From chemistry-request@server.ccl.net Tue May 23 08:36:26 2000 Received: from neptun.chem.uit.no (root@neptun.Chem.Uit.No [129.242.24.168]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA19772 for ; Tue, 23 May 2000 08:36:25 -0400 Received: from chem.uit.no (IDENT:bolvin@localhost.localdomain [127.0.0.1]) by neptun.chem.uit.no (8.9.3/8.9.3) with ESMTP id OAA12336 for ; Tue, 23 May 2000 14:39:25 +0200 Sender: bolvin@neptun.chem.uit.no Message-ID: <392A7BFC.3ED2EF48@chem.uit.no> Date: Tue, 23 May 2000 14:39:24 +0200 From: Helene BOLVIN X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Consistency failure with Gaussian 98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hallo I perform DFT geometry optimization with Gaussian 98. And very often, after one or many cycles of the geometry optimization, I get a consistency failure, always at the 3rd cycle of the SCF procedure. Cycle 3 Pass 1 IDiag 1: RMSU= 2.33D-02 CP: 2.63D-01 -2.55D-01 Warning! Spurious integrated density: NE= 58 NElCor= 0 Integral= 58.10848 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /usr/local/chemistry/g98/l502.exe. I have tried to restart with many options, as previously proposed in CCL: INT=GRID=UltraFine. SCF=NoVarrAcc Int=Rys1E but none works. The only way I have found is to perform a QC procedure for this point, and then start the geometry optimisation from this point til the next failure. But it is quite tedious. I would be pleased if any one has a better proposition. Helene Bolvin -- ***************************************************************** Helene BOLVIN Institutt for kjemi tlf: (+47) 77 64 40 61 Universitetet i Tromsoe fax: (+47) 77 64 47 37 N-9037 TROMSOE ***************************************************************** From chemistry-request@server.ccl.net Tue May 23 08:17:04 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA19700 for ; Tue, 23 May 2000 08:17:04 -0400 Received: from isosirri (isosirri.csc.fi [193.166.1.218]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id PAA03280 for ; Tue, 23 May 2000 15:16:52 +0300 From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Subject: Announcing gOpenMol version 1.4 Date: Tue, 23 May 2000 15:20:30 +0300 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0017_01BFC4CA.6EACCEC0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0017_01BFC4CA.6EACCEC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit We are very pleased to announce version 1.4 of the gOpenMol program. There are new functional enhancements added and performance improvements. The gOpenMol is a part of the OpenMol collaborative effort between Leif Laaksonen at the Center for Scientific Computing, Espoo and Geerd HF Diercksen at the Max-Planck-Institute for Astrophysics, Garching. The gOpenMol developed by Leif Laaksonen is a general purpose molecular graphics toolbox for the analysis and display of molecular structures, trajectories and properties. The program is available for Windows 95/98/NT/2000, Intel Linux and SGI platforms at the address: http://www.csc.fi/~laaksone/gopenmol/ The OpenMol Project, coordinated by Geerd HF Diercksen, is a concerted effort of several individuals and research groups to develop chemical software using modern information technology. http://ibm-8.mpa-garching.mpg.de:6565/~opmolsrv/OpenMol/homepage.shtml Yours, Leif Laaksonen Geerd HF Diercksen ------=_NextPart_000_0017_01BFC4CA.6EACCEC0 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;FUNET TITLE:Network Information Services Manager NOTE:My personal Web page: http://www.csc.fi/~laaksone/ TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358 +358400425203 TEL;WORK;FAX:+358 9 457 2302 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksone@csc.fi REV:19991226T172416Z END:VCARD ------=_NextPart_000_0017_01BFC4CA.6EACCEC0-- From chemistry-request@server.ccl.net Tue May 23 12:24:11 2000 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA20884 for ; Tue, 23 May 2000 12:24:10 -0400 Received: from tc.cornell.edu (LIGAND.TC.CORNELL.EDU [128.84.20.182]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id MAA22187; Tue, 23 May 2000 12:23:57 -0400 Sender: richard@tc.cornell.edu Message-ID: <392AAF8A.E53B9175@tc.cornell.edu> Date: Tue, 23 May 2000 12:19:22 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net, ccp4bb@dl.ac.uk Subject: stable Ih ice and P63/mmc space group References: <001001bfc142$515cc5e0$0200a8c0@pavilion> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Two related questions. One relates to simulation, the other to crystals so I'm posting to two lists. I was recently asked to generate an animation sequence of a solid melting into a fluid and then vaporizing. Since it was for purposes of illustration only (a low-level educational film) we did not need a great deal of accuracy in the model, just the basic behavior. I ended up using Argon and got nice results, but my first attempt with H2O has me a bit puzzled. I constructed a slab of Ih ice from the crystal structure. Because the structure is space and time averaged, or perhaps because the protons hop around a lot, the P63/mmc space group symmetry operators place 24 water molecules in the unit cell in 4 overlapping groups of 6. There are only 4 unique Oxygen positions, but each has 4 unique protons, so there appear to be clashes between neighboring protons. Sorry, this is hard to describe in words. I can simply choose four unique H2O molecules per unit cell and get a nice lattice with no clashes, which is what I did. When I minimize a block of ice, I was surprised to find that the the crystal structure appears to collapse .... or at least there is no minimum near the ice structure. I'm using a simple pairwise VDW+point charge model. Q1: Is a more advanced potential model (say with explicit H bonds) needed to have stable Ih ice, or is there a good set of point charges and VDW parameters that will work? Q2: The 24 symmetry operators fall into 4 groups of 6, each of which has the same z-value in common. For example: -x+y, -x, -z+1/2 -y , -x, -z+1/2 -x+y, -y, -z+1/2 x , x-y, -z+1/2 x , y, -z+1/2 -y , x-y, -z+1/2 I would have expected these operators to produce the six possible orientations of a single water molecule at a given lattice site. Instead, they seem to produce a doubly redundant set in which one OH bond is always fixed on the z axis. Am I missing something here? yes, I am applying these in fractional coordinates and shifting the result back into the unit cell, The fractional coordinates of the H2O molecule are: O (.333,.666,.063) H (.333,.666,.193) H (.455,.910,.018) with a,b = 4.516 and c = 7.354 angles = (90,90,120) Thanks Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Tue May 23 15:50:42 2000 Received: from server.ttpharma.com ([206.74.77.186]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA22108 for ; Tue, 23 May 2000 15:50:31 -0400 Received: from jerome ([192.168.4.24]) by server.ttpharma.com (8.9.3/8.8.7) with SMTP id OAA32158; Tue, 23 May 2000 14:51:29 -0500 From: "Jerome Baudry" To: Cc: Subject: number of rotatable bonds in drug-like molecules: references ? Date: Tue, 23 May 2000 15:47:51 -0400 Message-ID: <000001bfc4ef$c868c340$1804a8c0@ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear All The number of rotatable bonds in small molecules is often used as a filter to identify possible drug-like chemicals. The # of rotatable bonds is sometimes included in citations of the "rule of 5". However the rule-of-5 paper (Lipinski et al. Advanced Drug Discovery reviews, 1997)does not list this # of rotatable bond as a filter. Does anybody have a reference for a paper about the # of rotatable bonds as a 'drug-like' descriptor? What values are usually used, how does this descriptor correlate with the original r-o-5 descriptors, etc ...? Thanks a lot in advance Jerome --------------------------------- Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 From chemistry-request@server.ccl.net Tue May 23 18:06:30 2000 Received: from holyrood.ed.ac.uk (holyrood.ed.ac.uk [129.215.16.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA22761 for ; Tue, 23 May 2000 18:06:29 -0400 Received: from localhost (mhp02@localhost) by holyrood.ed.ac.uk (8.8.7/8.8.7) with ESMTP id XAA07439 for ; Tue, 23 May 2000 23:06:28 +0100 (BST) Date: Tue, 23 May 2000 23:06:28 +0100 (BST) From: Alistair Nelson To: chemistry@ccl.net Subject: Ozone MP2 IR Frequencies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCL'ers I have been trying to calculate IR Frequencies for Ozone using an MP2 wavefunction, but I have recently been informed that this will not work due to problems with ozone and IR freqs calculated using said wavefunction, I was just wondering if anyone had any references related to this problem? Cheers Alistair -- /------------------------------------------------------\ | Email: Alistair.nelson@ed.ac.uk ICQ# 16297649 | | http://thunder.prohosting.com/~nelsona/ (Personal) | | http://www.nelsona.co.uk/ (Spectrum stuff) | | http://www.ed.ac.uk/~zeke/ (PhD Stuff) | \------------------------------------------------------/ From chemistry-request@server.ccl.net Tue May 23 19:29:43 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA23115 for ; Tue, 23 May 2000 19:29:42 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JPR1ELDIY2002KA1@trentu.ca> for chemistry@ccl.net; Tue, 23 May 2000 19:29:38 EDT Date: Tue, 23 May 2000 19:33:46 -0400 From: elewars Subject: IR FREQS OF OZONE, ANSWER To: chemistry@ccl.net Message-id: <392B155A.A16FE52@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2000 May 23 Hello, Regarding the IR frequencies of ozone (question below): Ozone is a well-known "pathological" (Foresman and Frisch, p 118; J. B. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods, 2nd Ed., Gaussian Inc., Pittsburgh, 1996; see too p 35) molecule when it comes to accurate ab initio calculations (another is FOOF). See Jensen (F. Jensen, Introduction to Computational Chemistry, Wiley, New York, 1999), p 115 and particularly ("The vibrational frequencies of O3") p 287. O3 seems to respond well to DFT calculations. E. Lewars ============ Hello CCL'ers I have been trying to calculate IR Frequencies for Ozone using an MP2 wavefunction, but I have recently been informed that this will not work due to problems with ozone and IR freqs calculated using said wavefunction, I was just wondering if anyone had any references related to this problem? Cheers Alistair -- /------------------------------------------------------\ | Email: Alistair.nelson@ed.ac.uk ICQ# 16297649 | | http://thunder.prohosting.com/~nelsona/ (Personal) | | http://www.nelsona.co.uk/ (Spectrum stuff) | | http://www.ed.ac.uk/~zeke/ (PhD Stuff) | \------------------------------------------------------/ ================ =========== From chemistry-request@server.ccl.net Tue May 23 21:45:31 2000 Received: from msuiit.edu.ph ([202.78.82.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA23701 for ; Tue, 23 May 2000 21:45:26 -0400 Received: from cc1.msuiit.edu.ph (cc1 [202.78.82.30]) by msuiit.edu.ph (8.9.0/8.9.0) with ESMTP id JAA11034 for ; Wed, 24 May 2000 09:58:23 -0800 (GMT) Received: from CC1/SpoolDir by cc1.msuiit.edu.ph (Mercury 1.44); 24 May 00 09:57:17 GMT+0800 Received: from SpoolDir by CC1 (Mercury 1.44); 24 May 00 09:57:00 GMT+0800 From: "Marvin Jose F. Fernandez" To: chemistry@ccl.net Date: Wed, 24 May 2000 09:56:56 +0800 Subject: SCRF Priority: normal X-mailer: Pegasus Mail v3.40 (NDS) Message-ID: <104191F7288@cc1.msuiit.edu.ph> I'm not very familiar with this theory. I would like an expert opinion regarding the applicability of this theory to reactions in which the solvents are nitromethane or tetrahydrofuran. Please e-mail your response to this address:vinjo97@gopinoy.com From chemistry-request@server.ccl.net Tue May 23 23:02:23 2000 Received: from granger.mail.mindspring.net (granger.mail.mindspring.net [207.69.200.148]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA24096 for ; Tue, 23 May 2000 23:02:23 -0400 Received: from quantumnt (user-2injk6e.dialup.mindspring.com [165.121.208.206]) by granger.mail.mindspring.net (8.9.3/8.8.5) with SMTP id XAA10700 for ; Tue, 23 May 2000 23:02:17 -0400 (EDT) Message-ID: <000b01bfc52c$79367c30$0300a8c0@mindspring> Reply-To: "Jim Kress" From: "Jim Kress" To: "CCL" Subject: G98W and dual processors on NT Date: Tue, 23 May 2000 23:02:14 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 I am using G98W on a dual processor WinNT4.0SP5 machine with 1GB of RAM. I do NOT specify MKL_NPROCS to be 2. However, when I run G98W, it pauses with a 'low memory' warning. It states that I need 480MB of RAM to continue (which is the amount specified in the default.rou file) but that I have only (approx.) 231MB. If I allow it to proceed, it thrashes badly. If I specify a memory value of LE 256MB in the default.rou file, the program runs normally with no warnings or thrashing. The problem is not resolved by specification of MKL_NPROCS to be 1 In all cases I am using the qs.gjf example from the C:\G98W\quick subdirectory. Anybody know what I need to do to get this to run properly with the larger default.rou memory specification? I've asked Gaussian but they have not replied ... Thanks and I will summarize. Jim Check out my web site http://www.kressworks.com/ From chemistry-request@server.ccl.net Tue May 23 23:32:05 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA24267 for ; Tue, 23 May 2000 23:32:05 -0400 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Tue, 23 May 2000 22:32:02 -0500 Message-ID: <000d01bfc530$63ba0260$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "Alistair Nelson" , References: Subject: Re: CCL:Ozone MP2 IR Frequencies Date: Tue, 23 May 2000 22:30:20 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Ozone is a multireference case. MBPT(2) is particularly bad for ozone. For more on this and results of other methods on ozone, see: M. L. Leininger and H. F. Schaefer, J. Chem. Phys. 107(21), 1997, 9059. and references therein. C. W. Murray, N.C. Handy, and R.D. Amos, J. Chem. Phys. 98 (1993) 7145-7151. Watts & Stanton & Bartlett, CPL, 1991, 178, p. 471 B3LYP and pw91pw91 (recently I used both dft methods to study Cl + O3 reaction) are not so bad after all in this case even it is about or even faster than MP2. ---------------------------------------------------- Tapas Kar Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: Alistair Nelson To: Sent: Tuesday, May 23, 2000 5:06 PM Subject: CCL:Ozone MP2 IR Frequencies > Hello CCL'ers > > I have been trying to calculate IR Frequencies for Ozone using an MP2 > wavefunction, but I have recently been informed that this will not work > due to problems with ozone and IR freqs calculated using said > wavefunction, I was just wondering if anyone had any references related to > this problem? > > Cheers > > Alistair > > -- > /------------------------------------------------------\ > | Email: Alistair.nelson@ed.ac.uk ICQ# 16297649 | > | http://thunder.prohosting.com/~nelsona/ (Personal) | > | http://www.nelsona.co.uk/ (Spectrum stuff) | > | http://www.ed.ac.uk/~zeke/ (PhD Stuff) | > \------------------------------------------------------/ > > > -= 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 > > > > >