From chemistry-request@ccl.net Thu Feb 19 19:48:06 2004 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.120]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1K0m5Df011061 for ; Thu, 19 Feb 2004 19:48:05 -0500 Received: from alphahelix (alphahelix.Stanford.EDU [171.64.126.26]) by smtp1.Stanford.EDU (8.12.10/8.12.10) with ESMTP id i1K0moTH026950; Thu, 19 Feb 2004 16:48:51 -0800 Reply-To: From: "Joseph Han" To: "'Jie Zheng'" , Subject: RE: basic questions in MD Date: Thu, 19 Feb 2004 16:48:52 -0800 Message-ID: <002801c3f74b$4f926d30$1a7e40ab@alphahelix> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal In-Reply-To: X-Spam-Status: No, hits=0.0 required=7.0 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 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request~at~ccl.net] On Behalf Of Jie Zheng > Sent: Thursday, February 19, 2004 3:05 PM > To: chemistry~at~ccl.net > Subject: CCL:basic questions in MD > > > Hi, CCLer: > I have a few basic questions for molecular dynamics. > 1) why the system has to be neutral in molecular dynamics? From the > numerial point of views, it seems that to be neutral or not does not > affect the numerial algorithm. We still can get results. I > know there must > have some physical meaning behind this, anybody can give a answer? If the cell does not have a neutral change, then when you replicate it using periodic boundary conditions, the total charge becomes infinity. This does not make physical sense. > > 2) why the cutoff distance can not larger than the > half-size of box? If > we use the Ewald sum method to calculate nonbonded interactions, the > system and its images have been extend to infinite. If we use > the cutoff > method, the system is confined to the finite size by using periodic > boundary conditon. My question is that if we extend our > simulation system > to infinite as the Ewald sum does, the half-box cutoff is not > required for > the simluation systems. If the cutoff is greater than the half-size of the box, you will get self-interaction errors. Imagine a particle at the center of a cube. Embed a sphere with a radius half the edge of the cube. When you replicate the cell, if the radius of the sphere is greater than this size, it will interact with itself. Joseph Han Department of Chemical Engineering Stanford University 650-723-0420 FAX: 650-725-7294 From chemistry-request@ccl.net Thu Feb 19 21:44:34 2004 Received: from cyberwal.com.br ([200.198.82.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i1K2iTDf013181 for ; Thu, 19 Feb 2004 21:44:30 -0500 Received: (qmail 15658 invoked from network); 20 Feb 2004 02:25:26 -0000 Received: from unknown (HELO number42) (200.162.68.199) by 0 with SMTP; 20 Feb 2004 02:25:26 -0000 From: "Ian & Ana" To: "chemistry" Subject: CCL: extracting thermochemical data from G98w & pasting into excel Date: Thu, 19 Feb 2004 23:34:07 -0300 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C3F740.DE1E4840" 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 V6.00.2600.0000 Importance: Normal X-Spam-Status: No, hits=0.2 required=7.0 tests=HTML_70_80, HTML_FONTCOLOR_UNKNOWN,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_0006_01C3F740.DE1E4840 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCLers, I am calculating thermochemical properties (BDE, deltaH formation etc.), using G98W/G03 frequency calculations, by extracting the relevant data from the generated outputs and pasting into excel spreadsheets. I am estimating that I will have around 200 or more out files to exam. Does any one know of any ready made spreadsheet containing macros that would automate this rather tedious job. TIA Ian ------=_NextPart_000_0006_01C3F740.DE1E4840 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear = CCLers,<= /p>

 <= /p>

I am calculating = thermochemical properties (BDE, deltaH formation etc.), using G98W/G03 frequency = calculations, by extracting the relevant data from the generated outputs and pasting = into excel spreadsheets. I am estimating that I will have around 200 or more = out files to exam. Does any one know of any ready made spreadsheet = containing macros that would automate this rather tedious job.<= /p>

