From chemistry-request@ccl.net Fri Jul 18 12:36:43 2003 Received: from ufpe.br (h249.ip179.ufpe.br [150.161.179.249] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6IGaejq020085 for ; Fri, 18 Jul 2003 12:36:41 -0400 Received: (qmail 21913 invoked from network); 18 Jul 2003 16:36:46 -0000 Received: from h74.ip174.ufpe.br (HELO storm) (150.161.174.74) by 0 with SMTP; 18 Jul 2003 16:36:46 -0000 Message-ID: <00c301c34d4b$ddd7f6f0$4aaea196@storm> From: "Marcelo Zaldini Hernandes" To: "CCL" Subject: CCL: AGOA v2.0 announcement Date: Fri, 18 Jul 2003 13:44:33 -0300 Organization: UFPE MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00C0_01C34D32.B8786F70" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_00C0_01C34D32.B8786F70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers and AGOA users: I would like to announce the new version of the agoa program, AGOA = v2.0. Current improvements are: - Automatic selection of the number of water molecules around solute, = using the solvent accessible surface area (SASA); - A more flexible routine to explore numerical gradients of the = Molecular Electrostatic Potential (MEP); - The implementation of a cutoff radius for solvent (water) molecule, to = avoid high correlated structures of hydration; - Implementation of all geometries in cartesian coordinates; - And others... Details of the methodology and instructions about the availability = of the program could be found at: http://www.ufpe.br/farmacia/zaldini/agoa.html (link agoa v2.0) =20 or direct link: http://www.ufpe.br/farmacia/zaldini/instruc-agoa.html The program is free of charge only for academic usage. The software request could be also sent from an external server: http://server.com/WebApps/db-submit.cgi?id=3D105417 Best Regards, =20 ************************************************************** Prof. MARCELO ZALDINI HERNANDES, Ph.D. LQTM - Laboratorio de Quimica Teorica Medicinal UFPE - Universidade Federal de Pernambuco CCS - Centro de Ciencias da Saude Depto. de Ciencias Farmaceuticas Rua Prof. Arthur de Sa', s/n, Cidade Universitaria,=20 Recife, Pernambuco, Brasil CEP 50740-521 - Fone 81-32718511 FAX 81-32718510 http://www.ufpe.br/farmacia/zaldini mailto:zaldini|at|ufpe.br ************************************************************** --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.501 / Virus Database: 299 - Release Date: 14/7/2003 ------=_NextPart_000_00C0_01C34D32.B8786F70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
    Dear CCLers and AGOA = users:
 
    I would like to = announce the new=20 version of the agoa program, AGOA v2.0.
    Current = improvements=20 are:

-=20 Automatic selection of the number of water molecules around solute, = using the=20 solvent accessible surface area (SASA);

- A=20 more flexible routine to explore numerical gradients of the Molecular=20 Electrostatic Potential (MEP);

-=20 The implementation of a cutoff radius for solvent (water) molecule, to = avoid=20 high correlated structures of hydration;

-=20 Implementation of all geometries in cartesian coordinates;

-=20 And others...

    Details of the methodology and = instructions=20 about the availability of the program could be found at:

http://www.ufpe.br= /farmacia/zaldini/agoa.html     =20 (link agoa v2.0)  

or=20 direct link:   http://www= .ufpe.br/farmacia/zaldini/instruc-agoa.html

    The program is free of charge only for = academic=20 usage.

    The software request could be also sent=20 from an external server:

http://serve= r.com/WebApps/db-submit.cgi?id=3D105417

   =20 Best Regards,

   
 
**************************************************************Prof.=20 MARCELO ZALDINI HERNANDES, Ph.D.
LQTM - Laboratorio de Quimica = Teorica=20 Medicinal
 
UFPE - Universidade Federal de = Pernambuco
CCS -=20 Centro de Ciencias da Saude
Depto. de Ciencias Farmaceuticas
Rua = Prof.=20 Arthur de Sa', s/n, Cidade Universitaria,
Recife, Pernambuco, = Brasil
CEP=20 50740-521 - Fone 81-32718511 FAX 81-32718510
 
http://www.ufpe.br/farmacia/= zaldini
mailto:zaldini|at|ufpe.br
***********= ***************************************************
 

