From chemistry-request@ccl.net Mon May 30 09:05:57 2005 Received: from oceanite.ens-lyon.fr (oceanite.ens-lyon.fr [140.77.1.22]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UD5vVa005920 for ; Mon, 30 May 2005 09:05:57 -0400 Received: from localhost (oceanite.ens-lyon.fr [127.0.0.1]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 56AF63200BE for ; Mon, 30 May 2005 14:15:13 +0200 (CEST) Received: from oceanite.ens-lyon.fr ([127.0.0.1]) by localhost (oceanite [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 18195-08 for ; Mon, 30 May 2005 14:15:13 +0200 (CEST) Received: from [140.77.2.67] (mambo.ens-lyon.fr [140.77.2.67]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 226C432009F for ; Mon, 30 May 2005 14:15:13 +0200 (CEST) Message-ID: <429B03D1.3050206~at~ens-lyon.fr> Date: Mon, 30 May 2005 14:15:13 +0200 From: Paul Fleurat-Lessard Reply-To: Paul.Fleurat-Lessard~at~ens-lyon.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.7) Gecko/20050414 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: Energy decomposition with G03 Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at ens-lyon.fr Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4UD5vVa005924 Dear CCLers, I am using Gaussian03 to analyse a molecule consisting of two fragments linked by a weak bond (kind of H-bond). I would like to analyse the energetical origin of this bond with some kind of energy decomposition scheme. i thought that the Morokuma scheme was available in G03 but I cannot find the right keyword, can you help me ? Do you know some other tools that can provide such an analysis ? On the same topic, I would also like to analyse this complexe using a fragment approach (because in some cases, the two fragment are in fact part of a larger molecule that adopts a cyclic geometry). I was using such a tool within the exthuc program (FMO option), and I know that there is something similar in ADF... but I cannot find anything in G03... do you know a tool for this ? Thanks in advance, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard~at~ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 Si vous ne pouvez expliquer un concept ` un enfant de six ans, c'est que vous ne le comprenez pas complhtement. Albert Einstein From chemistry-request@ccl.net Mon May 30 05:55:13 2005 Received: from web30105.mail.mud.yahoo.com (web30105.mail.mud.yahoo.com [68.142.200.78]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4U9t9EE030412 for ; Mon, 30 May 2005 05:55:10 -0400 Received: (qmail 29931 invoked by uid 60001); 30 May 2005 08:55:08 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=FaPdmBZNxBnwUMzRkRG84JshHCSaRS5RFtqXA+kqOH/j+az3RIQH016eabDhxTg2H97FhoRQoq1C3uDiTycEG5VsUb1c+XWZrLQVstBJfnEsmmZANw1Idf1IrW1r1mYJeTqtwHBDK0QTriYzbNx0Pj65bjT0s7kyLpNzTFee584= ; Message-ID: <20050530085508.29929.qmail|at|web30105.mail.mud.yahoo.com> Received: from [202.127.145.15] by web30105.mail.mud.yahoo.com via HTTP; Mon, 30 May 2005 01:55:08 PDT Date: Mon, 30 May 2005 01:55:08 -0700 (PDT) From: Jinming zhou Subject: Is there a way to get CHEAT95 (the ff based on Charmm for carbohydrate) To: chemistry|at|ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1912918857-1117443308=:22955" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=4.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FORGED_YAHOO_RCVD,HTML_20_30,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --0-1912918857-1117443308=:22955 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I was trying to do the carbohydrate/protein simulation and need this urgently. please provide some information, thank you very much! Jinming Zhou Tel: +86-021-54925277 Email: zhoujm|at|mail.sioc.ac.cn CCL(Computer Chemstry Lab) Shanghai Institute of Organic Chemstry Chinese Academy of Sciences shanghai 200032 china --------------------------------- ~{R07<7"6xSDOc#,Pc6x71Ru~} ~{7gK*8_=`#,K.Bd6xJ/3vU_#,I=I was trying to do the carbohydrate/protein simulation and need this urgently.
please provide some information, thank you very much!