 <= /p>

TIA<= /p>

Ian

------=_NextPart_000_0006_01C3F740.DE1E4840-- From chemistry-request@ccl.net Thu Feb 19 22:01:45 2004 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1K31eDf014373 for ; Thu, 19 Feb 2004 22:01:41 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Thu, 19 Feb 2004 22:02:54 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Thu, 19 Feb 2004 22:02:32 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:basic questions in MD Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=1.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jay: 1) If you don't use particle Ewald mesh method, then it doesn't have to be neutral. 2) Read the amber manual. There is a discussion of why the cutoff distance is set the way it is. Pete >>> Jie Zheng 2/19/2004 6:04:32 PM >>> Hi, CCLer: I have a few basic questions for molecular dynamics. 1) why the system has to be neutral in molecular dynamics? From the numerial point of views, it seems that to be neutral or not does not affect the numerial algorithm. We still can get results. I know there must have some physical meaning behind this, anybody can give a answer? 2) why the cutoff distance can not larger than the half-size of box? If we use the Ewald sum method to calculate nonbonded interactions, the system and its images have been extend to infinite. If we use the cutoff method, the system is confined to the finite size by using periodic boundary conditon. My question is that if we extend our simulation system to infinite as the Ewald sum does, the half-box cutoff is not required for the simluation systems. I will appreciate for your clarification. Jay -= 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|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, jlabanow|at|nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Feb 20 04:23:38 2004 Received: from sun-blade.cnrs-orleans.fr (sun-blade.cnrs-orleans.fr [163.9.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1K9NbDf023013 for ; Fri, 20 Feb 2004 04:23:38 -0500 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.19]) by sun-blade.cnrs-orleans.fr (8.12.10/jtpda-5.4) with ESMTP id i1K9OOu0023910 ; Fri, 20 Feb 2004 10:24:24 +0100 (MET) Received: by dirac.cnrs-orleans.fr (Postfix, from userid 500) id 4123278D72; Fri, 20 Feb 2004 10:39:18 +0100 (CET) X-IMAP-Sender: hinsen In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v612) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: chemistry:at:ccl.net From: hinsen:at:cnrs-orleans.fr Subject: Re: CCL:basic questions in MD Date: Fri, 20 Feb 2004 10:04:06 +0100 To: Jie Zheng X-MailScanner: Found to be clean X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 20.02.2004, at 00:04, Jie Zheng wrote: > 1) why the system has to be neutral in molecular dynamics? From the > numerial point of views, it seems that to be neutral or not does not > affect the numerial algorithm. We still can get results. I know there > must > have some physical meaning behind this, anybody can give a answer? When you use periodic boundary conditions, you are effectively simulating an infinite system. With a non-zero total charge, you then get an infinite total charge and an infinite potential energy. Such a system would not be stable under real-life conditions (i.e. without the artifact of periodic boundary conditions). In fact, if you simulate such a system at constant pressure, i.e. with a variable box size, you will see the volume go up systematically. > 2) why the cutoff distance can not larger than the half-size of box? > If > we use the Ewald sum method to calculate nonbonded interactions, the > system and its images have been extend to infinite. If we use the > cutoff > method, the system is confined to the finite size by using periodic > boundary conditon. My question is that if we extend our simulation > system > to infinite as the Ewald sum does, the half-box cutoff is not required > for > the simluation systems. > What you want to do in a cutoff method is to sum over all pairs of atoms whose distance is below the cutoff. There is indeed no physical reason not to have a cutoff beyond half the box size, but if you do so, then for consistency you have to count in some atom pairs twice, because both the original atom and some of its images may be within the cutoff distance of a given other atom. The resulting algorithm becomes more complicated, which is why most implementations limit themselves to the simple case and impose the half-box-size limit on the cutoff. -- ------------------------------------------------------------------------ ------- Konrad Hinsen | E-Mail: hinsen:at:cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Fri Feb 20 09:10:44 2004 Received: from ccc018.chemie.uni-erlangen.de (ccc018.chemie.uni-erlangen.de [131.188.128.