From chemistry-request@ccl.net Tue Dec 2 21:42:11 2003 Received: from postal.usc.edu (postal.usc.edu [128.125.253.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB32fdxp027729 for ; Tue, 2 Dec 2003 21:41:40 -0500 Received: from usc.edu (localhost.usc.edu [127.0.0.1]) by postal.usc.edu (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HPA00441STFLM)at(postal.usc.edu> for chemistry)at(server.ccl.net; Tue, 02 Dec 2003 18:41:39 -0800 (PST) Received: from [128.125.23.1] by postal.usc.edu (mshttpd); Tue, 02 Dec 2003 18:41:39 -0800 Date: Tue, 02 Dec 2003 18:41:39 -0800 From: bradley douglass Subject: Best Graphical Interface for Autodock? To: chemistry)at(server.ccl.net Message-id: <82f91782e803.82e80382f917)at(usc.edu> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: en Priority: normal X-Spam-Status: No, hits=-0.1 required=7.0 tests=X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I am trying to find a graphically powerful and versatile viewing application to use in conjunction with Autodock; specifically for use in drug discovery. Any suggestions? I would like to restrict my search for apps that are FREE and Linux friendly. I've just started looking, but the best I've found so far is MolMol. Thanks in advance for your opinions. Brad Douglass University of Southern California bradd)at(usc.edu ************************************************************************ The highest purpose is to have no purpose at all. This puts one in accord with nature in her manner of operation. -- John Cage *********************************************************************** From chemistry-request@ccl.net Tue Dec 2 20:30:38 2003 Received: from father.chem.ubc.ca (chem.ubc.ca [137.82.7.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB31U6xp026591 for ; Tue, 2 Dec 2003 20:30:06 -0500 Received: from localhost (sacooke@localhost) by father.chem.ubc.ca (8.12.8/8.12.8) with ESMTP id hB31UB3R027596 for ; Tue, 2 Dec 2003 17:30:11 -0800 Date: Tue, 2 Dec 2003 17:30:11 -0800 (PST) From: Stephen Cooke To: chemistry..at..ccl.net Subject: Elec. Excited States Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I am interested in calculating the term energies along with the associated electronic state and potential energy curves for excited electronic states of heavy metal containing diatomic molecules such as WO, PtS, LuF etc. I was wondering what people consider to be the "state of the art" package and method for this type of calculation? For example a recent paper (2001) on WO by Ram et al. has used the MOLPRO package at the CMCRI level of theory with MO's first optimized in a state-averaged full-valence CASSCF calculation. Is there a better way or is this as good as it gets? Cheers, Steve -- From chemistry-request@ccl.net Wed Dec 3 04:04:12 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB393exp001866 for ; Wed, 3 Dec 2003 04:03:40 -0500 Received: from chem.vu.nl (oac17.chem.vu.nl [130.37.31.136]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1ARSv5-000NGFC; Wed, 3 Dec 2003 10:03 +0100 Date: Wed, 3 Dec 2003 10:05:30 +0100 Subject: Re: CCL:Lennard Jones potential parameters. Content-Type: multipart/alternative; boundary=Apple-Mail-4--206666084 Mime-Version: 1.0 (Apple Message framework v553) Cc: To: "Liuming Yan" From: Marcel Swart In-Reply-To: <0b6001c3b923$7557d430$1816fc81@yayay> Message-Id: X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=-0.3 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_10_20,HTML_MESSAGE,IN_REP_TO, MIME_LONG_LINE_QP,QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES, USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --Apple-Mail-4--206666084 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Whenever I find atoms for which there is no LJ parameter set available, I usually use the values from: "Molecular mechanics parameters", N.L. Allinger, X. Zhou and J. Bergsma J.Mol.Str.(Theochem) 312 (1994) 69-83 For Au, they are R=3D2.43 Angstrom, Eps=3D0.625 kcal/mol. NOTE: when combining these values with other force fields, you might=20 introduce mismatches, so be careful ! On Tuesday, Dec 2, 2003, at 23:27 Europe/Amsterdam, Liuming Yan wrote: > Dear all, > =A0 > =A0=A0=A0 I am trying to run some MD simulation using LJ potential, = but I=20 > can't find the potential parameters for the following atoms: > Au=A0 vs. Si > Au vs. O > =A0=A0=A0 Could tell me a reference on these parameters? > =A0 > Thanks! > > ********************************************* > Dr. Liuming Yan > Electrical Engineering Department > University of South Carolina > Columbia, SC29208 > Phone: 803-777-0392 > e-mail: yanli*at*engr.sc.edu > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Organische en Anorganische Chemie Faculteit der Exacte Wetenschappen Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands F +31-(0)20-4447488 E swart*at*chem.