From chemistry-request@server.ccl.net Wed May 14 04:58:20 2003 Received: from ns9.mmaweb.net ([64.71.143.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4E8wKt24996 for ; Wed, 14 May 2003 04:58:20 -0400 Received: from chemaxon.com (208.33-182-adsl-pool.axelero.hu [81.182.33.208]) by ns9.mmaweb.net (8.12.9/8.11.0) with ESMTP id h4E8wIXS011874 for ; Wed, 14 May 2003 04:58:19 -0400 (EDT) Message-ID: <3EC2051F.8010903@chemaxon.com> Date: Wed, 14 May 2003 10:58:07 +0200 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Fwd: PDB viewing and Mac OSX References: <78F8937D-8553-11D7-BD21-0003937E291E@saintmarys.edu> In-Reply-To: <78F8937D-8553-11D7-BD21-0003937E291E@saintmarys.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi Phil, > Does any one know of a plugin that can be used with a browser under > Mac OSX that will allow one to view 3-D chemical structures.? I am > thinking of a Chime-like plug-in, but MDL has no plans for OSX or > Linux. I am familiar with iMol but have been unable to install it as > a helper ap. Check out the MarvinView applet. It works under most current OS-s (Mac OS X is supported). Here are some examples: http://www.chemaxon.com/marvin/doc/dev/index.html#examples You can also consider downloading Marvin Beans that contains a JavaBean for viewing molecules. You can download these tools by following the Marvin link at http://www.chemaxon.com/products.html. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com -- Dr. Ferenc Csizmadia CEO ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3620 9570988 Tel: +361 4532660 Fax: +361 4532659 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Wed May 14 06:07:48 2003 Received: from kali.urz.unibas.ch ([131.152.1.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4EA7mt27667 for ; Wed, 14 May 2003 06:07:48 -0400 Received: from localhost (webmail.urz.unibas.ch [131.152.1.20]) by stud.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0HEV00C8CG50WO@stud.unibas.ch> for chemistry@ccl.net; Wed, 14 May 2003 12:07:48 +0200 (MET DST) Received: from 131.152.93.82 ( [131.152.93.82]) as user affmar00@kali-bac.backup.unibas.ch by webmail.unibas.ch with HTTP; Wed, 14 May 2003 12:07:48 +0200 Date: Wed, 14 May 2003 12:07:48 +0200 From: M.Affentranger@stud.unibas.ch Subject: Autodock: how to prepare file for a heme-Protein X-Originating-IP: 131.152.93.82 To: chemistry@ccl.net Message-id: <1052906868.3ec2157428693@webmail.unibas.ch> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 Dear CCLer I'm working on Cytochrome and I can't run the Autodock-job. I've got the parcial charges of Heme, but i'm a beginner in Autodock, and don't know how to prepare the input files for autodock... (the .pdbqs file isn't the problem, but what and how have i to change in the .dpf file???) i know there is something written in the oficial Autodock FAQ-site, but i dont get the point... I would be very thankful if you could explain me how to do it. thank you very much Martin Affentranger Lab 3025 Institute of Molecular Pharmacy Klingelbergstrasse 50 CH 4056 Basel Tel: +41 61 267 15 03 Fax: +41 61 267 15 52 mail: m.affentranger@stud.unibas.ch ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From chemistry-request@server.ccl.net Wed May 14 03:40:32 2003 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4E7eWt08554 for ; Wed, 14 May 2003 03:40:32 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.9/8.12.9/Guy-01-04-2003) with ESMTP id h4E7eUYc026027; Wed, 14 May 2003 09:40:31 +0200 (METDST) Received: from lctn.uhp-nancy.fr (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA21928; Wed, 14 May 2003 09:30:43 +0200 Message-ID: <3EC1F242.A207E41F@lctn.uhp-nancy.fr> Date: Wed, 14 May 2003 09:37:38 +0200 From: Xavier Assfeld X-Mailer: Mozilla 4.75 [fr] (Win98; U) X-Accept-Language: fr MIME-Version: 1.0 To: john thaler CC: chemistry@ccl.net Subject: Re: CCL:I Need Help: Warning message Gaussian98 References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: arcturus.ciril.fr Hi, john thaler a écrit : > I was running a frequency calculation in Gaussian98 on a molecule > similar to the sugar in the DNA backbone and it returned these errors > around the place where it reports the Zero point Calculation. I was > wondering if anybody knows what these errors means and how I can > fix them or maybe even ignore them? > > 1. > THIS MOLECULE IS AN ASYMMETRIC TOP. > ROTATIONAL SYMMETRY NUMBER 1. > WARNING-- ASSUMPTION OF CLASSICAL BEHAVIOR FOR > ROTATION MAY CAUSE SIGNIFICANT ERROR > > 2. WARNING-- EXPLICIT CONSIDERATION OF 15 DEGREES > OF FREEDOM AS VIBRATIONS MAY CAUSE SIGNIFICANT ERROR > these 15 degrees of freedom certainly correspond to pseudo-rotation of OH group (since you are studying a sugar molecule...) The potential energy profil of this rotation looks like a "sinusoïde" (sine function). In the harmonic approximation the shape of the potential energy surface is supposed to be a parabola. Hence it is difficult to think that a parabola can simulate a sine function... You can circumvent this problem with the Hindered Rotation keywords in G98. Hope this helps. -- ...Xav Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie théorique (T) 33 3 83 68 43 74 Université Henri Poincaré (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Wed May 14 02:56:28 2003 Received: from dmb.rug.ac.be ([157.193.78.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4E6uRt06920 for ; Wed, 14 May 2003 02:56:28 -0400 Received: from lmb032.rug.ac.be (lmb032.rug.ac.be [157.193.78.89]) by dmb.rug.ac.be (Postfix) with ESMTP id ABEDF5C05C; Wed, 14 May 2003 08:54:10 +0200 (CEST) Subject: Re: CCL:Protein folding and simulation problem finally solved ? From: Dominique Vlieghe To: Jan Torleif Pedersen Cc: chemistry@ccl.net In-Reply-To: <1052684880.1016.18.camel@localhost.localdomain> References: <1052684880.1016.18.camel@localhost.localdomain> Content-Type: text/plain Organization: DMBR Message-Id: <1052895304.12355.5.camel@LMB032.rug.ac.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 14 May 2003 08:55:04 +0200 Content-Transfer-Encoding: 7bit Hello, Would you trust a company that promises *the* solution for PROTEIN folding, PROTEIN-PROTEIN interactions and PROTEIN-drug interactions, but puts a picture of a DNA stretch on their web-site? Furthermore: no names, no references, not even a full-blown web-page... Regards, Dominique P.S. Is there a term for web-spam? On Sun, 2003-05-11 at 22:27, Jan Torleif Pedersen wrote: > Greetings, > > Apparently, the protein folding and simulation problem has been solved > by a small Cambridge, UK based company called Cambridge Proteomics > Ltd.(http://www.camprot.com). Is anybody familiar with this new and > revolutionary technology? - I would be quite interested in hearing from > anybody that has more information. > > Many Regards -- Jan > > Dr. Jan T. Pedersen > Section Head, Bioinformatics > H. Lundbeck A/S > Ottiliavej 9 > 2500 Valby > Denmark > phone: 36 43 28 87 > email: jatp@lundbeck.com > > > > > > -= 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 > > -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Dept. Molecular Biomedical Research & V.I.B., Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium Tel.: 32-9-2648749 Fax.: 32-9-2645348 email:dominique.vlieghe@dmb.rug.ac.be www:http://www.dmb.rug.ac.be/ ------------------------------ From chemistry-request@server.ccl.net Wed May 14 05:01:42 2003 Received: from cirse.saclay.cea.fr ([132.166.192.127]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4E91ft25188 for ; Wed, 14 May 2003 05:01:42 -0400 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by cirse.saclay.cea.fr (8.12.9/CEAnet-Internet.1.0) with ESMTP id h4E912LM010584 for ; Wed, 14 May 2003 11:01:02 +0200 (MEST) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.6) with ESMTP id ; Wed, 14 May 2003 10:57:20 +0200 Received: from mirabeau.saclay.cea.fr (mirabeau.saclay.cea.fr [132.166.189.103]) by nenuphar.saclay.cea.fr (8.12.9/CEAnet-Interne.1.0) with ESMTP id h4E8wqM9009851; Wed, 14 May 2003 10:58:52 +0200 (MEST) Received: by mirabeau.