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1KEAhDf027978 for ; Fri, 20 Feb 2004 09:10:43 -0500 Received: from localhost (localhost [127.0.0.1]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 1795E1185F; Fri, 20 Feb 2004 15:11:32 +0100 (CET) Received: from ccc018.chemie.uni-erlangen.de ([127.0.0.1]) by localhost (ccc018 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 18350-04; Fri, 20 Feb 2004 15:11:30 +0100 (CET) Received: from chemie.uni-erlangen.de (equinox.chemie.uni-erlangen.de [131.188.128.90]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 45D1A1184C for ; Fri, 20 Feb 2004 15:11:30 +0100 (CET) Sender: Harald.Lanig-.at.-chemie.uni-erlangen.de Message-ID: <40361592.A6C6E45E-.at.-chemie.uni-erlangen.de> Date: Fri, 20 Feb 2004 15:11:30 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: 18th Molecular Modelling Workshop - May 18-19, 2004 in Erlangen, Germany Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at chemie.uni-erlangen.de X-Spam-Status: No, hits=0.0 required=7.0 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 Dear list members, let me please point your attention to 18th Darmstaedter Molecular Modelling Workshop taking place in Erlangen, Germany from May 18 to 19, 2004. The registration is now open. Although the official conference language is German, this information may be useful to a lot of readers of this list. For further information please see the URL http://www.chemie.uni-erlangen.de/ccc/conference/darmstadt.html Kind regards, Harald Lanig ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 Mailto:lanig-.at.-chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ From chemistry-request@ccl.net Fri Feb 20 10:24:11 2004 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 i1KFO8Df030279 for ; Fri, 20 Feb 2004 10:24:08 -0500 Received: from minerva (minerva2.lib.duke.edu [152.3.237.232]) by compton.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with SMTP id i1KFOv64012727; Fri, 20 Feb 2004 10:24:57 -0500 (EST) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: questions about docking software Date: Fri, 20 Feb 2004 10:25:32 -0500 Message-ID: <018d01c3f7c5$c7987020$e8ed0398|at|myduke.lib.duke.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcP3xceVR5A8p7YsQv++PpY2bI4pdA== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.4 required=7.0 tests=MISSING_OUTLOOK_NAME, NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am going to do some protein-DNA docking, but have no idea of what kind of software is good for this kind of system. So I would like to ask the experts here if there is any good docking software I could download free (for academic use). Thanks so much! From chemistry-request@ccl.net Fri Feb 20 09:59:16 2004 Received: from iris.chimfarm.unipg.it (iris.chimfarm.unipg.it [141.250.13.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1KExEDf029298 for ; Fri, 20 Feb 2004 09:59:15 -0500 Received: from nettuno.chimfarm.unipg.it ([141.250.13.84] ident=1000) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 1AuKYg-0003dy-00 for chemistry{at}ccl.net; Fri, 20 Feb 2004 15:59:50 -0800 Date: Fri, 20 Feb 2004 15:51:04 +0000 (UTC) From: Mirco Meniconi X-X-Sender: mirco{at}nettuno.chimfarm.unipg.it To: chemistry{at}ccl.net Subject: atomic charges Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.6 required=7.0 tests=DATE_IN_PAST_06_12 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 all, I'm looking for a computational routine (program, script, etc) that can assign partial atomic carges. This routine must be called by command line and must read sdf (multiple is better) files, or pdb files. Thank you all -- Mirco Meniconi PhD candidate Dip. Chimica e Tecnologia del Farmaco via del liceo 1 06100 Perugia Universita' degli Studi di Perugia (Italia) phone: +39 075 585 5169 e-mail: mirco{at}unipg.it e-mail: mimenico{at}yahoo.it Prima ti ignorano. Poi ridono di te. Poi ti combattono. Poi tu vinci. From chemistry-request@ccl.net Fri Feb 20 16:26:02 2004 Received: from cholla.wustl.edu (cholla.wustl.edu [128.252.62.