From chemistry-request@server.ccl.net Mon Apr 14 16:35:54 2003 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3EKZr301367 for ; Mon, 14 Apr 2003 16:35:53 -0400 Received: from LAQUICOM02 (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.6) with SMTP id h3ELESk27847 for ; Mon, 14 Apr 2003 14:14:28 -0700 Message-ID: <011c01c302c5$6a5d2d10$8400000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: CBS basis sets Date: Mon, 14 Apr 2003 14:35:41 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0119_01C30293.1FA15260" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0119_01C30293.1FA15260 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear netters: In the CBS-QB3 chemistry model that is included with Gaussian (Petersson and coworkers), there are three basis sets involved: CBSB7, CBSB3 and CBSB4. Can somebody tell me how they line up with Pople style basis sets ? I know that CBSB7 =3D 6-311G(2d,d,p) but I would like to know about the other two. Thanks in advance Dr. Daniel Glossman-Mitnik *************************************************************************= *** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com *************************************************************************= *** -------------------------------------------------------------------------= ------- =20 ------=_NextPart_000_0119_01C30293.1FA15260 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Dear netters:

In the CBS-QB3 chemistry model that is included with Gaussian

(Petersson and coworkers), there are three basis sets = involved:

CBSB7, CBSB3 and CBSB4.

Can somebody tell me how they line up with Pople style basis

sets ?

I know that CBSB7 =3D 6-311G(2d,d,p)

but I would like to know about the other two.

Thanks in advance

&n= bsp; &nb= sp; =20 Dr. Daniel Glossman-Mitnik

********************************************************************= ********
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigacion en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109 = -=20 Mexico
Phone: (52) 614 4391151      FAX: = (52) 614=20 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
&n= bsp;         =20 dglossman@yahoo.com
**********= ******************************************************************