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id ; Wed, 14 May 2003 10:51:53 +0200 Message-ID: <3808A7D2DCEAD6118B63009027287265014786@azurite.saclay.cea.fr> From: VITORGE Pierre 094605 To: "'Dr. Richard L. Wood'" Cc: "'CHEMISTRY@ccl.net'" Subject: RE: Error estimation of gibbs free energy Date: Wed, 14 May 2003 10:58:51 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4E91gt25189 d(dG) = square root([d(dH)]^2 + [d(dS)]^2) cannot be true, if dh=0 and T is constant the above Eq. gives d(dG) = d(dS) while it is of course d(dG) = T d(dS) You probably mean: d(DG) = square root([d(DH)]^2 + [(Td(DS)+(DS)dT)]^2)? or d(DG) = square root([d(DH)]^2 + [Td(DS)]^2 + [(DS)dT]^2)? Pierre Vitorge CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-CNRS-Universite d'Evry) Universite d'Evry UMR 8587 pierre.vitorge@cea.fr http://perso.club-internet.fr/vitorgen/pierre/pierre.html -----Message d'origine----- De: Dr. Richard L. Wood [mailto:rlw28@cornell.edu] Date: lundi 12 mai 2003 15:58 À: Wong Lai Ho Cc: CHEMISTRY@ccl.net Objet: CCL:Error estimation of gibbs free energy Wouldn't the following be true d(dG) = square root([d(dH)]^2 + [d(dS)]^2)? dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH) is the error in delta H, dS is delta S and d(dS) is the error in delta S. This is taken from a simple error propagation analysis as taught in some physical/analytical chemistry laboratories. Richard Wong Lai Ho wrote: > Dear CCLers, > > I have a question regarding error estimation of the experimental values of > gibbs free energy. > As we knows that: > delta G(formation) > = delta H(formation) > - Temp * [entropy(molecule)-sum(entropy(atoms to form the molecules))] > > Can I claim that the experimental error bar of the gibbs free energy(delta > G) is equal to the error bar of the enthalpy change of formation(delta H)? > (since the error introduced by the entropy is usually very small) > Is there any papers or books talking about this error? > > I would be grateful if you can give some comments on this claim. > > Larry > -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 -= 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 From chemistry-request@server.ccl.net Wed May 14 20:12:46 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4F0Ckt15130 for ; Wed, 14 May 2003 20:12:46 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id UAA12475; Wed, 14 May 2003 20:09:21 -0400 (EDT) Message-ID: <3EC2DAAE.B8E16B45@cornell.edu> Date: Wed, 14 May 2003 19:09:18 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Dominique Vlieghe CC: Jan Torleif Pedersen , chemistry@ccl.net Subject: Re: CCL:Protein folding and simulation problem finally solved ? References: <1052684880.1016.18.camel@localhost.localdomain> <1052895304.12355.5.camel@LMB032.rug.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Heck, the website isn't even there. I got an "HTTP/1.1 404 Object Not Found" error when I tried to go there. Richard Dominique Vlieghe wrote: > Hello, > > Would you trust a company that promises *the* solution for PROTEIN > folding, PROTEIN-PROTEIN interactions and PROTEIN-drug interactions, but > puts a picture of a DNA stretch on their web-site? > > Furthermore: no names, no references, not even a full-blown web-page... > > Regards, > > Dominique > > P.S. Is there a term for web-spam? > > On Sun, 2003-05-11 at 22:27, Jan Torleif Pedersen wrote: > > Greetings, > > > > Apparently, the protein folding and simulation problem has been solved > > by a small Cambridge, UK based company called Cambridge Proteomics > > Ltd.