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1KLQ1Df004808 for ; Fri, 20 Feb 2004 16:26:01 -0500 Received: from cholla.wustl.edu (localhost.localdomain [127.0.0.1]) by cholla.wustl.edu (8.12.10/8.12.10) with ESMTP id i1KLQpoT002575 for ; Fri, 20 Feb 2004 15:26:51 -0600 Received: (from baker@localhost) by cholla.wustl.edu (8.12.10/8.12.10/Submit) id i1KLQpat002573 for CHEMISTRY_at_ccl.net; Fri, 20 Feb 2004 15:26:51 -0600 Date: Fri, 20 Feb 2004 15:26:51 -0600 From: "Nathan A. Baker" To: CHEMISTRY_at_ccl.net Subject: CCL: Adaptive Poisson-Boltzmann Solver v. 0.3.0 Message-ID: <20040220212651.GA2549_at_cholla.wustl.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i Organization: Washington University in St. Louis X-URL: http://www.biochem.wustl.edu/~baker X-PGP-Key: http://cholla.wustl.edu/~baker/pubkey.asc X-Spam-Status: No, hits=0.0 required=7.0 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 am pleased to announce the availablity of version 0.3.0 for the Adaptive Poisson-Boltzmann Solver (APBS) at: http://agave.wustl.edu/apbs/ This version of the software offers a number of improvements and added features which are summarized in the ChangeLog (see web site). Major highlights include: * A completely revised version of the documentation with links to APBS interfaces with several popular visualization packages * New scripts to easily parameterize PDB files and automatically generate APBS input scripts * Simpler input file syntax (backwards-compatible) * Several bug fixes * Routines to perform asynchronous parallel runs for on-demand resources (i.e., compute farms or sequential workstations) For more information, including download instructions, please visit the web site listed above. -- Nathan Baker -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc From chemistry-request@ccl.net Fri Feb 20 10:27:32 2004 Received: from iris.chimfarm.unipg.it (iris.chimfarm.unipg.it [141.250.13.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1KFRVDf030446 for ; Fri, 20 Feb 2004 10:27:32 -0500 Received: from nettuno.chimfarm.unipg.it ([141.250.13.84] ident=1000) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 1AuL03-0003tb-00 for chemistry:at:ccl.net; Fri, 20 Feb 2004 16:28:07 -0800 Date: Fri, 20 Feb 2004 16:19:18 +0000 (UTC) From: Mirco Meniconi X-X-Sender: mirco:at:nettuno.chimfarm.unipg.it To: chemistry:at:ccl.net Subject: CCL: atomic charges Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.6 required=7.0 tests=DATE_IN_PAST_06_12 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 all, I'm looking for a computational routine (program, script, etc) that can assign partial atomic carges. This routine must be called by command line and must read sdf (multiple is better) files, or pdb files. Thank you all -- Mirco Meniconi PhD candidate Dip. Chimica e Tecnologia del Farmaco via del liceo 1 06100 Perugia Universita' degli Studi di Perugia (Italia) phone: +39 075 585 5169 e-mail: mirco:at:unipg.it e-mail: mimenico:at:yahoo.it Prima ti ignorano. Poi ridono di te. Poi ti combattono. Poi tu vinci. From chemistry-request@ccl.net Fri Feb 20 15:13:05 2004 Received: from serenity.mcc.ac.uk (serenity.mcc.ac.uk [130.88.200.93]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1KKD3Df003692 for ; Fri, 20 Feb 2004 15:13:04 -0500 Received: from tcc02.ch.man.ac.uk ([130.88.83.2] helo=TCC02) by serenity.mcc.ac.uk with smtp (Exim 4.20) id 1AuH21-000Pru-DN for chemistry$at$ccl.net; Fri, 20 Feb 2004 20:13:53 +0000 Message-ID: <001e01c3f7ed$d69eff80$02535882@TCC02> Reply-To: "Mahesh" From: "Mahesh" To: Subject: parameters for Fe-S Date: Fri, 20 Feb 2004 20:12:17 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C3F7ED.D690A7A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *1AuH21-000Pru-DN*BXz26mOtdV.* X-Spam-Status: No, hits=0.1 required=7.0 tests=HTML_60_70,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_001B_01C3F7ED.D690A7A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL's: I am trying to do QM/MM calculations for Iron-Sulfur proteins,=20 May I know where I can I get MM parameters for Fe-S systems. Note: MM using Amber.=20 Thanks in Advance, Regards, Mahesh ------=_NextPart_000_001B_01C3F7ED.D690A7A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCL's:
I am trying to do QM/MM calculations = for=20 Iron-Sulfur proteins,
 
