From chemistry-request@server.ccl.net Tue May 29 07:23:38 2001 Received: from c0mailgw07.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4TBNbS12033 for ; Tue, 29 May 2001 07:23:37 -0400 Received: from mail18.prontomail.com (209.185.149.118) by c0mailgw07.prontomail.com (NPlex 5.5.015.3) id 3B137B7400000E9B for chemistry@ccl.net; Tue, 29 May 2001 04:20:26 -0700 Received: from c0web103 (216.163.180.10) by mail18.prontomail.com (NPlex 2.0.123) for chemistry@ccl.net; Tue, 29 May 2001 04:20:26 -0700 From: "markus mayer" Message-Id: Date: Tue, 29 May 2001 04:20:23 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: MD simulation of crystal melting X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear netters, I have an alloy which contains hydrogen. I want to identify the mobile species in this compounds before it melts. I intent to do a MD simulation and then study the spatial correlation function of each species. Now come the practical part. What code to use and what potential to use? I have checked some force field database but could not find the force field which contains all the element in my compound. So is it easy to generate such force field? and what program do you suggest? I used to do ab initio calculations so am totally unfamiliar with MD simulation. Forgive me if the question does not sound. thanks in advance markus ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Tue May 29 07:23:40 2001 Received: from c0mailgw07.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4TBNdS12038 for ; Tue, 29 May 2001 07:23:39 -0400 Received: from mail18.prontomail.com (209.185.149.118) by c0mailgw07.prontomail.com (NPlex 5.5.015.3) id 3B137B7400000EA7 for chemistry@ccl.net; Tue, 29 May 2001 04:20:34 -0700 Received: from c0web103 (216.163.180.10) by mail18.prontomail.com (NPlex 2.0.123) for chemistry@ccl.net; Tue, 29 May 2001 04:20:34 -0700 From: "markus mayer" Message-Id: <2F3A34FDFE355D115A450005B80ADEE6@markus.nandomail.com> Date: Tue, 29 May 2001 04:20:34 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: MD simulation of crystal melting X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear netters, I have an alloy which contains hydrogen. I want to identify the mobile species in this compounds before it melts. I intent to do a MD simulation and then study the spatial correlation function of each species. Now come the practical part. What code to use and what potential to use? I have checked some force field database but could not find the force field which contains all the element in my compound. So is it easy to generate such force field? and what program do you suggest? I used to do ab initio calculations so am totally unfamiliar with MD simulation. Forgive me if the question does not sound. thanks in advance markus ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Tue May 29 06:06:07 2001 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4TA5iS09332 for ; Tue, 29 May 2001 06:05:45 -0400 Received: (qmail 6497 invoked from network); 29 May 2001 12:07:12 -0000 Received: from test.fqspl.com.pl (HELO test) (10.10.10.50) by mail.fqspl.com.pl with SMTP; 29 May 2001 12:07:12 -0000 Message-ID: <00e401c0e827$3d6ce850$320a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: "Christian Pilger" , Cc: References: Subject: protein ionization Date: Tue, 29 May 2001 12:07:59 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, Christian Pilger wrote: From: "Christian Pilger" Subject: CCL:titratable amino acids and counter ions > while preparing a protein structure as input for MD simulations, I > encountered the following points, which I would like to ask your advice: > > - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? > Are all of them simply taken in their ionized forms ? I'm also very confused in general what to do with these residues, running QM calculation. The issue of the initially correct model definition is highly important for a quantum-chemical calculation of proteins. Certainly the ionization of these residues should depend on the environment the protein is placed in. Does someone know any MM or QM computational research papers modeling protein ionization as a response on the environment. I would greatly appreciate any hints. With kind regards, Victor. ================================================== Victor Anisimov, PhD, Senior Software Researcher - Computational Chemist FQS Poland, a Fujitsu company ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 ================================================== From chemistry-request@server.ccl.net Tue May 29 06:08:00 2001 Received: from alpha.si.unimib.it ([149.132.2.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4TA7xS09373 for ; Tue, 29 May 2001 06:07:59 -0400 Received: from mailserver.unimib.it (apandini.disat.unimib.it [149.132.36.68]) by alpha.si.unimib.it (Post.Office MTA v3.5.3 release 223 ID# 1007-68214U1500L100S0V35) with SMTP id it for ; Tue, 29 May 2001 12:07:56 +0200 Date: Tue, 29 May 2001 10:30:45 +0200 From: alessandro.pandini@unimib.it (Pandini Alessandro - Dip. di Scienze dell'Ambiente e del Territorio) To: chemistry@ccl.net Subject: CCL: Timescale of protein behaviour Message-ID: <20010529103045.C4820@apandini.disat.unimib.it> Reply-To: alessandro.pandini@unimib.it Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Balsa 1.1.2 Lines: 26 Dear CCLers, I am looking for information about timescale in protein behaviour at molecular level. I have a rough idea of the diffent time (really order of magnitude...) involved in molecular movements, but I couldn't find a review or a good reference about the topic. I am interest in a comparision between simulation, experimental studies and biological mechanism. Which are the limits and the future goals of simulation vs experiments? How could they pratically support each other? I will summurize answers. Thanks to anyone will email. Alex ----- Alessandro Pandini, PhD Student DISAT - Università degli Studi di Milano-Bicocca Piazza della Scienza, 1 20126 Milano Italy ----- From chemistry-request@server.ccl.net Tue May 29 12:57:11 2001 Received: from goliath.cnchost.com ([207.155.252.47]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4TGvBS22181 for ; Tue, 29 May 2001 12:57:11 -0400 Received: from guillermo ([63.127.188.75]) by goliath.cnchost.com id MAA25502; Tue, 29 May 2001 12:57:00 -0400 (EDT) [ConcentricHost SMTP Relay 1.11] Errors-To: Reply-To: From: "Dr. Guillermo A. Morales" To: "Artem Masunov" , Subject: RE: Databases to support Comb.Chem.? Date: Tue, 29 May 2001 09:54:45 -0700 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 In-Reply-To: Importance: Normal Dear Artem, Perhaps you would like to take a look at the Combinatorial Chemistry Software Section at my site CombiChemLab.com (http://www.combichemlab.com). You might find there an option that fits your needs. Hope this helps. Best of luck, Guillermo. ----- Dr. Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Artem Masunov Sent: Sunday, May 27, 2001 6:38 PM To: chemistry@ccl.net Subject: CCL:Databases to support Comb.Chem.? Dear CCLers, What software do you use nowadays to support combinatorial chemistry/high throughput screening? Comprehensive solutions from MSI seem to be too expensive for Academia (especially maintenance), and Windows based products (like Chem Finder from CambridgeSoft) do not seem to be able to handle large (hundreds of thousands) libraries.. Artem -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue May 29 22:53:31 2001 Received: from blakey.sci.ccny.cuny.edu (IDENT:root@[134.74.52.245]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4U2rUS32665 for ; Tue, 29 May 2001 22:53:30 -0400 Received: from localhost (amasunov@localhost) by blakey.sci.ccny.cuny.edu (8.11.0/8.11.0) with ESMTP id f4U2uIs03386 for ; Tue, 29 May 2001 22:56:19 -0400 Date: Tue, 29 May 2001 22:56:18 -0400 (EDT) From: Artem Masunov To: Subject: Summary + Question: Databases to support Comb.Chem. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thank you all who replied! The summary is below. Unfortunately, I only got responces from the vendors (except one).. What I hoped to get was input from the users. Dear Computational Chemists, experienced in ChemInformatics support for wet Combinatiorial Chemistry/High Throughput Screening lab!!! You researched the market, and selected the greatest value at minimal maintenence cost. What did you chose? Are you happy/unhappy with what you got? Please share with us.. Thank you in advance... Artem ------------- summary ------------- www.CombiChemLab.com www.combi-web.com www.DayLight.com www.MDLI.com www.MSI.com www.Accelrys.com www.ChemComp.com. www.ACDlabs.com www.JChem.com ------------- replies ------------- From: Dr. Guillermo A. Morales Perhaps you would like to take a look at the Combinatorial Chemistry Software Section at my site CombiChemLab.com (http://www.combichemlab.com). You might find there an option that fits your needs. ----------------------------------- From: Gavin Shear Advanced Chemistry Development (ACD) offers various tools for combinatorial/high throughput applications. For example, ACD clients are using our physicochemical (pKa, LogP, LogD, solubility) prediction software in high throughput drug discovery environments. These products also allow the user to create and utilize large training databases to improve predictions based on experimental data. Please see: http://www.acdlabs.com/clients/pr_pfizer0201.html Integration with third party applications such as ISIS/HOST, SpotFire, and more, is also available, as are tools such as ActiveX controls, and Java applets for integration to existing solutions. For Spectroscopy, and Chromatography, ACD offers SpecManager SQL, and enterprise solution for processing, databasing and analyzing experimental data. http://www.acdlabs.com/products/glob_sol_lab/spec_manager_sql/ For analysis of high throughput HNMR spectral plates, ACD/Combi NMR uses the ACD HNMR prediction engine, along with user trainable databases. Please see: http://www.acdlabs.com/products/spec_lab/complex_tasks/combinmr/ Please contact info@acdlabs.com, or sales@acdlabs.com for more information or visit our website: www.acdlabs.com ----------------------------------- From: Dimitri Bondarev You may want to try out the Molecular Operating Environment from http://www.chemcomp.com. We do have HTS and virtual combinatorial chemistry tools, and provide a 30-day evaluation (customer support included!). We also have an academic discount policy. ----------------------------------- FROM: Dr. Ferenc Csizmadia JChem is a software for handling chemical databases and structure files. http://www.jchem.com It runs under both Unix and Windows (even Mac) since it is written in Java. (At our web site you can try examples running on a Sun machine.) We are walking into the area of combinatorial chemistry with a new module, JKlustor, that can perform diversity calculations and clustering. http://www.jchem.com/doc/admin/JKlustor.html The software is developed continuously, we are open to suggestions on future directions. Please let me know if you have any question or if there are features that you miss. ----------------------------------- From: Eric Jamois I just saw your message on the CCL about selecting software for Combinatorial Chemistry. MSI has a tremendous amount of experience in this area through its Combinatorial Chemistry Consortium. I think we have invested more than any other company in the development of software for library design. Personally, I would approach selecting software from a different angle: First, evaluate the tools that are out there against my problem and select the vendor on that basis. Then work with the sales person to fit it in the budget envelope. This may require that you publish with the software...etc. ----------------------------------- Thank you all again!