(http://www.camprot.com). Is anybody familiar with this new and > > revolutionary technology? - I would be quite interested in hearing from > > anybody that has more information. > > > > Many Regards -- Jan > > > > Dr. Jan T. Pedersen > > Section Head, Bioinformatics > > H. Lundbeck A/S > > Ottiliavej 9 > > 2500 Valby > > Denmark > > phone: 36 43 28 87 > > email: jatp@lundbeck.com > > > > > > > > > > > > > > > -- > ------------------------------ > Dominique Vlieghe, Ph.D., > Bioinformatics Core, > Dept. Molecular Biomedical Research & V.I.B., > Ghent University, > K.L. Ledeganckstraat 35, > B-9000 Ghent, > Belgium > Tel.: 32-9-2648749 > Fax.: 32-9-2645348 > email:dominique.vlieghe@dmb.rug.ac.be > www:http://www.dmb.rug.ac.be/ > ------------------------------ > > -= 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 -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 From chemistry-request@server.ccl.net Wed May 14 21:20:13 2003 Received: from web21010.mail.yahoo.com ([216.136.227.64]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4F1KDt17236 for ; Wed, 14 May 2003 21:20:13 -0400 Message-ID: <20030515012012.26973.qmail@web21010.mail.yahoo.com> Received: from [148.218.36.120] by web21010.mail.yahoo.com via HTTP; Wed, 14 May 2003 18:20:12 PDT Date: Wed, 14 May 2003 18:20:12 -0700 (PDT) From: Cesar Millan Subject: RNA 3D structure software To: CHEMISTRY@ccl.net In-Reply-To: <1052906868.3ec2157428693@webmail.unibas.ch> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everyone! Does anyone knows a software that can build a 3D structure of RNA from sequence or 2D structure? All your help is really appreciate. Thanks. __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com From chemistry-request@server.ccl.net Wed May 14 14:32:06 2003 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4EIW6t08243 for ; Wed, 14 May 2003 14:32:06 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id h4EIW0O09495 for ; Wed, 14 May 2003 11:32:00 -0700 (PDT) Date: Wed, 14 May 2003 11:32:00 -0700 (PDT) From: Ioana Cozmuta To: "'CHEMISTRY@ccl.net'" Subject: Re: CCL:Error estimation of gibbs free energy In-Reply-To: <3808A7D2DCEAD6118B63009027287265014786@azurite.saclay.cea.fr> Message-ID: References: <3808A7D2DCEAD6118B63009027287265014786@azurite.saclay.cea.fr> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h4EIW6t08244 Hi, The most general formula from which you can always estimate the error del_f of a function f(x1, x2, x3, ...xn) is (del_f)^2= (df/dx1)^2*del_x1^2+(df/dx2)^2*del_x2^2+... where df/dxi are partial derivatives of the function f with respect to xi (i=1,n) and del_xi are the individual errors. So for example if f= x+y then (del_f)^2 = (del_x1)^2+(del_x2)^2 if f = x*y then (delf/f)^2= (del_x/x)^2+(del_y/y)^2 If x1, ...xn are functions of other variables I find the general formula above (with derivatives) much easier to use. Ioana On Wed, 14 May 2003, VITORGE Pierre 094605 wrote: > d(dG) = square root([d(dH)]^2 + [d(dS)]^2) > cannot be true, if dh=0 and T is constant the above Eq. gives > d(dG) = d(dS) > while it is of course > d(dG) = T d(dS) > > You probably mean: > d(DG) = square root([d(DH)]^2 + [(Td(DS)+(DS)dT)]^2)? > or > d(DG) = square root([d(DH)]^2 + [Td(DS)]^2 + [(DS)dT]^2)? > > Pierre Vitorge > CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-CNRS-Universite d'Evry) > Universite d'Evry UMR 8587 > pierre.vitorge@cea.fr > http://perso.club-internet.fr/vitorgen/pierre/pierre.html > > > -----Message d'origine----- > De: Dr. Richard L. Wood [mailto:rlw28@cornell.edu] > Date: lundi 12 mai 2003 15:58 > À: Wong Lai Ho > Cc: CHEMISTRY@ccl.net > Objet: CCL:Error estimation of gibbs free energy > > > Wouldn't the following be true > > d(dG) = square root([d(dH)]^2 + [d(dS)]^2)? > > dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH) is the > error > in delta H, dS is delta S and d(dS) is the error in delta S. > > This is taken from a simple error propagation analysis as taught in some > physical/analytical chemistry laboratories. > > Richard > > Wong Lai Ho wrote: > > > Dear CCLers, > > > > I have a question regarding error estimation of the experimental values of > > gibbs free energy. > > As we knows that: > > delta G(formation) > > = delta H(formation) > > - Temp * [entropy(molecule)-sum(entropy(atoms to form the molecules))] > > > > Can I claim that the experimental error bar of the gibbs free energy(delta > > G) is equal to the error bar of the enthalpy change of formation(delta H)? > > (since the error introduced by the entropy is usually very small) > > Is there any papers or books talking about this error? > > > > I would be grateful if you can give some comments on this claim. > > > > Larry > > > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Chemistry > Trinity University, San Antonio, TX 78212 > > > > > > > > > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Wed May 14 12:18:15 2003 Received: from web11703.mail.yahoo.com ([216.136.172.69]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4EGIFt05474 for ; Wed, 14 May 2003 12:18:15 -0400 Message-ID: <20030514161815.43186.qmail@web11703.mail.yahoo.com> Received: from [200.74.140.230] by web11703.mail.yahoo.com via HTTP; Wed, 14 May 2003 11:18:15 CDT Date: Wed, 14 May 2003 11:18:15 -0500 (CDT) From: =?iso-8859-1?q?Constanza=20Cardenas?= Subject: HELP: 2GB Scratch file limit in G98 on Linux/i386 To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CClers- We are using G98 Rev A.11 compiled with gcc-2.96 (linux/i386 2.4.18). However, the scatch files cannot grow beyond a 2GB limit. Apparently, SEEK uses 32 bit integers and this causes the file size limit. How have any of you overcome this scratch file size limit? TIA, Constanza _________________________________________________________ Do You Yahoo!? Información de Estados Unidos y América Latina, en Yahoo! Noticias. Visítanos en http://noticias.espanol.yahoo.com From chemistry-request@server.ccl.net Wed May 14 14:32:23 2003 Received: from bureau6.utcc.utoronto.ca ([128.100.132.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4EIWMt08258 for ; Wed, 14 May 2003 14:32:23 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1197]) by bureau6.utcc.utoronto.ca with SMTP id <464332-11312>; Wed, 14 May 2003 14:32:10 -0400 From: "William Wei" To: "CCLers" Cc: "William Wei" Subject: Summary: Gaussian Convergence failure! Date: Wed, 14 May 2003 14:33:24 -0500 Message-ID: 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) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Original question: After several Convergence failure (I changed conformations), what others I can do for it? My system is about 20 heavy atoms, include one benzal group in the end, and one Fluorine one Sulfur. After B3LYP/3-21G optimized, it can not convergence at B3LYP/6-31+G(D) level. Could anybody give me suggestion. I will summarize the result. Thank you. I got a lot of messages and I learned a lot from them. It is good to share these information with our community. Here they are: --------------------- I suppose, main part od the problem is connected with the presence of diffuse functions. Firstly, does your system really need them to be properly discribed? If so, I would suggest: 1. using UltraFineGrid, 2. maybe using scf=qc, which is slower, but more reliable algorithm, 3. maybe trying to converge it in a small basis containing diffuse function like 3-21+G, and later using these results as a guess in subsequent computations. Yours, Marcin Makowski ---------------------- Are you using the checkfile from the successful opt as a start for the 6-31+G(d) calc. perhaps you'd be better to opt at 6-31 first, then do for the bigger basis set. Regards Roma -------------------- Go at it slowly. Do a guess=read to try B3lYP/6-31G, then 6-31G(D) and then 6-31+G(D). I find this often works. I assume you are talking about SCF convergeence. Brian. ---------------------- try to suppress the (+) diffuse function. It worked for me for an organic molecule, once. Yours Alexandre HOCQUET ---------------------- You're not too specific on what you have already tried, so the advice I will give you is very basic stuff. You might actually need some more advanced tricks, but you should try these