May I know where I can I get MM = parameters for=20 Fe-S systems.
 
Note: MM using Amber.
 
Thanks in Advance,
 
Regards,
Mahesh
 
------=_NextPart_000_001B_01C3F7ED.D690A7A0-- From chemistry-request@ccl.net Fri Feb 20 11:34:53 2004 Received: from web20723.mail.yahoo.com (web20723.mail.yahoo.com [216.136.226.77]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i1KGYoDf032617 for ; Fri, 20 Feb 2004 11:34:50 -0500 Message-ID: <20040220163536.59268.qmail)at(web20723.mail.yahoo.com> Received: from [129.100.91.79] by web20723.mail.yahoo.com via HTTP; Fri, 20 Feb 2004 08:35:36 PST Date: Fri, 20 Feb 2004 08:35:36 -0800 (PST) From: "d. wanapun" Subject: Jaguar SCF convergence problem To: chemistry)at(ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-228054495-1077294936=:58679" X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_20_30,HTML_MESSAGE, HTML_TAG_BALANCE_A autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-228054495-1077294936=:58679 Content-Type: text/plain; charset=us-ascii I use Jaguar to do the transiton state optimization. After it ran for few "move" this error has aborted the program. Please let me know how to fix it ( I use the default convergence criteria and calculation) etot 34 N Y 2 U -861.39759988837 -8.8E-04 4.9E-04 1.0E-02 etot 35 Y Y 6 M -861.39768273142 8.3E-05 1.4E-03 1.1E-02 etot 36 N Y 2 U -861.39744731698 -2.4E-04 1.3E-03 9.7E-03 etot 37 Y Y 6 M -861.39731229606 -1.4E-04 3.9E-03 8.6E-03 etot 38 N Y 2 U -861.39671459558 -6.0E-04 4.0E+00 5.5E-03 etot 39 Y Y 6 M -952.94965913702 9.2E+01 1.3E+00 2.4E+01 ERROR: fatal error -- debug information follows etot 40 N N 2 U -905.48656491620 -4.7E+01 1.3E+00 2.4E+01 aborting scf due to large energy change Thanks D. D. Wanapun dwanapun)at(yahoo.com --------------------------------- Do you Yahoo!? Yahoo! Mail SpamGuard - Read only the mail you want. --0-228054495-1077294936=:58679 Content-Type: text/html; charset=us-ascii
I use Jaguar to do the transiton state optimization. After it ran for few "move" this error has aborted the program. Please let me know how to fix it ( I use the default convergence criteria and calculation)
 
etot  34  N  Y  2  U    -861.39759988837 -8.8E-04  4.9E-04  1.0E-02
etot  35  Y  Y  6  M    -861.39768273142  8.3E-05  1.4E-03  1.1E-02
etot  36  N  Y  2  U    -861.39744731698 -2.4E-04  1.3E-03  9.7E-03
etot  37  Y  Y  6  M    -861.39731229606 -1.4E-04  3.9E-03  8.6E-03
etot  38  N  Y  2  U    -861.39671459558 -6.0E-04  4.0E+00  5.5E-03
etot  39  Y  Y  6  M    -952.94965913702  9.2E+01  1.3E+00  2.4E+01

  ERROR: fatal error -- debug information follows
etot  40  N  N  2  U    -905.48656491620 -4.7E+01  1.3E+00  2.4E+01
  aborting scf due to large energy change
Thanks
D.
 
 
D. Wanapun

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