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-4--206666084 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Whenever I find atoms for which there is no LJ parameter set available, I usually use the values from: "Molecular mechanics parameters", N.L. Allinger, X. Zhou and J. Bergsma J.Mol.Str.(Theochem) 312 (1994) 69-83 For Au, they are R=3D2.43 Angstrom, Eps=3D0.625 kcal/mol. NOTE: when combining these values with other force fields, you might introduce mismatches, so be careful ! On Tuesday, Dec 2, 2003, at 23:27 Europe/Amsterdam, Liuming Yan wrote: ArialDear all, =A0 Arial=A0=A0=A0 I am trying to run some MD simulation using LJ potential, but I can't find the potential parameters for the following atoms: ArialAu=A0 vs. Si ArialAu vs. O Arial=A0=A0=A0 Could tell me a reference on = these parameters? =A0 ArialThanks! = Arial******************************************= *** Dr. Liuming Yan Electrical Engineering Department University of South Carolina Columbia, SC29208 Phone: 803-777-0392 e-mail: = 1999,1999,FFFFyanli*at*engr.sc.edu = Helvetica=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96 dr. Marcel Swart Organische en Anorganische Chemie Faculteit der Exacte Wetenschappen Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands F +31-(0)20-4447488 E swart*at*chem.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-4--206666084-- From chemistry-request@ccl.net Wed Dec 3 07:13:15 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3CCfxp031216 for ; Wed, 3 Dec 2003 07:12:43 -0500 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id hB3CAQPR039686; Wed, 3 Dec 2003 10:10:30 -0200 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id hB3CAONe041926; Wed, 3 Dec 2003 10:10:26 -0200 Date: Wed, 3 Dec 2003 10:10:24 -0200 (BDB) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Axel Mathieu cc: CCL Subject: Re: CCL:SOMFA TF2 File Format Converter In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Dr Mathieu, The program SOMFA2 itself is distributed with a file converter and a grid visualizer. Greets. On Mon, 1 Dec 2003, Axel Mathieu wrote: > Greetings CCL'ers, > I just came across SOMFA but unfortunately it works with its own TF2 file format. Did anybody script a file conversion tool for this file type? > APM > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Wed Dec 3 11:59:45 2003 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3GxExp005698 for ; Wed, 3 Dec 2003 11:59:14 -0500 Received: from dmbr032.fvms.ugent.be (dmbr032.fvms.ugent.be [157.193.200.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 63FC868004; Wed, 3 Dec 2003 17:59:12 +0100 (CET) Subject: Re: CCL:Best Graphical Interface for Autodock? From: Dominique Vlieghe To: bradley douglass Cc: chemistry[at]server.ccl.net In-Reply-To: <82f91782e803.82e80382f917[at]usc.edu> References: <82f91782e803.82e80382f917[at]usc.edu> Content-Type: text/plain Organization: Message-Id: <1070470525.13832.0.camel[at]dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 03 Dec 2003 17:55:25 +0100 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-4.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_XIMIAN version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) One word: AutoDockTools On Wed, 2003-12-03 at 03:41, bradley douglass wrote: > I am trying to find a graphically powerful and versatile viewing > application to use in conjunction with Autodock; specifically for use in > drug discovery. Any suggestions? > > I would like to restrict my search for apps that are FREE and Linux > friendly. > > I've just started looking, but the best I've found so far is MolMol. > > Thanks in advance for your opinions. > > Brad Douglass > University of Southern California > bradd[at]usc.edu > > > ************************************************************************ > The highest purpose is to have no purpose at all. > This puts one in accord with nature in her manner of operation. > -- John Cage > *********************************************************************** > > > > -= 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, jkl[at]ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University (new) 'Fiers-Schell-Van Montagu' building (new) Technologiepark 927 (new) B-9052 Ghent (Zwijnaarde), Belgium (new) Tel : +32-(0)9-33-13.693 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe[at]dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------ From chemistry-request@ccl.net Wed Dec 3 11:53:49 2003 Received: from Clarion.ucd.ie (avc.ucd.ie [193.1.172.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3GrIxp004405 for ; Wed, 3 Dec 2003 11:53:18 -0500 X-Confirm-reading-to: Laurence.Cuffe(at)ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Clarion.ucd.ie by Clarion.ucd.ie (PMDF V6.2-X17 #30693) id <0HPB00X01W8FX2(at)Clarion.ucd.ie> for chemistry(at)ccl.net; Wed, 03 Dec 2003 16:53:03 +0000 (GMT) Received: from noelfitz6 (noelfitz6.ucd.ie [137.43.24.17]) by Clarion.ucd.ie (PMDF V6.2-X17 #30693) with ESMTP id <0HPB00Z4EW7Z1O(at)Clarion.ucd.ie>; Wed, 03 Dec 2003 16:52:48 +0000 (GMT) Date: Wed, 03 Dec 2003 16:52:45 +0000 From: Laurence Cuffe Subject: Re: CCL:keto/enolate TS structure in Solvation model In-reply-to: <3fcb5433.4e6d.10387(at)ic.sunysb.edu> To: yonyang , chemistry(at)ccl.net Message-id: <3FCE14DD.12453.B1C31@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On 1 Dec 2003, at 14:46, yonyang wrote: >Dear CCL users: >I am playing around with a keto/enolate formation reaction catalyzed by >gernal acid and base(methyl amine/ammonium ion). I would like to locate >the TS structure in organic solvent such as THF or cyclohexane based on >the TS structure previously located in gas phase. Despite semi-empirical >method AM1 in spartan was able to locate the initial strucuture in >organic >solvation, but further optimization in Gaussian was unsuccesful and >failed >many times. Dear Yong you may find our paper: "Experimental and theoretical studies of rotational barriers in aceto, n-methylaceto and n-phenylacetohydroxamic acid" David A. Brown, Laurence P, Cuffe, Geraldine M. Fitzpatrick, Noel J. fitzpatrick, William K. Glass and Kara M. Herlihy in the collection of Czechoslovak Chemical Communications 2001, 66(1), 99-108 of interest. I think there's an abstract on the webpage: http://cccc.uochb.cas.cz/Vol/66/No01/20010099.html Finding solvated Transistion states is not easy and when we did find them we did not find the barrier heights reliable using DFT and PCM, although this may have changed with the new version of Gaussian. If your molecule has a dipole moment you might consider using the Onsager method, Its old fashioned, but also computationaly cheap and it seemed to improve over gas phase results for our systems. It may also provide a better starting point for more complex calculations. Hope this helps All the best Laurence Cuffe From chemistry-request@ccl.net Wed Dec 3 12:45:38 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3Hj7xp015567 for ; Wed, 3 Dec 2003 12:45:07 -0500 Received: from smeagol.unb.ca (smeagol.unb.ca [131.202.3.52]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id hB3HirdP007406; Wed, 3 Dec 2003 13:44:53 -0400 Received: from smeagol.unb.ca (localhost.localdomain [127.0.0.1]) by smeagol.unb.ca (8.12.8/8.12.8) with ESMTP id hB3HirvQ031014; Wed, 3 Dec 2003 13:44:53 -0400 Received: (from apache@localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id hB3Hir3L031006; Wed, 3 Dec 2003 13:44:53 -0400 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Wed, 3 Dec 2003 13:44:53 -0400 Message-ID: <1070473493.3fce21151fc0c(at)webmail.unb.ca> Date: Wed, 3 Dec 2003 13:44:53 -0400 From: "Flight, Robert Maxwell" Reply-to: robert.flight(at)unb.ca To: bradley douglass , Computational Chemistry List Subject: Re: CCL:Best Graphical Interface for Autodock? References: <82f91782e803.82e80382f917(at)usc.edu> In-Reply-To: <82f91782e803.82e80382f917(at)usc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.164.46 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-2.1, required 5, FROM_HAS_MIXED_NUMS, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, SPAM_PHRASE_03_05, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-2.3 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Brad, Not free, but Linux and Windows friendly is MOE, from Chemical Computing Group (www.chemcomp.com). You can prepare initial files for use in AutoDock by creating MOL2 files from MOE, then use AutoDockTools (free) to prepare them for docking. It is also really great for visualizing the docking results, as you can import the PDB files from docking runs into large databases that make it easy to screen through the results. If you are really looking for