---
Outgoing mail is certified = Virus=20 Free.
Checked by AVG anti-virus system (http://www.grisoft.com).
Version: = 6.0.501 /=20 Virus Database: 299 - Release Date: 14/7/2003
------=_NextPart_000_00C0_01C34D32.B8786F70-- From chemistry-request@ccl.net Fri Jul 18 11:56:58 2003 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6IFuwjq018566 for ; Fri, 18 Jul 2003 11:56:58 -0400 Received: (qmail 25671 invoked by uid 504); 18 Jul 2003 15:56:57 -0000 Received: from elewars|at|trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.16 ( Clear:. Processed in 0.02748 secs); 18 Jul 2003 15:56:57 -0000 X-Qmail-Scanner-Mail-From: elewars|at|trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.16 (Clear:. Processed in 0.02748 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 18 Jul 2003 15:56:56 -0000 Message-ID: <3F181984.D442B7FD|at|trentu.ca> Date: Fri, 18 Jul 2003 12:00:04 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Connie Chang , chemistry|at|ccl.net Subject: Re: CCL:`Long range Coulomb forces in PM3 semiempirical methods? References: <3F16C712.4060905|at|cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 July 18 Hello, If by long range coulombic forces you mean van der Waals forces, SE methods probably can't be relied on, although in particular cases they may give (happen to give) reasonable results. See: C. J. Cramer, _Essentials of Computational Chemistry_, Wiley, 2002, p 139: "For intermolecular interactions that are weak in nature, e.g. those arising from London forces (dispersion) or hydrogen bonding, semiempirical methods are in general unreliable." Standard SE methods don't really "include" van der Waals forces, because they were parameterized with an eye on heats of formation, geometries, ionization potentials, and dipole moments. E. Lewars =========== Connie Chang wrote: > Hi -- > > I was wondering if anyone out there knew if the PM3 semiempirical method > includes long range Coloumbic forces? > > Thanks! > Connie Chang > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl|at|ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jul 18 11:58:45 2003 Received: from compton.acpub.duke.edu (compton.acpub.duke.edu [152.3.233.74]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6IFwijq018656 for ; Fri, 18 Jul 2003 11:58:45 -0400 Received: from CONCORDIA (concordia.lib.duke.edu [152.16.191.233]) by compton.acpub.duke.edu (8.12.9/8.12.9/Duke-5.0.0) with SMTP id h6IFwhEC007874; Fri, 18 Jul 2003 11:58:43 -0400 (EDT) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: how to change convergence criteria? Date: Fri, 18 Jul 2003 11:50:28 -0400 Message-ID: <007101c34d44$4f6d3da0$eabf1098@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcNNRE9tJKcw/KcdSeSFxa+Na3sQSw== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear all, I am using Gaussian98 to do geometry optimization for a system including about 150 atoms. But the optimization seems to take a long long time. So I want to change the cutoff value of the convergence. How can I do that? Will you please give some suggestions? Thanks a lot! Best, Jeny From chemistry-request@ccl.net Fri Jul 18 14:33:19 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6IIXJjq023942 for ; Fri, 18 Jul 2003 14:33:19 -0400 Received: from cornell.edu (wing.ccmr.cornell.edu [128.84.241.85]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id OAA20993 for ; Fri, 18 Jul 2003 14:33:14 -0400 (EDT) Message-ID: <3F183D6A.9010206(at)cornell.edu> Date: Fri, 18 Jul 2003 14:33:14 -0400 From: Connie Chang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2) Gecko/20021203 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: CCL: Do-it-yourself Freq calculations in Gaussian Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello members of the CCL list, I am trying to do a Freq calculation in Gaussian03 with C140 -- two C70 fullerene cages linked by single bonds. Whereas the neutral case is very pliable and the Opt Freq combined job takes three hours, I am just having a devil of a time trying to do the same thing for the charged case -- charge = -1. I have several questions regarding this: 1). The optimization converges, but the freq calculation doesn't get beyond the first SCF Energy calculation! How is this possible since many/several SCF energy calculations were already performed during the optimization step? 