<= !--mail_content-->

------=_NextPart_000_0119_01C30293.1FA15260-- From chemistry-request@server.ccl.net Mon Apr 14 17:58:03 2003 Received: from igor.wag.caltech.edu ([131.215.26.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3ELw2303691 for ; Mon, 14 Apr 2003 17:58:02 -0400 Received: from wag.caltech.edu (DHCP-26-219 [131.215.26.219]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id OAA2465541 for ; Mon, 14 Apr 2003 14:57:57 -0700 (PDT) Date: Mon, 14 Apr 2003 14:57:59 -0700 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: PyQuante 1.1.1 available (Quantum Chemistry in Python) From: Richard Muller To: chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: <282C9AB2-6EC4-11D7-B447-000393B63452@wag.caltech.edu> X-Mailer: Apple Mail (2.552) PyQuante (http://pyquante.sourceforge.net) is a suite of programs for writing quantum chemistry software. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed. The resulting code is not nearly as fast as Jaguar, Gaussian, or GAMESS, but the resulting code is much easier to understand and modify. The goal of this software is not necessarily to provide a working quantum chemistry program (although it will hopefully do that), but rather to provide a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write everything. The program is released under the GNU General Public License and is thus freeware. PyQuante can be downloaded from http://pyquante.sourceforge.net. People can subscribe to the pyquante-users mailing list at http://lists.sourceforge.net/lists/listinfo/pyquante-users FEATURES * Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques. * Closed shell and unrestricted open-shell Hartree Fock * LDA DFT * MINDO/3 semiempirical energies and forces * Leapfrog Verlet dynamics and simple minimizers * Configuration Interaction Singles excited states * DIIS convergence acceleration * MP2 calculation of the correlation energy Here is an example of what the closed-shell Hartree-Fock scripts look like: (best viewed in a fixed-width font...) def rhf(atomlist): "General wrapper for restricted closed-shell hartree fock" bfs = getbasis(atomlist,basis) S,h,Ints = getints(bfs,atomlist) orbs = get_guess(h,S) nel = get_nel(atomlist,charge) nclosed,nopen = divmod(nel,2) enuke = get_enuke(atomlist) eold = 0. for i in range(MaxIter): D = mkdens(evecs,0,nocc) G = get2JmK(Ints,D) F = h+G evals,evecs = GHeigenvectors(F,S) energy = get_energy(h,F,D,enuke) print energy if abs(energy-eold) < ConvCriteria: break eold = energy return energy Rick Muller rpm@wag.caltech.edu http://wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Mon Apr 14 14:33:28 2003 Received: from mail1.WPI.EDU ([130.215.36.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3EIXR329136 for ; Mon, 14 Apr 2003 14:33:27 -0400 Received: from mcafee.wpi.edu (mcafee.WPI.EDU [130.215.36.86]) by mail1.WPI.EDU (8.12.9/8.12.9) with SMTP id h3EIXRH5000844 for ; Mon, 14 Apr 2003 14:33:27 -0400 Received: from smtp.wpi.edu(130.215.36.186) by mcafee.wpi.edu via csmap id 13499; Mon, 14 Apr 2003 14:35:10 -0400 (EDT) Received: from grover.WPI.EDU (root@grover.WPI.EDU [130.215.25.67]) by smtp.WPI.EDU (8.12.9/8.12.9) with ESMTP id h3EIXQK2019696 for ; Mon, 14 Apr 2003 14:33:27 -0400 Received: from grover.WPI.EDU (rconnors@localhost [127.0.0.1]) by grover.WPI.EDU (8.12.8/8.12.8) with ESMTP id h3EIXQxL024006 for ; Mon, 14 Apr 2003 14:33:26 -0400 (EDT) Received: from localhost (rconnors@localhost) by grover.WPI.EDU (8.12.8/8.12.8) with ESMTP id h3EIXQYq025146 for ; Mon, 14 Apr 2003 14:33:26 -0400 (EDT) X-Authentication-Warning: grover.WPI.EDU: rconnors owned process doing -bs Date: Mon, 14 Apr 2003 14:33:26 -0400 (EDT) From: Robert E Connors To: chemistry@ccl.net Subject: CCL:ZINDO MO's Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am running zindo calculations with Gaussian98 and having trouble printing out the mo's (orbital eigenvectors). Pop=reg doesn't seem to do it. Any suggestions? Thanks, ------------------------------------------------------------------------ Robert E. Connors Professor of Chemistry Worcester Polytechnic Institute Worcester,MA 01609 email:rconnors@wpi.edu phone:(508) 831-5394 fax:(508) 831-5933 From chemistry-request@server.ccl.net Mon Apr 14 21:41:10 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3F1a7308628 for ; Mon, 14 Apr 2003 21:37:45 -0400 Received: from zhang1 (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id HAA15838; Tue, 15 Apr 2003 07:56:44 +0800 (CST) Message-Id: <200304142356.HAA15838@ns.ciac.jl.cn> From: "zjwu" To: "chemistry@ccl.net" CC: "help@gaussian.com" Subject: Re:CCL:PCM frequency calculation X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====002_Dragon517742747754_=====" Date: Tue, 15 Apr 2003 7:54:6 +0800 This is a multi-part message in MIME format. --=====002_Dragon517742747754_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Hi, Douglas, Thanks a lot for your comments. Meanwhile I would also like to thank Maciek Haranczyk and Mirco Meniconi for their concerns and answers about my questions on PCM frequency calculations. I have just finished one CPCM frequency calculation, it seems as Dr. Haranczyk said, it takes a lot of time to finish the calculation. On my case, Onsager frequency calculation takes about one hour, but CPCM model takes about 14 hours (keywords, freq=numer, scrf=cpcm). I will also try to use the default parameters as Doug suggested and will report results when it is available. Thank you very much again for you all. Best wishes, wu ------------------ Prof. Zhijian Wu, Ph.D Key Laboratory of Rare Earth Chemistry and Physics Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China Email: zjwu@ciac.jl.cn Dr. Wu, G98 does not implement analytic second derivatives for the PCM methods. You don't need to use FREQ=NUMER, the correct option will be selected by default, but the program will do a number of gradient calculations with each atom in turn displaced along cartesian directions. Formally 6 points per atom will be done but symmetry can be used to reduce this. So while it seems like it goes on forever it probably does not. >> >> Dear cclers, >> Does anybody know how to run PCM frequency calculation on PCM optimized geometry? I have tried to run PCM frequency calculation with the keywords: >> #B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water) >> but it seems the frequency calculation never stops. Any suggestions are appreciated. >> Regards, >> Zhijian Wu >> >> --=====002_Dragon728447207021_===== >> Content-Type: text/html; >> charset="GB2312" >> Content-Transfer-Encoding: 7bit >> >> < !DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> >> < HTML> < HEAD> >> < META http-equiv=Content-Type content="text/html; charset=gb2312"> >> < META content="MSHTML 6.00.2462.0" name=GENERATOR> < /HEAD> >> < BODY> >> Dear cclers, >> Does anybody know how to run PCM frequency calculation on PCM optimized >> geometry? I have tried to run PCM frequency calculation with the keywords: >> #B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water) >> but it seems the frequency calculation never stops. Any suggestions are >> appreciated. >> Regards, >> Zhijian Wu < /BODY> < /HTML> >> >> --=====002_Dragon728447207021_=====-- >> >> >> >> >> >> -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com --=====002_Dragon517742747754_===== Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: 7bit

