From chemistry-request@ccl.net Fri Dec 12 08:41:03 2003 Received: from faro.ibmc.up.pt (faro.ibmc.up.pt [193.137.38.3]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBCDeU8a006167 for ; Fri, 12 Dec 2003 08:40:31 -0500 Received: (qmail 6512 invoked by uid 504); 12 Dec 2003 13:39:55 -0000 Received: from fmaia)at(gmx.net by faro.ibmc.up.pt by uid 0 with qmail-scanner-1.16 (uvscan: v4.1.40/v4121. spamassassin: 2.60. Clear:. Processed in 0.059916 secs); 12 Dec 2003 13:39:55 -0000 Received: from unknown (HELO xtal6.ibmc.up.pt) (193.137.38.253) by 0 with SMTP; 12 Dec 2003 13:39:55 -0000 To: chemistry)at(ccl.net Subject: Autodock .vs GOLD From: Filipe Maia Organization: IBMC Content-Type: text/plain; format=flowed; charset=iso-8859-1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Date: Fri, 12 Dec 2003 13:46:56 -0000 Message-ID: User-Agent: Opera7.23/Linux M2 build 518 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Greetings dear CCL readers, Can anyone compare the performance of Autodock3 and GOLD when docking a ligand with several hydrophobic interactions to a protein? Which one is more accurate? (speed is not an issue). Best regards From chemistry-request@ccl.net Fri Dec 12 01:58:32 2003 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBC6vX8a017006 for ; Fri, 12 Dec 2003 01:57:55 -0500 Received: (eyou send program); Wed, 10 Dec 2003 10:04:01 +0800 Message-ID: <271021841.16896~at~mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Wed, 10 Dec 2003 10:04:01 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: namd-l~at~ks.uiuc.edu Date: Wed, 10 Dec 2003 10:04:01 +0800 CC: CHEMISTRY~at~ccl.net Reply-To: "" Subject: where to find the force field parameters for F and P atom? Content-Type: text/plain X-Spam-Status: No, hits=5.2 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I want to do a MD calculation with the system including F and P atom. However I can't find these relevant parameters in AMBER or CHARMM force field parameters. If you can give me some suggestions or clues on where I can find them, I will be very appreciated your help! From chemistry-request@ccl.net Thu Dec 11 23:11:52 2003 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBC4Aq8a006761 for ; Thu, 11 Dec 2003 23:11:15 -0500 Received: (eyou send program); Thu, 11 Dec 2003 17:36:27 +0800 Message-ID: <271135387.19562~at~mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Thu, 11 Dec 2003 17:36:27 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: CHEMISTRY~at~ccl.net Date: Thu, 11 Dec 2003 17:36:27 +0800 Reply-To: "" Subject: format for adding force field parameter in the G03 input file Content-Type: text/plain X-Spam-Status: No, hits=5.2 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I have a questionon on Molecular Mechanics caluclation of ONIOM method. I want to use AMBER force field at low layer, however some parameters are not available in this program. For example, the following is a part of output fiel: -------------------------------------------------- Bondstretch undefined between atoms 1689 4232 Bondstretch undefined between atoms 1825 1827 Bondstretch undefined between atoms 2029 2031 Bondstretch undefined between atoms 2531 2532 Angle bend undefined between atoms 153 154 155 Angle bend undefined between atoms 154 155 157 Angle bend undefined between atoms 154 156 158 ---------------------------------------------------------- So I must input the parameter by myself. In the manual of G03, there is a sentence" SoftOnly Read parameters from the input stream and use only them, ignoring hard-wired parameters", but I don't know the format for adding parameter in the input file. Could you please tell me the detailed format for adding parameter in the input file? Thank you for your help! YingXiong From chemistry-request@ccl.net Fri Dec 12 14:12:29 2003 Received: from gw1-mail.cict.fr (gw1-mail.cict.fr [195.220.59.