free software, I know that AutoDockTools is free and a very versatile tool for molecular modelling, but I don't have much experience with it outside of converting files for use in AutoDock. Hope this helps. Cheers, -Robert Quoting bradley douglass : > I am trying to find a graphically powerful and versatile viewing > application to use in conjunction with Autodock; specifically for use in > drug discovery. Any suggestions? > > I would like to restrict my search for apps that are FREE and Linux > friendly. > > I've just started looking, but the best I've found so far is MolMol. > > Thanks in advance for your opinions. > > Brad Douglass > University of Southern California > bradd(at)usc.edu > > > ************************************************************************ > The highest purpose is to have no purpose at all. > This puts one in accord with nature in her manner of operation. > -- John Cage > *********************************************************************** > > > > -= 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, jkl(at)ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight(at)unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Douglas Adams, Hitch Hikers Guide to the Galaxy From chemistry-request@ccl.net Wed Dec 3 11:53:42 2003 Received: from Clarion.ucd.ie (cigr.ucd.ie [193.1.172.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3GrBxp004393 for ; Wed, 3 Dec 2003 11:53:11 -0500 X-Confirm-reading-to: Laurence.Cuffe*at*ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Clarion.ucd.ie by Clarion.ucd.ie (PMDF V6.2-X17 #30693) id <0HPB00X01W8FX2*at*Clarion.ucd.ie> for chemistry*at*ccl.net; Wed, 03 Dec 2003 16:53:03 +0000 (GMT) Received: from noelfitz6 (noelfitz6.ucd.ie [137.43.24.17]) by Clarion.ucd.ie (PMDF V6.2-X17 #30693) with ESMTP id <0HPB00Z4EW7Z1O*at*Clarion.ucd.ie>; Wed, 03 Dec 2003 16:52:48 +0000 (GMT) Date: Wed, 03 Dec 2003 16:52:46 +0000 From: Laurence Cuffe Subject: Re: CCL:keto/enolate TS structure in Solvation model In-reply-to: <3fcb5433.4e6d.10387*at*ic.sunysb.edu> To: yonyang , chemistry*at*ccl.net Message-id: <3FCE14DE.13452.B1FB4@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On 1 Dec 2003, at 14:46, yonyang wrote: >Dear CCL users: >I am playing around with a keto/enolate formation reaction catalyzed by >gernal acid and base(methyl amine/ammonium ion). I would like to locate >the TS structure in organic solvent such as THF or cyclohexane based on >the TS structure previously located in gas phase. Despite semi-empirical >method AM1 in spartan was able to locate the initial strucuture in >organic >solvation, but further optimization in Gaussian was unsuccesful and >failed >many times. Dear Yong you may find our paper: "Experimental and theoretical studies of rotational barriers in aceto, n-methylaceto and n-phenylacetohydroxamic acid" David A. Brown, Laurence P, Cuffe, Geraldine M. Fitzpatrick, Noel J. fitzpatrick, William K. Glass and Kara M. Herlihy in the collection of Czechoslovak Chemical Communications 2001, 66(1), 99-108 of interest. I think there's an abstract on the webpage: http://cccc.uochb.cas.cz/Vol/66/No01/20010099.html Finding solvated Transistion states is not easy and when we did find them we did not find the barrier heights reliable using DFT and PCM, although this may have changed with the new version of Gaussian. If your molecule has a dipole moment you might consider using the Onsager method, Its old fashioned, but also computationaly cheap and it seemed to improve over gas phase results for our systems. It may also provide a better starting point for more complex calculations. Hope this helps All the best Laurence Cuffe From chemistry-request@ccl.net Wed Dec 3 12:37:53 2003 Received: from mail.mans.edu.eg ([193.227.50.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3HbKxp015314 for ; Wed, 3 Dec 2003 12:37:21 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: CCL: Molecular Orbital Computations on Molecular Complexes content-class: urn:content-classes:message Date: Wed, 3 Dec 2003 19:33:34 +0200 Message-ID: <095F5EDC6A006F41AFF7804586108ACF38E4ED*at*mail.mans.edu.eg> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: Molecular Orbital Computations on Molecular Complexes Thread-Index: AcO5w5PV8PYXD56uTGSHHxLJXgiAxA== From: "Tarek M. El-Gogary" To: X-Spam-Status: No, hits=1.6 required=7.0 tests=BASE64_ENC_TEXT version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id hB3Hbrxp015328 Dear All, I am going to make an essay and give a talk on 'Molecular Orbital Computations on Molecular Complexes'. I very much appreciate if you could make some helpful guideline and suggestions about sub-titles and provide some sources (reviews, books, papres and web sites) about such topic. Best regards Tarek From chemistry-request@ccl.net Wed Dec 3 14:24:45 2003 Received: from mail.mans.edu.eg ([193.227.50.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3JODxp030118 for ; Wed, 3 Dec 2003 14:24:13 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: CCL:Molecular Complexes content-class: urn:content-classes:message Date: Wed, 3 Dec 2003 21:20:28 +0200 Message-ID: <095F5EDC6A006F41AFF7804586108ACF38E4EE_at_mail.mans.edu.eg> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL:Molecular Complexes Thread-Index: AcO50oKgeAlxB+ysQHSmZhuHJ3aE+w== From: "Tarek M. El-Gogary" To: X-Spam-Status: No, hits=1.6 required=7.0 tests=BASE64_ENC_TEXT version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id hB3JOjxp030129 Dear CCLers, I am looking for an accurate definition for the term, Molecular Complexes. I understand that Van der Wal complexes, charge transfer complexes, intercalation complexes and H-Bonding complexes all do fall within Molecular complexes. Please make some comments. Best regards Tarek From jkl@ccl.net Wed Dec 3 17:55:01 2003 -0500 Date: Wed, 03 Dec 2003 17:28:44 -0500 From: "Andrew T. Chu" Subject: DivCon educational version released To: chemistry*at*ccl.net Reply-to: achu*at*quantumbioinc.com Message-id: DivCon is now available through QuantumBio Inc, www.quantumbioinc.com. DivCon is a linear-scaling semi-empirical quantum mechanical software program that carries out divide-and-conquer (D&C) methodology to study intermolecular interactions large biomolecules and ligands. Some of the features are: 1. Support multiple semi-empirical Hamiltonians: AM1, PM3, PM3-PDDG, MNDO-PDDG, MNDO, MNDO/d 2. Multiple geometry optimization algorithms available: - Conjugate Gradient, Steepest Descent, BFGS, LBFGS - Options for DIIS, LSEARCH, and restrained atoms (BELLY) calculations. 3. Derivation of atomic charges using several charge models: CM1, CM2, Mulliken. 4. Transition structure optimization routines. 5. MC simulation capabilities available 6. Frequency calculations - used to compute force constants and resulting vibrational frequencies. 7. Output options include: - Atomic charges, Final eigenvectors, Density of state analysis, Ionization potential, HOMO-LUMO gap, Final/incremental density matrix, Trajectory data, Energy decomposition analyses, Molecular dipole moment. 8. Long-range electrostatics (based on the included charge models) can be handled using Particle Mesh Ewald (PME). Visit http://www.quantumbioinc.com/contact/academic.htm for educational licensing and pricing information, or email sales*at*quantumbioinc.com. Best Regards, Andrew Chu achu*at*quantumbioinc.com From chemistry-request@ccl.net Wed Dec 3 21:38:17 2003 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB42bjxp006952 for ; Wed, 3 Dec 2003 21:37:46 -0500 Received: from oemcomputer (PPP82.fukuoka-ip.dti.ne.jp [211.132.92.82]) by smtp4.dti.ne.jp (3.08s) with SMTP id hB42bfrL013217 for ; Thu, 4 Dec 2003 11:37:42 +0900 (JST) Message-ID: <00a201c3ba0e$896964c0$525c84d3@oemcomputer> From: "Telkuni" To: Subject: CCL: Summary) Amber is MM or MD? Date: Thu, 4 Dec 2003 11:30:08 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, CCLers. I've asked the classification and nature of Amber as written in title. --- original question --- > Although I think it is very basic knowledge, I want to know the truth. > > Some papers and books treat AMBER as Molecular Mechanic method > describing with force fields and bonding parameters. But others treat > AMBER as Molecular Dynamic method describing with potential functions. > > Does AMBER belong MM or MD? and or both of them? > > >...All responses, I will appreciate. And I will summarize them. Here is the summary. Thank you very much for the people who sent me the replies. 1) from Konrad Hinsen --------------------- Both. MM refers to the kind of model that is used to describe the chemical system, MD to a particular simulation method. 2) from David F. Green --------------------- Telkuni, Molecular Mechanics is a term used to describe a type of model for molecular systems. In a Molecular Mechanics model (sometimes also referred to as an Emprical Force Field model), the molecular properties are treated by terms derived from macroscopic physics. For example, bond terms may be treated as a harmonics oscillator, electrostatic interactions may be treated by Coulomb's Law, and so on. In this sense, Molecular Mechanics is a term which differeniates a model from Quantum Mechanics (including ab initio and semi-empirical models), where the underlying description of a molecule is based on microscopic physics (i.e. quantum mechanics). Molecular Dynamics, on the other hand, describes a similuation technique, in which Newton's Laws of motion are propogated over an energy surface. Thus MD should be used to differentiate from other techniques for conformational sampling over an energy surface (such as Monte Carlo). MD can be employed using a Molecular Mechanics force field, or a Quantum Mechanical description of the energetics, just as MC methods can. AMBER includes a Molecular Mechanics force field designed primarily for simulation of biomolecules, comparable in structure, but differing in details from the other biomolecular force fields such as CHARMM, OPLS, or GROMOS, and perhaps varying a little more from MM force fields designed for simulation of other molecules (such as MM3). In addition, AMBER provides a set of code for preforming many types of simulations, including MD. Again, many other packages implement many of the same features, including CHARMM, GROMACS, NAMD, and many more. There are really three independent portions to molecular simulations: (1) the force field, (2) the simulation method, (3) and the software implementation. The confusion arises in that the software package name is often also used for the force field name, particular in the case of AMBER and CHARMM. I hope this clears some things up. David ** And, I've copyed here Dr.Feenstra's CCL-mail answring the question of Dr.Tamulis, becouse it is concerning my questuion. > Dear Prof. Telkuni Tsuru and other Netters, > > I am working with quantum mechanical Hartree-Fock and Density Functional > Methods. Would you be so kind and explane me more detail what it is the > difference between methods: > 1) MM, describing with force fields and bonding parameters and > 2) MD, describing with potential functions ? In the terms you use, there is no difference. Both use *potential functions* to describe *bonding paramaters*, together these are called a *force field*. One can view Molecular *Dynamics* as a special case of Molecular *Mechanics* where dynamics comes in through assigning velocities to all atoms (and hence a system *temperature*), and integrating the (Newtons) equations of *motion*. > Which is more exact in comparison with quantum mechanical methods? IMHO, that is not a sensible question. The realm, if you will, of both methods (i.e. 'QM' vs 'MM/MD') and possible applications, is so different that there is no sensible way in which to compare them. Furthermore, many parameters in the forcefields have their basis in QM calculations, so that MM/MD can be said to be derived from QM, which implies it is less accurate. But on the other hand, the MM/MD parameters are also based on (other) experimental knowledge (often thermodynamical parameters like heat of vaporization) which make them on a certain level of application at least in principle more correct (and at the same time they are, obviously, empyrical parameters with limited applicability). 4) from --------------------- 5) from --------------------- 6) from --------------------- From chemistry-request@ccl.net Wed Dec 3 13:18:25 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3IHsxp017015 for ; Wed, 3 Dec 2003 13:17:54 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HPC00M9M05VII^at^mailserver.unimi.it> for chemistry^at^server.ccl.net; Wed, 03 Dec 2003 19:17:55 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HPC0074405RTK^at^smtp.unimi.it> for chemistry^at^server.ccl.net; Wed, 03 Dec 2003 19:17:51 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 5223F2831F; Wed, 03 Dec 2003 19:21:13 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 47111282D3; Wed, 03 Dec 2003 19:21:13 +0100 (CET) Date: Wed, 03 Dec 2003 19:21:11 +0100 (CET) From: Alessandro Contini Subject: Re: CCL:Best Graphical Interface for Autodock? In-reply-to: <82f91782e803.82e80382f917^at^usc.edu> To: bradley douglass Cc: chemistry^at^server.