Hi, Douglas,

Thanks a lot for your comments. Meanwhile I would also like to thank Maciek Haranczyk and Mirco Meniconi for their concerns and answers about my questions on PCM frequency calculations.

I have just finished one CPCM frequency calculation, it seems as Dr. Haranczyk said, it takes a lot of time to finish the calculation. On my case, Onsager frequency calculation takes about one hour, but CPCM model takes about 14 hours (keywords, freq=numer, scrf=cpcm). I will also try to use the default parameters as Doug suggested and will report results when it is available.

Thank you very much again for you all.

Best wishes,

------------------

Prof. Zhijian Wu, Ph.D

Key Laboratory of Rare Earth Chemistry and Physics

Changchun Institute of Applied Chemistry

Chinese Academy of Sciences

Changchun 130022

China

Email: zjwu@ciac.jl.cn

Dr. Wu,

G98 does not implement analytic second derivatives for the PCM methods.

You don't need to use FREQ=NUMER, the correct option will be selected by

default, but the program will do a number of gradient calculations with each

atom in turn displaced along cartesian directions. Formally 6 points per

atom will be done but symmetry can be used to reduce this.

So while it seems like it goes on forever it probably does not.

>> Dear cclers,

>> Does anybody know how to run PCM frequency calculation on PCM optimized geometry? I have tried to run PCM frequency calculation with the keywords:

>> #B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water)

>> but it seems the frequency calculation never stops. Any suggestions are appreciated.

>> Regards,

>> Zhijian Wu

>> --=====002_Dragon728447207021_=====

>> Content-Type: text/html;

>> charset="GB2312"

>> Content-Transfer-Encoding: 7bit

>> < !DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

>> < HTML> < HEAD>

>> < META http-equiv=Content-Type content="text/html; charset=gb2312">

>> < META content="MSHTML 6.00.2462.0" name=GENERATOR> < /HEAD>

>> < BODY>

>> Dear cclers,

>> Does anybody know how to run PCM frequency calculation on PCM optimized

>> geometry? I have tried to run PCM frequency calculation with the keywords:

>> #B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water)

>> but it seems the frequency calculation never stops. Any suggestions are

>> appreciated.

>> Regards,

>> Zhijian Wu < /BODY> < /HTML>

>> --=====002_Dragon728447207021_=====--

Douglas J. Fox

Technical Support

Gaussian, Inc.

help@gaussian.com

--=====002_Dragon517742747754_=====-- From chemistry-request@server.ccl.net Tue Apr 15 03:18:11 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3F7IA314742 for ; Tue, 15 Apr 2003 03:18:10 -0400 Received: (qmail 14836 invoked by uid 505); 15 Apr 2003 07:08:49 -0000 Received: from victor@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.045022 secs); 15 Apr 2003 07:08:49 -0000 Received: from unknown (HELO PION) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 15 Apr 2003 07:08:49 -0000 Message-ID: <00d201c3031f$2b274810$2d0a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: Subject: New linear scaling method Date: Tue, 15 Apr 2003 09:18:09 +0200 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 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear Colleagues, The cost of drug design is escalating in spite of many strong experimental techniques emerged last decade, promising the cost saving. Combinatorial chemistry, gene expression technique have opened new horizons for drug design but have contributed their part to the continuing growth of the cost, as well. Thus it seems the task of fulfilling the promise to reduce the cost of drug design is impossible without the progress being made in the computational chemistry. The predictive capability of the computational tools strongly depends on theoretical methodology employed. The description or real physics of atomic level phenomena by using the Quantum Mechanics becomes an ultimate requirement. However a severe limitation of the QM methodology is an enormous computer resource demand. This requires new ideas being developed how to avoid the performance bottleneck and the recently created LocalSCF approach is one of them. LocalSCF solution of the SCF task is implemented at present for the semiempirical framework with the thought of quantum chemical calculations of real life complex proteins. The method represents the first full variational approach to the linear scaling problem. This makes the method faster, more stable and more accurate than the traditional cut-off based linear scaling methods known at present. Developed for a popular PC platform the LocalSCF can handle 100,000+ atoms real life complex proteins. Thus, for example, 10 steps of full geometry optimization on the 90,000+ protein (Hsluv Protease-Chaperone Complex, PDB id 1G3I) require 27 hours on a single processor Pentium-4 / 2.4GHz computer. The method allows simple control for balancing between speed and accuracy and for validation of the quality of the density matrix upon selection of a faster calculation mode. This time I can respond on the old question, which appeared some time ago on the CCL list, asking what is the biggest system calculated by a QM method? To the best of my knowledge this is a LocalSCF calculation of the GroEL-GroES chaperonin complex containing 119,273 atoms (PDB id 1AON). The energy calculation at the frozen geometry was performed on a regular 32-bit Windows PC and took 4 hours 30 minutes. The RAM requirement was 1.3GB. If one had a good molecular structure the 2Gb memory limit would allow calculating nearly 200,000 atoms real 3D molecular system. Is this enough or still there is a need to switch to a 64-bit platform? Besides of the present capabilities the method has strong future perspectives for those who are interested in developing the method further. The LocalSCF methodology allows highly effective parallelization of the code. The ability to treat different parts of the molecule with different accuracy allows implementation of a full QM alternative to the popular QM/MM approaches. The LocalSCF method can be extended for the DFT and ab initio frameworks as well. These are features to be developed. A brochure describing present capabilities of the computer program is available on request. The LocalSCF manuscript is submitted for publication to the Chemical Physics Letters. The preprint of the paper is available from the Chemistry Preprint Server http://preprint.chemweb.com/physchem/0304005 Please don't hesitate to contact me if there are any questions. With kind regards, Victor -- Victor Anisimov, PhD FQS Poland, Fujitsu Krakow, Poland Tel: +48 12 429-4345, Fax: + 48 12 429-6124 E-mail: victor@fqspl.com.pl From chemistry-request@server.ccl.net Tue Apr 15 16:03:02 2003 Received: from webmail.Stanford.EDU ([171.64.12.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3FK32310856 for ; Tue, 15 Apr 2003 16:03:02 -0400 Received: (from wwwd@localhost) by webmail.Stanford.EDU (8.12.9/8.12.9) id h3FK300f002015; Tue, 15 Apr 2003 13:03:00 -0700 (PDT) X-Authentication-Warning: webmail.Stanford.EDU: wwwd set sender to gorelsky@stanford.edu using -f To: Robert E Connors Subject: Re: CCL:ZINDO MO's Date: Tue, 15 Apr 2003 13:03:00 -0700 From: "S. I. Gorelsky" Cc: chemistry@ccl.net Message-ID: <1050436980.3e9c6574149c3@webmail.stanford.edu> References: In-Reply-To: X-Mailer: Stanford Webmail v1.1.6 17-June-2002 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit Please use the overlay option IOp(5/33=2) to get the ZINDO orbitals. Serge Quoting Robert E Connors : > I am running zindo calculations with Gaussian98 and having trouble > printing out the mo's (orbital eigenvectors). Pop=reg doesn't seem to > do > it. Any suggestions? > Thanks, > > ---------------------------------------------------------------------- -- > Robert E. Connors > Professor of Chemistry > Worcester Polytechnic Institute > Worcester,MA 01609 > email:rconnors@wpi.edu > phone:(508) 831-5394 > fax:(508) 831-5933 > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > Dr. S.I. Gorelsky Department of Chemistry, Stanford University Box 155, Mudd Bldg., 333 Campus Drive, Stanford, California 94305-5080 U.S.A. From jkl@ccl.net Tue Apr 15 16:08:54 2003 -0400 Return-Path: Reply-To: From: "Mark Thompson" To: Subject: Updated set of INDO/s parameters on the ArgusLab (Si and P) Date: Tue, 15 Apr 2003 13:06:52 -0700 Message-ID: <000501c3038a$8e52ff40$0300a8c0@attbi.com> We've posted an updated set of INDO/s parameters on the ArgusLab website. These include parameters for Si and P. (click on the downloads button on the homepage). Please send email to info@arguslab.com for any questions or problems with this download. ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 =================================