From chemistry-request@ccl.net Sun Mar 6 22:53:05 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j273r5s8028541 for ; Sun, 6 Mar 2005 22:53:05 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j273r5WE028539 for chemistry * ccl.net; Sun, 6 Mar 2005 22:53:05 -0500 Date: Sun, 6 Mar 2005 22:53:05 -0500 Message-Id: <200503070353.j273r5WE028539 * server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request * ccl.net using -f From: "Xunlei, , Ding" To: chemistry * ccl.net X-Web-Message-Number: 050306224557-28266 Subject: W:Does Dmol3 has check file ? X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net After I have finished an optimization calculation, I want to do some analysis calculations on the same system, such as electronic populaion. Then must I do a new SCF calculation? Can I use the results of optimization calculation, like Gaussian software, by using the check file? Thank you! From chemistry-request@ccl.net Sun Mar 6 20:50:41 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.205]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j271oes8021880 for ; Sun, 6 Mar 2005 20:50:40 -0500 Received: by rproxy.gmail.com with SMTP id r35so980635rna for ; Sun, 06 Mar 2005 17:50:40 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding; b=Z8Q13cFFe1Vl5dkf4cuUxvSnovdpiX57aEFfbPMZzhO2L632pJgtXrhx0xDIJwaudoHPJjIb9jUOYddb7Qr9rdVoGfZNm5kzH9o8jGXuFu5dvUTM/m2reSX5t3Xzpzoc7/nnYJ5ncytPYEOyp7xDIHJuYxuq5OA9qyFmGVvGOhQ= Received: by 10.38.72.55 with SMTP id u55mr30145rna; Sun, 06 Mar 2005 17:50:39 -0800 (PST) Received: by 10.38.151.50 with HTTP; Sun, 6 Mar 2005 17:50:39 -0800 (PST) Message-ID: Date: Sun, 6 Mar 2005 20:50:39 -0500 From: john furr Reply-To: john furr To: chemistry [a] ccl.net Subject: Dynamol Beta Test 2 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dynamol is proud to announce it's second beta release of the Dynamol Drug Discovery Software. What's New? 1) Windows Release 2) Several bug fixes (sure there are plenty more) 3) Systematic Conformational Search (Certainly not perfect yet) 4) Four new chemical programming functions. 5) Decreased dependency issues with Linux., Also as a heads up I would like to inform everyone that we have decided to maintain a monthly/bi-monthly beta release program. These releases will remain free to academic and non-profit organizations (indefinitely) Once the software is made available commercially we will then charge for-profit companies a license fee as other vendors do. However academic and non-profit's will be able to purchase a license or continue using the free beta releases. Please download the software and then post you gripes/likes/complaints to the user forums. We are interested in hearing were you would like to see Dynamol go...or not go for that matter. http://www.dynamol.com Enjoy! Thanks John Furr john.furr [a] dynamol.com From chemistry-request@ccl.net Sun Mar 6 22:33:03 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j273X2s8027713 for ; Sun, 6 Mar 2005 22:33:02 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j273X2el027711 for chemistry !=! ccl.net; Sun, 6 Mar 2005 22:33:02 -0500 Date: Sun, 6 Mar 2005 22:33:02 -0500 Message-Id: <200503070333.j273X2el027711 !=! server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request !=! ccl.net using -f From: "Xunlei, , Ding" To: chemistry !=! ccl.net X-Web-Message-Number: 050306222240-27296 Subject: W:How to plot the specified orbitals in DMol3 ? X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I want to plot some orbitals much below the HOMO. If I use the key word "Plot Fermi NN", NN will be set to more than 30, and the program will stop with an error for too many orbitals to be plotted. Then how to plot the specified orbitals in DMol3 ? Thank you very much ! From chemistry-request@ccl.net Mon Mar 7 12:06:17 2005 Received: from smtp.prodigy.net.mx (nlpproxy03.prodigy.net.mx [148.235.52.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j27H5nu8015411 for ; Mon, 7 Mar 2005 12:05:50 -0500 Disposition-notification-to: dglossman~at~prodigy.net.mx Received: from smtp.prodigy.net.mx (nlpproxy03 [148.235.52.23]) by smtp.prodigy.net.mx (iPlanet Messaging Server 5.2 HotFix 2.01 (built Aug 26 2004)) with ESMTP id <0ICZ00JPJRHIOW~at~smtp.prodigy.net.mx>; Mon, 07 Mar 2005 11:05:43 -0600 (CST) Received: from chiquita(customer-148-223-46-1.uninet-ide.com.mx [148.223.46.1]) bysmtp.prodigy.net.mx(iPlanet Messaging Server 5.2 HotFix 2.01 (built Aug 26 2004))with ESMTP id <0ICZ00M5XRH7OY~at~smtp.prodigy.net.mx>; Mon, 07 Mar 2005 11:05:42 -0600 (CST) Date: Fri, 07 Jan 2005 10:05:31 -0700 From: "Dr. Daniel Glossman-Mitnik" Subject: CCL: a question about Koopmans' theorem To: chemistry~at~ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Mailer: Microsoft Outlook, Build 10.0.2627 Content-type: multipart/alternative; boundary="----=_NextPart_000_0011_01C4F4A0.6CF58170" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-imss-version: 2.022 X-imss-result: Passed X-imss-scores: Clean:99.90000 C:2 M:3 S:5 R:5 X-imss-settings: Baseline:4 C:4 M:4 S:4 R:4 (8.0000 8.0000) X-Spam-Status: No, hits=6.4 required=7.5 tests=COMBINED_FROM, DATE_IN_PAST_96_XX,DNS_FROM_RFCI_DSN,HTML_70_80, HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C4F4A0.6CF58170 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 =20 Dear netters: =20 I am a bit confused about Koopmans=92 theorem. In Essentials of Computational Chemistry, C.J. Cramer, Wiley, 2002, we can read on page 181: =93=85Koopmans=92 theorem equates the energy of the HOMO with the IP=85=94. On page 182, = we can read =93=85Koopmans=B4 theorem can be formally applied to electron affinities (EAs) as well. i.e., the EA can be taken to be the orbital energy of the lowest unoccupied (virtual) orbital=85=94 =20 That is IP =3D -E(HOMO) and EA =3D E(LUMO)=20 =20 But many articles, quote the opposite for the EA. =20 As an example, in Reactivity Descriptors, PK Chattaraj et al, in the book Computational Medicinal Chemistry for Drug Discovery, we can read on page 302: =93=85 In ab initio MO theory, I and A can be approximated as = the=20 negative of energies of HOMO and LUMO, respectivelu, using Koopmans=92 theorem=85=94 =20 That is IP =3D -E(HOMO) and EA =3D -E(LUMO) =20 Beyond the validity of this approximation, specially for anions, which one is correct : EA =3D E(LUMO) or EA =3D -E(LUMO) ?? =20 Thanks for your help =20 Daniel=20 =20 =20 ************************************************************ Dr. Daniel Glossman-Mitnik Grupo NANOCOSMO - CIMAV Nanociencia y Nanotecnolog=EDa Computacional Simulaci=F3n y Modelado Molecular Miguel de Cervantes 120 - Comp. Ind. Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391130 Part.: (52) 614 4987113 Cel.: (52) 614 1635322 E-mail: daniel.glossman~at~cimav.edu.mx dglossman~at~prodigy.net.mx ************************************************************* =20 =20 ------=_NextPart_000_0011_01C4F4A0.6CF58170 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear netters:

I am a bit confused = about Koopmans’ theorem. In Essentials of = Computational

Chemistry,=A0 C.J. Cramer, Wiley, 2002, we can = read on page 181: “…Koopmans’

theorem equates the = energy of the HOMO with the IP…”. On page 182, = we

can read “…Koopmans=B4 theorem can be formally applied to electron = affinities

(EAs) as well. i.e., = the EA can be taken to be the orbital energy of the = lowest

unoccupied (virtual) orbital…”

That is=A0 IP =3D -E(HOMO)=A0=A0 and=A0 EA =3D E(LUMO)

But many articles, = quote the opposite for the EA.

As an example, in = Reactivity Descriptors, PK Chattaraj et al, in the = book

Computational = Medicinal Chemistry for Drug Discovery, we can read = on

page 302: = “… In ab initio MO theory, I and A can be approximated as the =

negative of energies = of HOMO and LUMO, respectivelu, using = Koopmans’

theorem…”

That is=A0 IP =3D -E(HOMO)=A0 and=A0 EA =3D = -E(LUMO)

Beyond the validity of = this approximation, specially for anions, which = one

is correct :=A0=A0=A0 EA =3D E(LUMO)=A0=A0 or=A0 EA =3D -E(LUMO)=A0 ??

Thanks for your help

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 Daniel

************************************************= ************

= Dr. Daniel Glossman-Mitnik

= Grupo NANOCOSMO - CIMAV

Nanociencia y Nanotecnolog=EDa Computacional

Simulaci=F3n y Modelado = Molecular

Miguel de Cervantes 120 - Comp. Ind. Chihuahua

Chihuahua, Chih. 31109 - MEXICO

Tel.: (52) 614 4391151 FAX: = (52) 614 4391130

Part.: (52) 614 4987113 Cel.: (52) = 614 1635322

E-mail: daniel.glossman~at~cimav.edu.mx

= dglossman~at~prodigy.net.mx

************************************************= *************

------=_NextPart_000_0011_01C4F4A0.6CF58170-- From chemistry-request@ccl.net Mon Mar 7 10:57:54 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j27Fvsu8012190 for ; Mon, 7 Mar 2005 10:57:54 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j27FvroZ012188 for chemistry~at~ccl.net; Mon, 7 Mar 2005 10:57:53 -0500 Date: Mon, 7 Mar 2005 10:57:53 -0500 Message-Id: <200503071557.j27FvroZ012188~at~server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request~at~ccl.net using -f From: "Giancarlo, , Terraneo" To: chemistry~at~ccl.net X-Web-Message-Number: 050307100250-8068 Subject: W:how to install AIMPAC programs X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi everybody I have problem to install AIMAPC software, I have installed, following the procedure in the web site, te programs grdvec and contor, but I'm not able to install the otherones. When I try to compile the other programs with g77 I have this message: ex.for EXT94b. ---------------------------------- EXT94b.f: In subroutine `props': EXT94b.f:863: SUBROUTINE BOND(X,Y,Z,BL,NCAL,PN,IFunc,Iwhole) 1 EXT94b.f:3348: (continued): CALL BOND(X1,Y1,Z1,BL2,NCAL,PN) 2 Too few arguments passed to `bond' at (2) versus definition at (1) [info -f g77 M GLOBALS] -------------------------- I don't know to go on , I have tried several things but nothing works....Could samebody help me ? thanks a lot best regard Giancarlo Terraneo PhD student