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 References: <82f91782e803.82e80382f917^at^usc.edu> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hB3IIPxp017031 Hi, did you already tried AutodockTools? it's a graphical front end written in python. It works great under linux and can automate most of the autodock processes. It's freely available at http://www.scripps.edu/pub/olson-web/doc/autodock/tools.html Reguards, Alessandro Contini On Tue, 2 Dec 2003, bradley douglass wrote: > I am trying to find a graphically powerful and versatile viewing > application to use in conjunction with Autodock; specifically for use in > drug discovery. Any suggestions? > > I would like to restrict my search for apps that are FREE and Linux > friendly. > > I've just started looking, but the best I've found so far is MolMol. > > Thanks in advance for your opinions. > > Brad Douglass > University of Southern California > bradd^at^usc.edu > > > ************************************************************************ > The highest purpose is to have no purpose at all. > This puts one in accord with nature in her manner of operation. > -- John Cage > *********************************************************************** > > > > -= 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, jkl^at^ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini^at^unimi.it From chemistry-request@ccl.net Wed Dec 3 14:19:31 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3JIxxp030007 for ; Wed, 3 Dec 2003 14:18:59 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id E269E9AD8; Wed, 3 Dec 2003 20:18:58 +0100 (CET) To: chemistry^at^ccl.net Subject: Resp Esp charge Derive (RED v-1.0) release Message-ID: <1070479138.3fce3722d38fd^at^webmail.u-picardie.fr> Date: Wed, 03 Dec 2003 20:18:58 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.9 required=7.0 tests=NO_COST,USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I am pleased to announce the release of program RED version 1.0. (http://www.u-picardie.fr/labo/lbpd/RED/) R.E.D. (Resp Esp charge Derive) calculate automatically 'RESP' and 'ESP' charges starting > from an un-optimized PDB structure. R.E.D. sequentially executes (i) either program "GAMESS" or program "Gaussian" to minimize the studied structure and to compute the corresponding Molecular Electrostatic Potential, and (ii) program "RESP" to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically generated. Moreover, a new RESP fitting procedure is proposed allowing to get highly reproducible 'RESP' and 'ESP' charges whatever the QM software is and whatever the starting Cartesian coordinates are. R.E.D. makes the development of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure. A graphical user-friendly interface, X R.E.D., has been also developed to execute R.E.D. and modify R.E.D. variables. R.E.D. and X R.E.D. use is described in a downloadable manual. Program R.E.D. has been written with the "Perl" programming language and program X R.E.D. with the "tcl/tk" programming language, making R.E.D. and X R.E.D. highly flexible and portable. These two programs have been tested on PC-LINUX and SGI-IRIX workstations and should work on other UNIX platforms. R.E.D. and X R.E.D. are "free" (i.e. provided at no cost) for all academic users after signing a license. Best regards, Francois F.-Y. Dupradeau -- The Scripps Research Institute, San Diego, CA Faculte de Pharmacie, UPJV, Amiens, France -- http://www.u-picardie.fr/labo/lbpd/fyd.htm From chemistry-request@ccl.net Wed Dec 3 16:19:24 2003 Received: from gdr.neokimia.com (dir-rnd.med.usherbrooke.ca [132.210.158.206]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3LImxp000524 for ; Wed, 3 Dec 2003 16:18:53 -0500 Received: from mercure.neokimia.com (exchange.neokimia.com [192.168.1.3]) by gdr.neokimia.com (8.12.10/8.12.10) with ESMTP id hB3LIlBW019483; Wed, 3 Dec 2003 16:18:47 -0500 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: SOMFA TF2 File Format Converter Date: Wed, 3 Dec 2003 16:18:43 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: SOMFA TF2 File Format Converter Thread-Index: AcO5wE2eKVtiluvRS6usVeV135MWcwAIWotA From: "Axel Mathieu" To: "andre mauricio de oliveira" , X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 0, Requis: 5) X-NK-Spam-Version: SpamAssassin version 2.60 X-Scanned-By: MIMEDefang 2.38 X-Spam-Status: No, hits=-0.5 required=7.0 tests=EMAIL_ATTRIBUTION version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hB3LJOxp000541 Thanks for your reply ... I understand that SOMFA comes with its own CIF to TF2 converter (am I mistaken?) but I was wondering if others had scripted other converters for more file types. Did anybody? I would thus not have to go through my filetypes -> PDB -> CIF -> TF2 (I would like to limit the conversion steps). APM -----Original Message----- From: andre mauricio de oliveira [mailto:amolive!at!dedalus.lcc.ufmg.br] Sent: 3 dicembre, 2003 07:10 To: Axel Mathieu Cc: CCL Subject: CCL:SOMFA TF2 File Format Converter Dear Dr Mathieu, The program SOMFA2 itself is distributed with a file converter and a grid visualizer. Greets. On Mon, 1 Dec 2003, Axel Mathieu wrote: > Greetings CCL'ers, > I just came across SOMFA but unfortunately it works with its own TF2 file format. Did anybody script a file conversion tool for this file type? > APM > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil -= 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, jkl!at!ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Dec 3 18:55:02 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3NsUxp004853 for ; Wed, 3 Dec 2003 18:54:31 -0500 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id hB3NqIPR027108; Wed, 3 Dec 2003 21:52:18 -0200 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id hB3NqHH7027106; Wed, 3 Dec 2003 21:52:17 -0200 Date: Wed, 3 Dec 2003 21:52:17 -0200 (BDB) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Axel Mathieu cc: chemistry..at..ccl.net Subject: RE: SOMFA TF2 File Format Converter In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hB3Nt2xp004864 Dear Dr Mathieu, SOMFA2 does not need to be run with its TF2 format. It is able to run both .csr and .tf2 formats, although .tf2 run faster. I myself have worked with it by using only .cssr format in a direct way. Cheers. On Wed, 3 Dec 2003, Axel Mathieu wrote: > Thanks for your reply ... I understand that SOMFA comes with its own CIF to TF2 converter (am I mistaken?) but I was wondering if others had scripted other converters for more file types. Did anybody? I would thus not have to go through my filetypes -> PDB -> CIF -> TF2 (I would like to limit the conversion steps). > > APM > > -----Original Message----- > From: andre mauricio de oliveira [mailto:amolive..at..dedalus.lcc.ufmg.br] > Sent: 3 dicembre, 2003 07:10 > To: Axel Mathieu > Cc: CCL > Subject: CCL:SOMFA TF2 File Format Converter > > > > Dear Dr Mathieu, > > The program SOMFA2 itself is distributed with a file converter and a grid > visualizer. > > Greets. > > > > > On Mon, 1 Dec 2003, Axel Mathieu wrote: > > > Greetings CCL'ers, > > I just came across SOMFA but unfortunately it works with its own TF2 file format. Did anybody script a file conversion tool for this file type? > > APM > > > > Andre Mauricio de Oliveira > > VOICE +55-031-374-1325 > +55-031-499-5765 > FAX +55-031-499-5700 > > Laboratorio de QSAR e Modelagem Molecular > Nucleo de Estudos em Quimica Medicinal (NEQUIM) > NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim > Departamento de Quimica ICEx > Federal University of Minas Gerais > Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 > Belo Horizonte MG Brazil > > > > -= 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, jkl..at..ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Wed Dec 3 16:37:15 2003 Received: from chemik.chem.univ.gda.pl (chemik.chem.univ.gda.pl [153.19.29.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB3Lacxp001441 for ; Wed, 3 Dec 2003 16:36:39 -0500 Received: from chemik.chem.univ.gda.pl (chemik.chem.univ.gda.pl [153.19.29.1]) by chemik.chem.univ.gda.pl (8.12.10/8.12.10) with ESMTP id hB3La0QD017950 for ; Wed, 3 Dec 2003 22:36:00 +0100 (CET) Received: from localhost (maharan@localhost) by chemik.chem.univ.gda.pl (8.12.10/8.12.10/Submit) with ESMTP id hB3LZwHQ017944 for ; Wed, 3 Dec 2003 22:35:59 +0100 (CET) X-Authentication-Warning: chemik.chem.univ.gda.pl: maharan owned process doing -bs Date: Wed, 3 Dec 2003 22:35:58 +0100 (CET) From: Maciej Haranczyk To: CHEMISTRY..at..ccl.net Subject: Thermodynamic corrections at MM level (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.4 required=7.0 tests=USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I did some DFT (B3LYP) calculations on small DNA fragments (~200atoms). I would like to calculate thermodynamic corrections (EZPV,H,G) for these systems but since I do not have fully optimized geometries (I had to freeze nucleic acid bases layers because B3LYP does not deal with dispersion (pi-stacking)) I cannot run frequency calculation at B3LYP level. I would like to calculate thermodynamic corrections with MM approach and then add it to B3LYP energies. Since I am not familiar with MM programs I would be grateful if someone suggested me any free program than can do that or paper on this topic. Regards, Maciej