 
 
 
 


Jinming Zhou
Tel: +86-021-54925277
Email: zhoujm|at|mail.sioc.ac.cn
CCL(Computer Chemstry Lab)
Shanghai Institute of Organic Chemstry
Chinese Academy of Sciences
shanghai 200032 china
---------------------------------
~{R07<7"6xSDOc#,<QD>Pc6x71Ru~}
~{7gK*8_=`#,K.Bd6xJ/3vU_#,I=<dV.KDJ1R2!#~}
--~{E7QtP^~}
----------------------------------

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http://mail.yahoo.com --0-1912918857-1117443308=:22955-- From chemistry-request@ccl.net Mon May 30 11:16:23 2005 Received: from pastinakel.tue.nl (pastinakel.tue.nl [131.155.2.7]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UFGKdJ013425 for ; Mon, 30 May 2005 11:16:20 -0400 Received: by pastinakel.tue.nl (Postfix, from userid 40) id F11EB14BDF5; Mon, 30 May 2005 17:16:14 +0200 (CEST) Received: from stex2.campus.tue.nl (stex2.campus.tue.nl [131.155.81.192]) by pastinakel.tue.nl (Postfix) with ESMTP id 473E314BBCF for ; Mon, 30 May 2005 17:16:14 +0200 (CEST) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Subject: Periodic calculations in Gaussian03 Date: Mon, 30 May 2005 17:16:14 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Periodic calculations in Gaussian03 Thread-Index: AcVlKoTH3w8XNCPwSmmE/cUxxy7dLA== From: "Ojwang, J.G.O." To: X-Spam-DCC: : X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4UFGNdJ013431 Dera all, Has anyone ever done periodic calculations in gaussian03? I've tried to perfrom periodic calculation for even a simpler sytem like NaH but everytime I get an error message. The reason for my preference of gaussian03 is to take advantage of the variety of packages it offers especially in analysing bond overlap population like NPA and MPA. Regards, Ojwang' From chemistry-request@ccl.net Mon May 30 15:00:27 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UJ0M89024327 for ; Mon, 30 May 2005 15:00:22 -0400 Received: from accra.ks.uiuc.edu (IDENT:U2FsdGVkX19rYEpnpG5n8hIHZ1t9Vgiy0vmvQR5DbYY *o* accra.ks.uiuc.edu [130.126.120.220]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j4UI5FKx000398 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 30 May 2005 13:05:15 -0500 (CDT) Date: Mon, 30 May 2005 13:05:15 -0500 (CDT) From: deyulu To: chemistry *o* ccl.net Subject: CCL:potential from part of the system Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCL: I want to obtain the potential field from only part of my system, eg., the electrostatic potentail that a real ion feels from the rest of the system. Does anyone know if there is a quick way to do this from a Gaussian checkpoint file? Thanks Deyu ************************************************************** Deyu Lu Tel: 217-367-7102(h), 217-244-8946(O) Office: 3111, Beckman Institute, UIUC Address: 2118 S. Orchard St., Apt. 203, Urbana, IL, 61801 ************************************************************** From chemistry-request@ccl.net Mon May 30 16:15:42 2005 Received: from pantheon-po08.its.yale.edu (pantheon-po08.its.yale.edu [130.132.50.50]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UKFcjf027466 for ; Mon, 30 May 2005 16:15:38 -0400 Received: from ares.its.yale.edu (ares.its.yale.edu [130.132.52.16]) by pantheon-po08.its.yale.edu (8.12.11/8.12.11) with ESMTP id j4UKFbbk013035 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 30 May 2005 16:15:37 -0400 Received: from ares.its.yale.edu (localhost [127.0.0.1]) by ares.its.yale.edu (8.12.11/8.12.11) with ESMTP id j4UKFbF4017992; Mon, 30 May 2005 16:15:37 -0400 Received: from localhost (jag86@localhost) by ares.its.yale.edu (8.12.11/8.12.11/Submit) with ESMTP id j4UKFbK0017988; Mon, 30 May 2005 16:15:37 -0400 X-Authentication-Warning: ares.its.yale.edu: jag86 owned process doing -bs Date: Mon, 30 May 2005 16:15:37 -0400 (EDT) From: Jose Gascon X-X-Sender: jag86 :: ares.its.yale.edu To: deyulu cc: chemistry :: ccl.net Subject: Re: CCL:potential from part of the system In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-YaleITSMailFilter: Version 1.2b (attachment(s) not renamed) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Deyu, if your Gaussian Job included a calculation of point charges (esp or chelpg) then the electrostatic potential from a subset of atoms is the sum of coulombic terms over that subset. My suggestion is, take those point charges, take the coordinates of your system and make a small program to calculate the electrostatic potential wherever you want. Jose On Mon, 30 May 2005, deyulu wrote: > Dear CCL: > I want to obtain the potential field from only part of > my system, eg., the electrostatic potentail that a real ion > feels from the rest of the system. Does anyone know if there > is a quick way to do this from a Gaussian checkpoint file? > > Thanks > Deyu > > ************************************************************** > > Deyu Lu > > Tel: 217-367-7102(h), 217-244-8946(O) > Office: 3111, Beckman Institute, UIUC > Address: 2118 S. Orchard St., Apt. 203, Urbana, IL, 61801 > > ************************************************************** > > -= This is automatically added to each message by the 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Mon May 30 16:34:34 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4UKYUWf028322 for ; Mon, 30 May 2005 16:34:31 -0400 Received: from accra.ks.uiuc.edu (IDENT:U2FsdGVkX1/vJU88OsqHxrGFpANXPchWB3hPKJO0dw4 +*+ accra.ks.uiuc.edu [130.126.120.220]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j4UKYUKx003735 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Mon, 30 May 2005 15:34:30 -0500 (CDT) Date: Mon, 30 May 2005 15:34:30 -0500 (CDT) From: deyulu To: Jose Gascon cc: chemistry +*+ ccl.net Subject: Re: CCL:potential from part of the system In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Jose: Thank you for your suggestion. I think it will work, but the accuracy of the potential is largely limited by the very point charge approximation. I wonder if there is a way to use the nuclear charges and electron wavefunctions of a desired part of the system to compute potential. I would imagine this could be achieved by setting the coefficients of some atomic orbitals to zero. Best Deyu ************************************************************** Deyu Lu Tel: 217-367-7102(h), 217-244-8946(O) Office: 3111, Beckman Institute, UIUC Address: 2118 S. Orchard St., Apt. 203, Urbana, IL, 61801 ************************************************************** On Mon, 30 May 2005, Jose Gascon wrote: > > Deyu, if your Gaussian Job included a calculation > of point charges (esp or chelpg) then the > electrostatic potential from a subset of atoms > is the sum of coulombic terms over that subset. > My suggestion is, take those point charges, take > the coordinates of your system and make a small > program to calculate the electrostatic potential > wherever you want. > Jose > > On Mon, 30 May 2005, deyulu wrote: > >> Dear CCL: >> I want to obtain the potential field from only part of >> my system, eg., the electrostatic potentail that a real ion >> feels from the rest of the system. Does anyone know if there >> is a quick way to do this from a Gaussian checkpoint file? >> >> Thanks >> Deyu >> >> ************************************************************** >> >> Deyu Lu >> >> Tel: 217-367-7102(h), 217-244-8946(O) >> Office: 3111, Beckman Institute, UIUC >> Address: 2118 S. Orchard St., Apt. 203, Urbana, IL, 61801 >> >> ************************************************************** >> >> -= This is automatically added to each message by the 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 is mail bouncing from ccl.net domain due to spam filters, please >> use the Web based form from CCL Home Page >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> >> > >