things first. I assume that you have optimized the geometry in the B3LYP/3-21G* job, and now the SCF won't converge with the larger basis set? I would at first avoid the diffuse functions, and instead run a single point job at the B3LYP/6-31G* level, reading in the initial guess from the checkpoint file from B3LYP/3-21G* job (Guess=Read keyword). You should also increase the number of SCF cycles, by specifying SCF(MaxCycle=1000) or an even higher number if nessecary. Hopefully, this will lead to SCF convergence. Then you can move on with optimizing the geometry or running the 6-31+G(D) job, again reading the initial guess from the checkpoint file. Once you have a wavefunction that converges, you might also want to run a job specifying the Stable keyword just to make sure. Hope it helps! Peter --------------------- Try scf=qc, it is slower but usually it works when the default algorithm fail. Michele Lunelli -------------------- Most programs will let you use the SCF MOs from one run as the input to start the next run. I would go 3-21 -> 6-31+G -> 6-31+G(D), all in one job. Are you using Gaussian? John McKelvey -------------------- I had the same problem earlier. Check the .out file to see if the failure is in the scf calculation. If so, try using scf=qc in the route section. Joey -------------------- Can you try to increase the maxcycle number for scf? For example, scf=(maxcycle=256) option. Yubo -------------------- Here are some possible approaches to solving your problem. If it is the '+' that caused the convergence difficulty then try doing a single point B3LYP/6-31G(d) calculation first. If the job converged you may then proceed to a 6-31+G(d) calculation with the guess=read option. Gaussian is capable of taking advantage of an initial guess generated from a smaller basis set. Did you also try any hartree-fock calculation? If the HF method converged easily then you may try a BHandHLYP singlet point job. Use the BHandHLYP orbitals which should be similar to B3LYP as the initial guess for subsequent calculations. Is your B3LYP/6-31+G(d) job a single point energy calculation? If the convergence failure occurs during geometry optimization reducing the step size may help. In the most difficult case the SCF solution will keep oscillating. You may then consider measures like reducing the convergence criteria (with scf=sp; ok for single point job, not recommended for geometry optimization) or the scf=qc which could take forever. Wai-To Chan -------------------- I assume your convergence failure is not an SCF convergence problem (this is not clear from your message). Then, if you have done a frequency calculation for the B3LYP/3-21G optimized structure, try using the force constants for the calculation at the higher level, i.e. use opt=readfc (note that the name of the checkpoint file must be the one you used for the lower level calculation). Dmitri -------------------- I am not sure where your problem is, because you did not attach your input gaussian file with the structure of the molecule. But, if I have a problem with convergence in Gaussian (it is true especially for metal complexes) I usually use the QC option in SCF calculations So, write "SCF=QC" in your input file. Unfortunately you will need more time for your calculations :-( Best regards Kzys -------------------- Yes, qc is often needed for such systems (namely S-Fe bonding). One usually starts with a HF calculation and a small basis, then increases the basis using options scf(qc,conver=8), then b3lyp calculation (with the same options) pierre.vitorge@cea.fr ---------------------- You might also want to consider reading in the results from the 3-21g calculation as the guess for the higher basis-set 'guess=check'. You might also want to check that the HOMO-LUMO is not causing problems - use 'vshift=x' to increase it. DFT typically gets this separation wrong. Mark Russell ----------------------- Thank you guys, I appreciate it very much. William