2). Because my advisor was fed up with the convergence problems of the Freq calculation, he told me to calculate the Hessian myself using Gaussian and the Force keyword. So, I optimize the molecule, and then I change the coordinates one by one by delta and calculate the Forces that result on each atom. After many jobs (I use a batch file), I reassemble my results into a hessian by taking the derivative of the force with respect to displacement using a central difference derivative. I first try this with the neutral case since I already have values for the frequencies based on my successful Opt Freq run for the neutral molecule. My frequencies don't match up at all -- there are many negative eigenvalues for my Hessian despite the fact that my Hessian seems to be symmetric. Am I going about this wrong? Is there a subtlety I am missing? 3). What things can be tweaked to get the SCF energy to converge? I've already tried SCF=Tight and SCF=QC. Any other ways people know of? Thank you and sorry for the long questions... -Connie From chemistry-request@ccl.net Fri Jul 18 17:23:22 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6ILNMjq031106 for >ccl.net>; Fri, 18 Jul 2003 17:23:22 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1369]) by bureau6.utcc.utoronto.ca with SMTP id <464164-22264>; Fri, 18 Jul 2003 17:23:16 -0400 From: "William Wei" >utoronto.ca> To: "CCLers" >ccl.net> Subject: Asking for free molecular surface software-MS Date: Fri, 18 Jul 2003 17:24:34 -0500 Message-ID: >utoronto.ca> 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 IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Importance: Normal Dear CCLers, Could anyone give me a clue that where I can get a free MS software using for DOCK program? Thank you and have a nice weekend. William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william<>phm.utoronto.ca william.wei<>utoronto.ca From chemistry-request@ccl.net Fri Jul 18 15:10:51 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6IJAojq025609 for >ccl.net>; Fri, 18 Jul 2003 15:10:50 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Fri, 18 Jul 2003 16:13:26 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B90<>correio.cetem.gov.br> From: Ian Hovell >cetem.gov.br> To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= >ccl.net> Subject: CCL: constraining the symmetry Date: Fri, 18 Jul 2003 16:13:18 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear CCLers Benzene has two symmetries C2h and C2v I would like to carry out a frequency calculation using G98w, taking only C2v into consideration. Would some kind soul point me in the right direction. Ian Hovell From chemistry-request@ccl.net Fri Jul 18 19:22:56 2003 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6INMsjq001146 for >ccl.net>; Fri, 18 Jul 2003 19:22:55 -0400 Received: from ceasar (pc200.dialup.uoi.gr [195.130.119.200]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id CAA190597; Sat, 19 Jul 2003 02:16:24 +0300 (EEST) Message-ID: <001701c34d83$75dae480$0100a8c0@ceasar> From: "George Papamokos" >cc.uoi.gr> To: "Connie Chang" >cornell.edu>, >ccl.net> References: <3F15A267.5020905<>cornell.edu> Subject: Re: CCL:Long range Coloumb forces included in PM3 semiempirical methods? Date: Sat, 19 Jul 2003 02:21:59 +0300 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 6.00.2600.0000 Disposition-Notification-To: "George Papamokos" >cc.uoi.gr> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear Connie, If you want to include long range interactions in your calculation, you probably need to go to a much heavier level of theory wich includes electron correlation. Semiempirical, HF and DFT methods fail when it comes, for example, to dispersion forces ( London bonds). George Papamokos Ph.D. Student Ioannina University Dept. of Chemistry Sector of Physical Chemistry ----- Original Message ----- From: "Connie Chang" >cornell.edu> To: >ccl.net> Sent: Wednesday, July 16, 2003 10:07 PM Subject: CCL:Long range Coloumb forces included in PM3 semiempirical methods? > Hi -- > > Does anyone know if long range Coloumb forces are included in > semi-empirical methods like PM3? > > Thanks, > Connie > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY<>ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl<>ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > >