From chemistry-request@server.ccl.net Thu Oct 14 03:42:31 1999 Received: from sheridan.dina.kvl.dk (sheridan.dina.kvl.dk [130.225.40.227]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA16271 for ; Thu, 14 Oct 1999 03:42:30 -0400 Received: from ssx2.dina.kvl.dk (ssx2.dina.kvl.dk [130.225.40.231]) by sheridan.dina.kvl.dk (8.9.0.Beta5/8.9.0.Beta5) with ESMTP id JAA27682 for ; Thu, 14 Oct 1999 09:37:10 +0200 Received: from localhost (antony@localhost) by ssx2.dina.kvl.dk (8.8.8+Sun/8.8.8) with SMTP id JAA16241 for ; Thu, 14 Oct 1999 09:36:58 +0200 (MET DST) X-Authentication-Warning: ssx2.dina.kvl.dk: antony owned process doing -bs Date: Thu, 14 Oct 1999 09:36:58 +0200 (MET DST) From: Jens Antony To: chemistry@ccl.net Subject: Installation of g98 Rev A7 Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-559023410-851401618-939802065=:23850" Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---559023410-851401618-939802065=:23850 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Dear all! We are installing the new version of Gaussian98 on an SGI R10000. The compilation finishes without obvious error messages. When executing the program, however, it stops without reading the input and writes a core file. The output for example on test000 finishes with the following lines immediately after the Gaussian citation: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ rrrrrrrrrrrr @@@@@@@@@@@@@@@@@@@@@@@@@@@ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Route card not found. Error termination via Lnk1e in /pack/g98a7/g98/l1.exe. Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds. File lengths (MBytes): RWF= 0 Int= 0 D2E= 0 Chk= 0 Scr= 0 Thank you very much for your help. Jens ---559023410-851401618-939802065=:23850-- From chemistry-request@server.ccl.net Thu Oct 14 03:51:08 1999 Received: from email.guomai.sh.cn (qrkewxfprh@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA16337 for ; Thu, 14 Oct 1999 03:51:06 -0400 Received: from guomai.sh.cn ([202.101.13.65]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.05.24.18.28.p7) with ESMTP id <0FJL008OR1YY3O@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Thu, 14 Oct 1999 15:54:35 +0800 (CST) Date: Thu, 14 Oct 1999 15:47:47 +0800 From: Yubo Fan Subject: Why aren't DFT methods suitable for long distance interactions? To: CHEMISTRY@ccl.net Message-id: <38058AA2.2F21D28C@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.6 [en] (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, everyone, Many articles and books say that DFT methods are not suitable for intermolecular interaction calculations. That means I can use DFT to calculate many H-bonding or Pi-Pi systems. I don't know the reason. Can anybody explain it? Thank you very much Y. Fan ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Wed Oct 13 16:19:54 1999 Received: from mtiwmhc01.worldnet.att.net (mtiwmhc01.worldnet.att.net [204.127.131.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13581 for ; Wed, 13 Oct 1999 16:19:53 -0400 Received: from nt ([12.74.128.162]) by mtiwmhc01.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <19991013201230.EAIQ12280@nt> for ; Wed, 13 Oct 1999 20:12:30 +0000 Message-Id: <3.0.32.19991013141644.00997560@postoffice.worldnet.att.net> X-Sender: mrmopac@postoffice.worldnet.att.net X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 13 Oct 1999 14:16:51 -0600 To: CHEMISTRY@ccl.net From: "James J. P. Stewart" Subject: Help: I need interatomic distances Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Interatomic distances and angles are needed for the following solids: MgBr2 Mg-Br Br-Mg-Br Mg-Br-Mg PbF2 Pb-F Pb-Pb' Pb-Pb" PbMgO3 Any distance. ZnF2 Zn-F, Zn'-F any angles ZnS Zn-S I've checked Wells and various other sources, but all they give is the lattice type. Any info, with references, would be most useful. Jimmy Stewart ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart@fujitsu.com | | 15210 Paddington Circle | WWW: http://home.att.net/~MrMOPAC | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | Fax: USA +(719) 488-9758 | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From chemistry-request@server.ccl.net Wed Oct 13 15:19:27 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA12856 for ; Wed, 13 Oct 1999 15:19:26 -0400 Received: from venezia.ks.uiuc.edu (IDENT:barryi@venezia.ks.uiuc.edu [130.126.120.96]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id OAA09171; Wed, 13 Oct 1999 14:14:04 -0500 (CDT) Received: (from barryi@localhost) by venezia.ks.uiuc.edu (8.8.7/8.6.9)id PAA22369; Wed, 13 Oct 1999 15:14:10 -0400 From: Barry Isralewitz Message-Id: <199910131914.PAA22369@venezia.ks.uiuc.edu> Subject: Re: CCL:Question About Structure/Viewing Software To: aiz0001@jove.acs.unt.edu (Anita Ilze Zvaigzne) Date: Wed, 13 Oct 1999 14:14:10 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: from Anita Ilze Zvaigzne at "Oct 8, 99 02:57:45 am" X-Mailer: ELM [version 2.4ME+ PL15 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello, re: Also, I have a PDB-type file > generated by using AMBER, and I want to prepare a 3D image that can be > pasted into Microsoft Word 97 as well as PowerPoint for the purpose of > publication. As you may have seen recently on this list, the 3D molecule viewer "VMD" has just come out in a new release. VMD (which is free academic software) is about the best program for studying 3D molecular features I've come across, thanks to some excellent interface design decisions and its performance on playing back trajectories of dynamics simulations. Advanced users even have the option of using the scripting language TCL to easily add features / do analysis while VMD is running. The interactive onscreen images themselves are publication quality; VMD also works with several raytracers to make extra-beautiful pictures. See: http://www.ks.uiuc.edu/Research/vmd/ Plus, after years of Unix existence, its recently been ported to Windows ! VMD performance on a Windows box with a modern gaming card (Voodoo, etc) is shockingly good, even compared to a new workstation like the Sun Ultra 10/Elite3D. [Ob. bias admission: my office is about 200 feet from that of the chief VMD developers!] Cheers, Barry --- Barry Isralewitz Theoretical Biophysics Group Beckman 3121 Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Thu Oct 14 07:56:53 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.222.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA18505 for ; Thu, 14 Oct 1999 07:56:47 -0400 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 3300 invoked from network); 14 Oct 1999 11:51:00 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 14 Oct 1999 11:51:00 -0000 Received: (qmail 19972 invoked by uid 10283); 14 Oct 1999 11:50:42 -0000 Message-ID: <19991014115042.19971.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? To: yubofan@guomai.sh.cn (Yubo Fan) Date: Thu, 14 Oct 1999 13:50:42 +0200 (MSZ) Cc: chemistry@ccl.net In-Reply-To: <38058AA2.2F21D28C@guomai.sh.cn> from "Yubo Fan" at Oct 14, 99 03:47:47 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit There is no such general statement. It depends on the physics of the interaction. For H-bonded systems for example, there is *experience* that DFT does not work too well, or that it is acceptable only for specific functionals. For dispersion forces on the other hand, it is clear that DFT cannot treat them: although the opposite is claimed from time to time, it should be obvious that there is no long-range correlation in local or gradient-corrected functionals. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 700 6485 Theoretical Chemistry | Fax (University): +49 234 709 4109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 14 07:53:53 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.222.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA18490 for ; Thu, 14 Oct 1999 07:53:51 -0400 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 432 invoked from network); 14 Oct 1999 11:48:14 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 14 Oct 1999 11:48:14 -0000 Received: (qmail 19765 invoked by uid 10283); 14 Oct 1999 11:47:56 -0000 Message-ID: <19991014114756.19764.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Installation of g98 Rev A7 To: antony@dina.kvl.dk (Jens Antony) Date: Thu, 14 Oct 1999 13:47:56 +0200 (MSZ) Cc: chemistry@ccl.net In-Reply-To: from "Jens Antony" at Oct 14, 99 09:36:58 am X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit My experience compiling g98 rev a7 on SGI R10000 was similar: I could compile the program but the executable immedeately bombs (in the malloc function in my case). I guess there must some OS incompatibilies between different versions/patchlevels of IRIX. Without 64-bit integers (i.e. with the 'old' Makefile), everything is OK. So if you have less than 2 GB memory, you might be happy with this solution. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 700 6485 Theoretical Chemistry | Fax (University): +49 234 709 4109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 14 09:34:05 1999 Received: from ns.mnc.md (root@ns.mnc.md [212.0.192.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA18981 for ; Thu, 14 Oct 1999 09:33:57 -0400 Received: from ppp-09.core-a.mnc.md (ppp-09.core-a.mnc.md [212.0.192.76]) by ns.mnc.md (8.8.7/8.8.7) with ESMTP id QAA16440 for ; Thu, 14 Oct 1999 16:27:31 +0300 Date: Thu, 14 Oct 1999 15:45:30 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.36) S/N 5172A37D Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <5656.991014@mnc.md> To: chemistry@ccl.net Subject: HyperChem & DDE Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit +======================---------------- --- -- - - - - . | Dear chemistry, : . Is there any list devoted to HyperChem and HyperChem scripts and DDE? I have a problem with linking Excel with HyperChem. Problem is so: I would like to have a log-file of calculations, but it is impossible to make log when you use DDE. So a made next script (see below), but it doesn't work properly: 1) DDERequest(HCC, QVal$(2, i)) returns 'Error 2023' 2) DDEExecute HCC, "[read-script...]" doesn't work on 2nd run (i=1 Ok, but i=2 it do nothing). Could anybody help me? ------------------- script begins ----------------------------------- For j = 1 To NMols Open MolPath$ & Left(MolData(2, j), InStr(MolData(2, j), ".")) & "scr" For Output As #1 Print #1, "stop-logging" Print #1, "omsgs-not-to-file" Print #1, "start-logging " & MolPath$ & MolData(7, j) & " true" Print #1, "write-file " & MolPath$ & MolData(7, j) & "" Print #1, "errors-are-omsgs" Print #1, "query-response-has-tag false" Print #1, "one-line-arrays false" Print #1, "append-omsgs-to-file " & MolPath$ & MolData(7, j) & "" ''''' Open File & run single point ZINDO ''''''''''''''''''''' Print #1, "open-file " & MolPath$ & MolData(2, j) & "" Print #1, "calculation-method semiempirical" Print #1, "semi-empirical-method zindos" Print #1, "scf-convergence 0.00100" Print #1, "max-iterations 200" Print #1, "excited-state false" Print #1, "quantum-total-charge " & MolData(3, j) & "" Print #1, "multiplicity " & MolData(4, j) & "" Print #1, "configuration-interaction SinglyExcited" Print #1, "do-single-point" Print #1, "export-dipole No" Print #1, "export-ir No" Print #1, "export-orbitals Yes" Print #1, "export-UV Yes" Print #1, "export-property-file " & MolPath$ & MolData(9, j) & "" Print #1, "stop-logging" Print #1, "omsgs-not-to-file" Print #1, "start-logging " & MolPath$ & "$temp$.tmp" & " true" Print #1, "write-file " & MolPath$ & "$temp$.tmp" & "" Print #1, "stop-logging" Print #1, "omsgs-not-to-file" Print #1, "exit-script" Close #1 S$ = "[read-script " & MolPath$ & Left(MolData(2, j), InStr(MolData(2, j), ".")) & "scr]" DDEExecute HCC, S$ For i = 1 To nqval Var = DDERequest(HCC, QVal$(2, i)) Sheets(MolData(1, j) & "O").Cells(i, 1).Value = QVal$(1, i) Sheets(MolData(1, j) & "O").Cells(i, 2).Value = Var Next Open MolPath$ & MolData(9, j) For Input As #1 Next ------------------- script ends ------------------------------------- Best regards, Mike mailto:mike@mnc.md . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Thu Oct 14 10:23:59 1999 Received: from mail.chemie.fu-berlin.de (root@envelope.chemie.fu-berlin.de [160.45.24.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA19246 for ; Thu, 14 Oct 1999 10:23:56 -0400 Received: from Dirac.Chemie.FU-Berlin.DE (dirac.chemie.fu-berlin.de[160.45.24.166]) (1847 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Thu, 14 Oct 1999 16:18:11 +0200 (CEST) (Smail-3.2.0.108) Received: by Dirac.Chemie.FU-Berlin.DE (Smail3.2.0.98) id ; Thu, 14 Oct 1999 16:18:10 +0200 (MEST) Message-Id: From: melchers@chemie.fu-berlin.de (Bernd Melchers) Subject: Re: CCL:Installation of g98 Rev A7 To: antony@dina.kvl.dk (Jens Antony) Date: Thu, 14 Oct 1999 16:18:10 +0200 (MEST) Cc: chemistry@ccl.net In-Reply-To: from "Jens Antony" at Oct 14, 99 09:36:58 am X-Mailer: ELM [version 2.4 PL24 ME8d] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit 'Jens Antony wrote:' > > Dear all! > > We are installing the new version of Gaussian98 on an SGI R10000. The > compilation finishes without obvious error messages. When executing the > program, however, it stops without reading the input and writes a core You need a Makefile suitable for your compiler version. Our gaussian98 A6 generates core dumps with compiler versions 7.3.1 (IRIX 6.5.5) but not with compiler 7.2.x. There is a new Makefile available from gaussian for 7.3.0 Compilers but it produces code which is 30 % slower. And occasionally dumps core, also. It seems, the people at gaussian have to do some further developement. But who should be blamed for bad code, the compiler developer at sgi or the programmer at gaussian??? Ciao Bernd -- Bernd Melchers | melchers@FU-Berlin.DE Freie Universitaet Berlin | "We don't write software, we compose it." AG Macromolecular Modelling - Prof. Dr. E.W. Knapp for more information see http://userpage.chemie.fu-berlin.de/~melchers/ From chemistry-request@server.ccl.net Thu Oct 14 11:27:43 1999 Received: from estradiol.cbr.tulane.edu (estradiol.cbr.tulane.edu [129.81.225.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19657 for ; Thu, 14 Oct 1999 11:27:42 -0400 Received: from estradiol.cbr.tulane.edu (estradiol.cbr.tulane.edu [129.81.225.60]) by estradiol.cbr.tulane.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA14576 for ; Thu, 14 Oct 1999 10:22:06 -0500 (CDT) Sender: hall@estradiol.cbr.tulane.edu Message-ID: <3805F51D.E2586C9D@estradiol.cbr.tulane.edu> Date: Thu, 14 Oct 1999 10:22:06 -0500 From: Andrew Hall Organization: Center for Bioenvironmental Research X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Sybyl output to NAMD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are working on protein-ligand dynamics using NAMD and would like to be able to take the MOL2 output of Sybyl for the small molecules and easily use it in the NAMD sims. I was hoping someone had followed a similar path and there are available Perl or other scripts which will convert from MOL2 format into (e.g.) a topology file for Xplor or other pathways which will make input into NAMD possible. Thanks, A. -- Andrew Hall hall@estradiol.cbr.tulane.edu Center for Bioenvironmental Research Tulane University/Xavier University From chemistry-request@server.ccl.net Thu Oct 14 07:56:59 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA18511 for ; Thu, 14 Oct 1999 07:56:58 -0400 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Thu, 14 Oct 1999 12:50:54 +0100 Received: (from mitchell@localhost) by biochem.ucl.ac.uk (8.9.2/8.9.1) id MAA13202 for chemistry@ccl.net; Thu, 14 Oct 1999 12:51:01 +0100 (BST) Date: Thu, 14 Oct 1999 12:51:01 +0100 (BST) From: John Mitchell Message-Id: <199910141151.MAA13202@biochem.ucl.ac.uk> To: chemistry@ccl.net Subject: Re: CCL:How are H-bonds parameterized in force fields? Well, those of you who have read my thesis probably don't need to read any further in this reply. In addition to agreeing with Irene, I'd make the following comments 1) The repulsion doesn't vanish because of some mystical violation of the Pauli principle. The reasons are: a) The charge density around polar hydrogens is greatly reduced relative to non-polar hydrogens, so the charge overlap is reduced, so the repulsion is reduced b) Induction and charge transfer effects, which Williams and others can safely ignore in less polar situations become significant for hydrogen bonds. So these effects roughly cancel out with some more of the repulsion. The consequence is that ignoring polar hydrogen repulsion happens to give a reasonable model in many cases due to cancellation of errors. 2) In general, I don't think there is any need to think of hydrogen bonds as covalent. They can be described well by perturbation theory, for instance, and a good representation of non-bonded interactions should take care of hydrogen bonding automatically. There are some possible pathological cases, for instance where the symmetry leads to a double well potential for the hydrogen position. John. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Dr John B.O. Mitchell, Centre for Theoretical and Computational Chemistry, Department of Chemistry, University College London, Phone: 020-7679-4665 20 Gordon Street, Fax: 020-7679-7463 London WC1H OAJ, United Kingdom. Email address: mitchell@biochemistry.ucl.ac.uk Home page URL: http://www.biochem.ucl.ac.uk/~mitchell/index.html >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< From chemistry-request@server.ccl.net Thu Oct 14 15:23:44 1999 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA21364 for ; Thu, 14 Oct 1999 15:23:43 -0400 Received: from degas.scripps.edu (degas.scripps.edu [137.131.252.44]) by relay2.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id MAA25794; Thu, 14 Oct 1999 12:16:02 -0700 (PDT) Received: (from lou@localhost) by degas.scripps.edu (8.9.2/TSRI-3.0.1) id MAA11093; Thu, 14 Oct 1999 12:16:02 -0700 (PDT) Date: Thu, 14 Oct 1999 12:16:02 -0700 (PDT) From: Lou Noodleman Message-Id: <199910141916.MAA11093@degas.scripps.edu> To: yubofan@guomai.sh.cn Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? Cc: chemistry@ccl.net X-Sun-Charset: US-ASCII Dear Yubo Fan and CCL, DFT, especially in the form of gradient corrected potentials has proved suitable for many applications involving H-bonds. This includes water clusters, H-bond donor-acceptor systems, for metal ions in solution (redox processes)(see Li et al Inorg. Chem. 1996, 35, 4694-4702), and for transition metal complexes in proteins (metalloproteins)(Li et al., Inorg. chem. 1999, 38,929-939, Konecny et al., Inorg. Chem. 1999, 38, 940-950). Overall, fairly polar, dipolar, or especially charged H bonds look to be well-represented in most cases. One Ref. is Pudzianowski, J.Phys.Chem.1996, 100, 4781-4789. Another example is the recent discussion and controversy in the literature over low-barrier hydrogen bonds (LBHB) or more generally, short strong hydrogen bonds (SSHB). Hydrogen bond energies are quite similar for density functional (BLYP) versus ab initio MP2 results (for substituted formate-formic acid dimers) (see Kumar and McAlister J.A.C.S. 1998, 120, 3159). Whatever the outcome of this controversy, DFT methods look suitable for analyzing these issues. DFT does have some specific deficiencies for delocalized 3-electron bonds, which are too stable. So, for example, the ground state of the [(H2O)2]+ radical cation is incorrectly found as the "hemibond" structure rather than the correct proton transferred OH-H3O+ isomer.(Sodupe et al., J.Phys.Chem.A 1999, 103, 166-170.) This corresponds to a problem that my coworkers and I identified in DFT long ago (Noodleman, Post, Baerends Chem. Phys. 1982, 64, 159. This can be partially remedied by looking for broken symmetry DFT solutions with charge asymmetry.) Overall, however, this is an atypical problem. In terms of H-bonded systems, it appears that quite weak H-bonds are difficult for DFT. Weak long range Van der Waals interactions (dispersion energies) are also evidently not well treated by standard DFT methods from what I have seen (as might be expected). Louis Noodleman Department of Molecular Biology The Scripps Research Institute, TPC15 La Jolla, CA 92037 . From chemistry-request@server.ccl.net Thu Oct 14 12:35:32 1999 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA20173 for ; Thu, 14 Oct 1999 12:35:31 -0400 Received: (qmail 13185 invoked from network); 14 Oct 1999 16:29:48 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 14 Oct 1999 16:29:48 -0000 Received: from egppp1.physics.upatras.gr by pythagoras.physics.upatras.gr with SMTP (1.36.108.4/16.2) id AA09346; Thu, 14 Oct 1999 19:35:29 GMT Message-Id: <001301bf1660$d93a2080$5d9f8c96@stelios> From: "garoufal" To: Subject: about ArgusLab Date: Thu, 14 Oct 1999 19:26:19 +0300 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0010_01BF1679.FDDF7FC0" X-Priority: 3 X-Msmail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0010_01BF1679.FDDF7FC0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCLers I have downloaded and installed ArgusLab and I have a problem. The parameters for all the supported Hamiltonians (AM1,PM3,MNDO,EHT) are included in a directory and can be easily accessed. There is no evidence about where the parameters of the INDO1/S method are. I want to use this approximation to systems that mainly contain Si. The program gives me an error saying that there are not parameters for Si. Is there a way=20 to access the INDO1/S parameters or add new parameters to the program? Thanks in advance Christos S. Garoufalis Department of Physics, University of Patras, Greece ------=_NextPart_000_0010_01BF1679.FDDF7FC0 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear CCLers
 
I have downloaded and installed=20 ArgusLab
and I have a problem.
The parameters for all the supported = Hamiltonians (AM1,PM3,MNDO,EHT)
are included in a directory and can = be easily=20 accessed.
There is no evidence about where the = parameters
of the INDO1/S method = are.
I want to use this approximation to = systems=20 that
mainly contain Si. The program gives = me an=20 error
saying that there are not parameters = for Si. Is=20 there a way
to access the INDO1/S parameters or = add new=20 parameters to
the program?
 
Thanks in advance
Christos S. Garoufalis
Department of Physics, University of = Patras,=20 Greece
 
------=_NextPart_000_0010_01BF1679.FDDF7FC0-- From chemistry-request@server.ccl.net Thu Oct 14 11:59:28 1999 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.90.174] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19965 for ; Thu, 14 Oct 1999 11:59:28 -0400 Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.3/UCB 8.8.8/8.7) with SMTP id LAA17136; Thu, 14 Oct 1999 11:00:40 -0500 Date: Thu, 14 Oct 1999 11:00:40 -0500 (CDT) From: Tapas Kar To: Meike Reinhold cc: chemistry Subject: Re: CCL:symmetry in G98 In-Reply-To: <3804AD16.58C52F9F@york.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try with "SCF=SYMM" On Wed, 13 Oct 1999, Meike Reinhold wrote: > Date: Wed, 13 Oct 1999 17:02:30 +0100 > From: Meike Reinhold > To: chemistry > Subject: CCL:symmetry in G98 > > HI All, > > I have asked this question already some time ago, but I am still not > totally clear about the use of symmetry in Gaussian. > Maybe somebody would be so nice to point me to a good reference or so. > The question is: > I want to calculate the geometry and the frequencies of a highly > symmetric molecule (in this case D6H). The variables have been chosen in > order to be D6H, this means the bond length, etc. which generate the > symmetry have all the same variable. > If I use only the default input without the symmetry keyword, than G98 > recognizes the symmetry, but during the optimization it aborts the > calculation because the molecule has no longer D6H symmetry (this is > what I make out from the error message). > Symmetry saves time and helps in a lot of ways. > COuld somebody explain me what exactly happens in simple words? > Thanks, > Meike Reinhold > Ph.D. Student > Chemistry Department > York University > UK > > -= 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 > > > > > > -------------------------------------------- Tapas Kar, Ph. D Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 14 11:44:41 1999 Received: from chemsun.chem.umn.edu (chemsun.chem.umn.edu [128.101.157.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA19754 for ; Thu, 14 Oct 1999 11:44:41 -0400 From: giesen@chem.umn.edu Received: (qmail 1690 invoked by uid 395); 14 Oct 1999 10:39:06 -0500 Message-ID: <19991014153906.1689.qmail@chemsun.chem.umn.edu> Subject: CCL:Installation of g98 Rev A7 (fwd) To: CHEMISTRY@ccl.net Date: Thu, 14 Oct 1999 10:39:06 -0500 (CDT) X-Mailer: ELM [version 2.4ME+ PL40 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Doug Fox from Gaussian was kind enough to help me with this problem. There are two issues: 1) The compilers need to be version 7.3 (I had 7.2.1 when I had the problem) or a patched version of the 7.2 compilers. A quick, convenient way to check F77 compiler versions is the command versions | grep 'Fortran 77 Headers' and 2) A revised makefile must be obtained from Gaussian. Dave Giesen Eastman Kodak ----- Forwarded message from Christoph.van.Wuellen@ruhr-uni-bochum.de ----- From chemistry-request@server.ccl.net Thu Oct 14 14:09:10 1999 Received: from oz.che.rochester.edu (janeou@oz.che.rochester.edu [128.151.211.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20666 for ; Thu, 14 Oct 1999 14:09:09 -0400 Received: (from janeou@localhost) by oz.che.rochester.edu (8.9.3/8.9.3) id OAA17478; Thu, 14 Oct 1999 14:03:32 -0400 (EDT) Date: Thu, 14 Oct 1999 14:03:32 -0400 (EDT) From: Jane-Jane Ou Message-Id: <199910141803.OAA17478@oz.che.rochester.edu> To: CHEMISTRY@ccl.net Subject: Constant Volume Simulation of Amber Cc: janeou@oz.che.rochester.edu Dear CCLers: How to run constant volume simulation with Amber wihout water molecules or other solvent? Are the control words for volume dimensions in the input file of edit module? If they are, how to use them? Thank you very much. Best regards, Jane From chemistry-request@server.ccl.net Thu Oct 14 15:27:18 1999 Received: from deliverator.sgi.com (deliverator.sgi.com [204.94.214.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA21394 for ; Thu, 14 Oct 1999 15:27:17 -0400 Received: from nodin.corp.sgi.com (fddi-nodin.corp.sgi.com [198.29.75.193]) by deliverator.sgi.com (980309.SGI.8.8.8-aspam-6.2/980310.SGI-aspam) via ESMTP id MAA26111; Thu, 14 Oct 1999 12:20:17 -0700 (PDT) mail_from (omar@boston.sgi.com) Received: from sgibos.boston.sgi.com (sgibos.boston.sgi.com [169.238.32.4] (may be forged)) by nodin.corp.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA15230; Thu, 14 Oct 1999 12:21:32 -0700 (PDT) Received: from arkham.boston.sgi.com (arkham.boston.sgi.com [169.238.35.21]) by sgibos.boston.sgi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id PAA92042; Thu, 14 Oct 1999 15:21:31 -0400 (EDT) Received: from localhost (omar@localhost) by arkham.boston.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id PAA06243; Thu, 14 Oct 1999 15:21:30 -0400 (EDT) Date: Thu, 14 Oct 1999 15:21:30 -0400 (EDT) From: Omar Stradella To: Christoph.van.Wuellen@ruhr-uni-bochum.de cc: Jens Antony , chemistry@ccl.net Subject: Re: CCL:Installation of g98 Rev A7 In-Reply-To: <19991014114756.19764.qmail@sgi249.rz.ruhr-uni-bochum.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 14 Oct 1999 Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > My experience compiling g98 rev a7 on SGI R10000 was similar: I could compile > the program but the executable immedeately bombs (in the malloc function in > my case). I guess there must some OS incompatibilies between different > versions/patchlevels of IRIX. > > Without 64-bit integers (i.e. with the 'old' Makefile), everything is OK. > So if you have less than 2 GB memory, you might be happy with this solution. Some old versions of the compiler had problems with -i8 (I assume that's what you call 64-bit integers, even though you can have 64-bit integers without using -i8). There is no connection between -i8 and being able to address more than 2GB of memory, that's enabled by using 64-bit pointers (-64), -i8 allows you to create bigger files. Omar. +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. SGI / Chemistry and Biology Applications Group One Cabot Road, Hudson, MA 01749, USA N 42 22'40" W 71 33'44" E-mail: omar@boston.sgi.com Phone: +1-978-567-2258 FAX: +1-978-562-4755 http://www.sgi.com/chembio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From chemistry-request@server.ccl.net Thu Oct 14 20:51:58 1999 Received: from hestia.its.deakin.edu.au (root@hestia.its.deakin.edu.au [128.184.136.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA23465 for ; Thu, 14 Oct 1999 20:51:56 -0400 Received: from [128.184.88.60] (ara10.bcs.deakin.edu.au [128.184.88.60]) by hestia.its.deakin.edu.au (8.9.3/8.9.3) with ESMTP id KAA28941 for ; Fri, 15 Oct 1999 10:46:07 +1000 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: lim@128.184.136.2 Message-Id: Date: Fri, 15 Oct 1999 10:48:17 +1000 To: chemistry@ccl.net From: "Kieran F Lim (Lim Pak Kwan)" Subject: CCL: Q: greek letters in HTML? How can I put greek letters into a HTML page? Can someone please point me to a reference/help site? thanks Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Thu Oct 14 23:47:34 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA24077 for ; Thu, 14 Oct 1999 23:47:34 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id XAA18483; Thu, 14 Oct 1999 23:43:07 -0400 (EDT) Date: Thu, 14 Oct 1999 23:43:07 -0400 (EDT) From: Iraj Daizadeh To: "Kieran F Lim (Lim Pak Kwan)" cc: chemistry@ccl.net Subject: Re: CCL:Q: greek letters in HTML? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII latex2html --- everything should be done in tex/latex...just for your reference. iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh On Fri, 15 Oct 1999, Kieran F Lim (Lim Pak Kwan) wrote: > How can I put greek letters into a HTML page? > Can someone please point me to a reference/help site? > > thanks > > Kieran > ------------------------------------------------------------ > Dr Kieran F Lim Biol. and Chemical Sciences > (Lim Pak Kwan) Deakin University > ph: + [61] (3) 5227-2146 Geelong VIC 3217 > fax: + [61] (3) 5227-1040 AUSTRALIA > mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim > > -= 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 > > > > > >