance _____________________________________________________________ Eric VANGREVELINGHE -------- Graduate Student in Chemistry ___ _ e-mail: vangreve@univ-orleans.fr `T\_ww/|@,_ _ http://web.univ-orleans.fr/ICOA ~ ~~~ =(_)\___[/(_)`> I.C.O.A. Institut de Chimie Organique et Analytique URA 499-UFR Sciences BP 6759 45067 ORLEANS Cedex 2 FRANCE tel: (33) 38 49 45 77 fax: (33) 38 41 72 81 _____________________________________________________________ From chpajt@bath.ac.uk Wed Jul 10 15:13:12 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id OAA04565; Wed, 10 Jul 1996 14:14:27 -0400 (EDT) Received: from bath.ac.uk (actually host ss1.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Wed, 10 Jul 1996 19:14:24 +0100 Date: Wed, 10 Jul 1996 19:14:20 +0100 (BST) From: A J Turner To: A J Turner cc: CHEMISTRY@www.ccl.net Subject: Re M imaginary frequencies In-Reply-To: <31E3E2D4.397D@univ-orleans.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! There are a few points that are maybe worth thinking about. 1: Mopac is not stable under restarts - in my experiance. Ie if you have and EF job that ran half way and was restarted , then compare to a complete run - the answers will not be the same. This sometime erroniously results in to jobs giveing different answers - and you think - err why did that happen! 2: The hessian update does seem to fail sometime on EF. I often use hess=3 recalc=3 or recalc=1. Most people say this is excessive - but I find it kills off these imaginary frequencies. 3: I once accedantally started EF on a transition state - absolutelyy 100% on the torsion barrier - eay for a z-matrix. I said that this was a minimum! IE - it cn fail in this way. 4: My version of mopac 6.0 has ddmin - something odd here. Anyhow - hess=3 recalc=3 or recalc=1 has never ever failed me yet. Good luck Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From Steve.Bowlus@sandoz.com Wed Jul 10 16:13:12 1996 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.7.5/950822.1) id PAA04939; Wed, 10 Jul 1996 15:05:16 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id AA21169; Wed, 10 Jul 1996 21:05:15 +0200 X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-Mts-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700002002879000002] X400-Content-Type: P2-1988 (22) Message-Id: <0034700002002879000002*@MHS> To: Subject: Mopac: Summary: Structure of excited states Date: Wed, 10 Jul 1996 21:07:24 +0200 My thanks to those who replied to my query on optimizing structures of excited states in Mopac. This appears to be less straightforward than I expected. . .ah, well, fools rush in. . . Below are the replies I received, subjected to some (unmarked) snipping: >>Andreas Parusel, Vienna (andreas@majestix.msp.univie.ac.at): I read your posting in the ccl about excited states. I am working also with these problems in the VAMP package, but I do have the same problems. As fas as I know, you have to change the structure of the MOLECULE a bit ( for my large molecules for ex. -Ph --> -CH3) then it works better. Sometimes it works if you coose another converger ... PULAY or IIS ... you could try this. Or you have to optimize the excited state with GNORM=20 f. ex. and lowering the gradient step by step ... this are all possibilities that work sometimes but not always! >>Dr. Jose Ignacio Garcia-Laureiro (jig@qorg.unizar.es): In general, geometric optimizations at the CI level are MUCH more time demanding than "normal" ones, but I realize that 10 cpu hours on an Indigo2 is too much... You may take a look to the following reference: M.J.S. Dewar, S. Olivella, J.J.P. Stewart J. Am. Chem. Soc., 108 (1986) 5771-5779 These authors recommend to start with an UHF geometry optimization, which is as fast as an normal RHF one, but leads to a better starting point for a further CI optimization. >>Dr. Peter Gedeck (gedeck@organik.uni-erlangen.de): As far as I think SHIFT only damp SCF oscillations and does not change the behaviour of the EF geometry optimization. You should try setting DMAX to a smaller value. This restricts the maximum step size of the geometry optimization and might thus damp the oscillations. Also try different geometry optimizers. Another problem that can occur is a crossing of excited states during the course of the geometry optimization. If such a crossing occurs the calculated gradients suddenly belong to a different state than in the steps before and you can imagine that this way your calculation must fail. A possible way to reduce the problem here is to define the multiplicity of the state you want to optimize. E.g use: root=1 singlet for the S0 state root=2 singlet for the S1 state root=1 triplet for the T1 state This way at least we get rid of the problem of crossing singlet and triplet states. It might be that some of the keywords are not correct because I usually use VAMP and not Mopac but there are definitly similar keywords. >>Lutfur Khundkar (LKHUNKR@NEU.EDU): I have tried a few excited state calculations using MOPAC 6 using OS/2 on a 486D50. My molecules were relatively small, but what I would consider medium to large for semiempirical calculations, specially geometry optimizations. I have worked with about 16 heavy and 12 H atoms. There are some special keywords (SINGLET and TRIPLET) that you can use to restrict yuour basis set. However, geomtry optimizations do take a long time.From what I understand from talking to a few people, C.I.=2 is not really a useful choice --- unless you are interested in very approximate numbers. My own experience with a limited set of molecules has been that even the energies that you get seem to depend on the level of CI. I find that CI=4 (single geometry SCF calculations) and less gives results that are reasonably similar, but CI=5 makes a significant difference to the energies and relative ordering of states (I use dipole moments to "identify" my states --- its an approximate handle for me, since thats what I am interested in). I remember seeing a post to this list several months back about MECI in Mopac that discussed an alternative to using the preset CI keyword. You can define your microstates to be used in MECI by Mopac, although this does not address your initial concern about how long it takes to get a converged calcualtion. From boyd@chem.iupui.edu Wed Jul 10 18:13:13 1996 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.7.5/950822.1) id RAA05667; Wed, 10 Jul 1996 17:35:11 -0400 (EDT) Received: from macgw.chem.iupui.edu (134.68.137.71) by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01I6WXHA61CG006LBE@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Wed, 10 Jul 1996 16:33:36 -0500 Date: Wed, 10 Jul 1996 16:22:55 -0500 From: Boyd Subject: Gordon Conference on Computational Chemistry To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT CCLers: Last week, the 6th biennial Gordon Research Conference on Computational Chemistry was held in New Hampton, New Hampshire. At the conference, which was chaired this year by Dr. Tom Halgren (Merck), elections were held for the future guidance of the conference. By policy, the chair of this conference alternate between someone from academia and someone from industry. Last week the conferees elected Dr. Terry Stouch to be Vice Chair. So when the conference next meets in the summer of 1998, Dr. Jeffry Madura will be Chair. In the year 2000, Terry will be Chair. For information about these future conferences, contact: Jeffry D. Madura, Ph.D. Department of Chemistry University of South Alabama Mobile, AL 36688 USA Phone: 334-460-7430 - FAX: 334-460-7359 E-mail: jmadura@jaguar1.usouthal.edu Terry R. Stouch, Ph.D. Room H3812, Department of Macromolecular Modeling Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 4000, Princeton, NJ 08543-4000 USA Phone: 609-252-5442 - FAX: 609-252-6030 E-mail: stouch@bms.com On behalf of everyone at the conference, we thank Tom Halgren for his superb organization of a most stimulating meeting, truly at the cutting edge of science. Donald B. Boyd, Ph.D. Member of the Steering Committee of Past Chairs Indiana University-Purdue University at Indianapolis E-mail: boyd@chem.iupui.edu