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBCJBv8a018046 for ; Fri, 12 Dec 2003 14:11:57 -0500 Received: from gw1-mail.cict.fr (gw1-mail.cict.fr [127.0.0.1]) by gw1-mail.cict.fr (8.12.10/8.12.9) with ESMTP id hBCJC5GP029845 for ; Fri, 12 Dec 2003 20:12:05 +0100 Received: from irsamc.ups-tlse.fr (irsamc.ups-tlse.fr [130.120.88.41]) by gw1-mail.cict.fr (8.12.10/8.12.9) with ESMTP id hBCJC5PU029841 for ; Fri, 12 Dec 2003 20:12:05 +0100 Received: from irsamc4.ups-tlse.fr (irsamc4.ups-tlse.fr [130.120.88.67]) by irsamc.ups-tlse.fr (8.11.6/8.11.6) with ESMTP id hBCJBs404524 for ; Fri, 12 Dec 2003 20:11:54 +0100 Date: Fri, 12 Dec 2003 20:11:51 +0100 (CET) From: EVANGELISTI Stefano X-X-Sender: stefano-.at.-irsamc4.ups-tlse.fr To: chemistry-.at.-ccl.net Subject: CCL: EUCO-CC5 Second_Announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT 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) SECOND ANNOUNCEMENT SECOND ANNOUNCEMENT SECOND ANNOUNCEMENT SECOND ANNOUNCEMENT Notice: A few changes have been made compared to the First Announcement THE FIFTH EUROPEAN CONFERENCE ON COMPUTATIONAL CHEMISTRY (EUCO-CC5) will be held in the AGELONDE complex, at LA LONDE LES MAURES on the Mediterranean coast, close to Hyhres les Palmiers, FRANCE, from the 15th to the 20th June, 2004 This congress is the fifth in this series, after the similar ones held in Nancy, Lisboa, Budapest, and Assisi. The conference is organized by the Working Party on Computational Chemistry of the Federation of European Chemistry Societies (FECS). Local organization is undertaken by the "Laboratoire de Physique Quantique" of P. Sabatier University, Toulouse (F) and the "Groupe de Chimie Thiorique et Modilisation Moliculaire", Aix-Marseille Universities I and III, Marseille (F). Additional information can be found on the web site http://www.irsamc.ups-tlse.fr/EUCOCC5 The following topics will be covered during the conference: Quantum Chemistry Spectroscopy Statistical Mechanics and Thermodynamics Molecular Dynamics and Kinetics Molecular Modelling Cheminformatics and Chemometrics Bioinformatics The conference program will include plenary lectures, Oral Communications, and two Poster Sessions. Plenary lectures will be given by the following speakers: Kurt Binder (Mainz - Germany) Victor I. Danilov (Kiev - Ukraine) Robert Glen (Cambridge - United Kingdom) Fracesc Illas (Barcelona - Spain) Massimo Olivucci (Siena - Italy) Andras Perczel (Budapest - Hungary) Hans-Joachim Werner (Stuttgart - Germany) Gilles Zerah (Paris - France) Oral Communications will be selected on the basis of a written presentation (a manuscript of no more than 6 pages, plus two figures). All these papers will be reviewed, and the selected contributions will be published on a special issue of the JOURNAL of COMPUTATIONAL METHODS in SCIENCES and ENGINEERING that will be ready for the time of the conference. The manuscripts must be sent, in electronic form, >>>>>>>>>>>>>>>>>>>>> BEFORE January 15, 2004 to <<<<<<<<<<<<<<<<<<<<< eucocc5.-at-.irsamc.ups-tlse.fr The format must be LaTeX or Word for Windows. Figures must be in .eps or .ps form. In addition to this, the congress proceedings will be published on the INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (instructions will be given subsequently) The inscription prices are single-room accomodation 650 Euros (750 after March 31) double-room accomodation 550 Euros (650 after March 31) These fees include all the meals during the congress period, and the congress banquet. For the Local Committee Stefano EVANGELISTI We apologize to those who will receive multiple copies of this e-mail. -- Stefano EVANGELISTI Laboratoire de Physique Quantique Universite Paul Sabatier 118 R.te de Narbonne F-31062 Toulouse FRANCE Phone: +33(0)561.55.76.94 Fax: +33(0)561.55.60.65 E-mail: stefano.-at-.irsamc.ups-tlse.fr stefano.-at-.fci.unibo.it From chemistry-request@ccl.net Fri Dec 12 10:24:12 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 hBCFNa8a010874 for ; Fri, 12 Dec 2003 10:23:41 -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 hBCFMZDa018416; Fri, 12 Dec 2003 11:22:45 -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 hBCFMJvQ000377; Fri, 12 Dec 2003 11:22:19 -0400 Received: (from apache@localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id hBCFMFaS000352; Fri, 12 Dec 2003 11:22:15 -0400 Received: from dellbox.chem.unb.ca (dellbox.chem.unb.ca [131.202.164.145]) by webmail.unb.ca (IMP) with HTTP for ; Fri, 12 Dec 2003 11:22:15 -0400 Message-ID: <1071242535.3fd9dd27d6dce..at..webmail.unb.ca> Date: Fri, 12 Dec 2003 11:22:15 -0400 From: Joey Harriman To: yxiong..at..mail.ccnu.edu.cn Cc: namd-l..at..ks.uiuc.edu, CHEMISTRY..at..ccl.net Subject: Re: CCL:where to find the force field parameters for F and P atom? References: <271021841.16896..at..mail.ccnu.edu.cn> In-Reply-To: <271021841.16896..at..mail.ccnu.edu.cn> 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: 131.202.164.145 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=-0.9, required 5, DEAR_SOMETHING, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, SPAM_PHRASE_02_03, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=0.3 required=7.0 tests=DEAR_SOMETHING,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, If you are doing an MD in amber7 you can make a force field modification file including the missing parameters. You could try to get these parameters from a variety of different sources. The best of course would be to run the ab initio calculations to get these values. As a less expensive solution you could try to get the parameters > from gaff (in Amber 7) or from a molecular mechanics program such a macromodel that is well parametrized. Hope this helps. Cheers, Joey Quoting yxiong..at..mail.ccnu.edu.cn: > Dear sir, > I want to do a MD calculation with the system including F and P atom. However I > can't find these relevant parameters in AMBER or CHARMM force field parameters. If > you can give me some suggestions or clues on where I can find them, I will be very > appreciated your help! > > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o..at..unb.ca 476-6543 ---------------------------------- From chemistry-request@ccl.net Fri Dec 12 16:09:16 2003 Received: from hellmouth3.gatech.edu (hellmouth3.gatech.edu [130.207.165.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBCL8j8a027998 for ; Fri, 12 Dec 2003 16:08:45 -0500 Received: from hellmouth3.gatech.edu (localhost [127.0.0.1]) by hellmouth3.gatech.edu (Postfix) with SMTP id 019C9221820; Fri, 12 Dec 2003 16:08:46 -0500 (EST) (envelope-from ok16|at|mail.gatech.edu) Received: from acmez.gatech.edu (acmez.prism.gatech.edu [130.207.171.28]) by hellmouth3.gatech.edu (Postfix) with ESMTP id 496FC221594; Fri, 12 Dec 2003 15:55:12 -0500 (EST) (envelope-from ok16|at|mail.gatech.edu) Received: by acmez.gatech.edu (Postfix, from userid 11564) id 243124ECAD; Fri, 12 Dec 2003 15:55:12 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by acmez.gatech.edu (Postfix) with ESMTP id 1B8304FE82; Fri, 12 Dec 2003 15:55:12 -0500 (EST) (envelope-from ok16|at|mail.gatech.edu) Date: Fri, 12 Dec 2003 15:55:11 -0500 (EST) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Cc: Subject: Summary of 5d and 6d functions in basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.1 required=7.0 tests=FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR,USER_AGENT_PINE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers; I summarized answers to following question of mine. Dear CCLers; According to Gaussian and other program manuals, some basis sets employ 6d, and others do 5d. For example, 6-31G* basis set use 6d (Cartesian d function) but 6-311G* basis set use 5d (pure d function). And in GaussianXX program, when the keyword of "Gen" is applied, using 5d is default. Is any particular reason for that? I would appreciate it if anyone could kindly give some advice on this maater. Thank you very much for your attention. The answers are; --------------------------------------------------------------------------------------- Date: Wed, 10 Dec 2003 17:04:20 -0000 From: Herbert Fruechtl To: 'Ohyun Kwon' Subject: CCL: RE: 5d and 6d functions in basis set Parts/Attachments: 1 Shown 71 lines Text 2 OK 20 lines Text ---------------------------------------- The "correct" treatment of the angular part of the basis set (cartesian or spherical) is generally the one that was used for its development, so you would have to look up the original reference (unless you just trust Gaussian to get it right). Generally, older basis sets tend to be of the cartesian variety, because this is easier to program, and integral codes for these basis functions were available earlier. Spherical harmonics are mathematically cleaner, because they don't introduce additional functions of lower angular momentum. Differences in speed vary between programs. Some calculate spherical functions from the cartesians by projecting out the additional functions, which is obviously slower than just the cartesian functions. Others are optimised for spherical functions, and you pay a penalty if you use cartesian functions. For post-HF methods, often the number of basis functions determines the cost of calculations, which also favours spherical functions. HTH, Herbert --------------------------------------------------------------------------------- Date: Wed, 10 Dec 2003 12:26:25 -0500 (EST) From: Joslyn Y Kravitz To: Ohyun Kwon Subject: Re: CCL:5d and 6d functions in basis set I've just been dealing with this. If you use 5D, you get the orbital information in a form that translates directly to the regular 5 d orbitals you usually think of, dxy, dz^2, etc. I think this is preferrable if you are looking at atomic orbital contributions to MO's. The 6D puts the electron density into 6 d-type orbitals, which is probably more "accurate" since more basis functions give a better approximation and the dz^2 is really a linear combination of two orbitals anyway. But I think the 5D way is more "intuitive." One note of caustion, if you use a basis set that defaults to (6D, 10F) but you want to use 5D, you also may have to specify 7F or else the orbitals don't come put right. While this explanation is not the most scientific, I hope it helps. Joslyn Kravitz ---------------------------------------------------------------------------------- Date: Wed, 10 Dec 2003 13:05:16 -0500 From: Stefan Fau To: Ohyun Kwon Cc: CCL - all Subject: CCL: Re: 5d and 6d functions in basis set [ The following text is in the "iso-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] Hi Ohyun, my speculation on this is as follows: cartesian d-functions are linear combinations of the five "pure" d-functions and an s-function of the same exponent. Therefore, using cartesian d-functions introduces an additional s-function into the basis set. This may lead to near linear dependence problems in larger basis sets. Since many smaller basis sets are part of Gaussians basis set library, it is probably more likely that the GEN keyword is used to specify large basis sets. Hence the 5D default. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau|at|qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 ------------------------------------------------------------------------------------ Date: Wed, 10 Dec 2003 14:26:51 -0500 (EST) From: Doug Fox Reply-To: gaussian.com!help%gaussian.com|at|gaussian.com To: Ohyun Kwon Subject: Re: CCL:5d and 6d functions in basis set Dr. Kwon, The 6d case is easier to code but less satisfying if you compare with the hydrogenic solution where there are only 5 angular momentum functions with l=2. Second, that 6th function is sort of a 2S function, spherically symmetric with a node, and as an s function it overlaps strongly with the other s functions in the basis set. This can cause linear dependence problems and if you have carefully chosen the set of s functions adding a random function is unlikely to be an improvement. So eliminating these functions cuts down the cost slightly while achieving the goal of adding polarization functions to the basis set. >