From chemistry-request@server.ccl.net Mon Jan 22 21:10:07 2001 Received: from femail3.sdc1.sfba.home.com (femail3.sdc1.sfba.home.com [24.0.95.83]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0N2A7d11226 for ; Mon, 22 Jan 2001 21:10:07 -0500 Received: from C1353359A ([65.4.172.51]) by femail3.sdc1.sfba.home.com (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010123020802.FMDV20325.femail3.sdc1.sfba.home.com@C1353359A>; Mon, 22 Jan 2001 18:08:02 -0800 Message-ID: <003201c084e0$f3214b00$33ac0441@sttln1.wa.home.com> From: "Mark A. Thompson" To: "Maija Lahtela" , References: Subject: Re: CCL:Visualization of double and triple bonds Date: Mon, 22 Jan 2001 18:05:25 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Yes. Try ArgusLab http://www.seanet.com/~mthompson/ArgusLab Mark ----- Original Message ----- From: Maija Lahtela To: Sent: Monday, January 22, 2001 5:31 AM Subject: CCL:Visualization of double and triple bonds > Dear CCLers, > > I would like to > know if there are molecular modeling program such as RasMol, > WebLAbviewer that could present double bond as two tubes and triple bond > with three tubes ( the way as student are used books of chemistry in high > school or collage). > > Yours, > Maija L.-K. > > ***************************************************** > Maija Lahtela-Kakkonen, Researcher > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela@csc.fi, Internet:www.csc.fi > **************************************************** > > > > -= 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 Jan 23 06:44:34 2001 Received: from cpc.pp.molsci.csiro.au (firewall-user@cpc.molsci.csiro.au [138.194.241.18]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0NBiVd13646 for ; Tue, 23 Jan 2001 06:44:32 -0500 Received: by cpc.pp.molsci.csiro.au; id WAA14564; Tue, 23 Jan 2001 22:33:45 +1100 Received: from tigger.pp.molsci.csiro.au(138.194.245.49) by cpc.pp.molsci.csiro.au via smap (V4.2) id xma014562; Tue, 23 Jan 01 22:33:03 +1100 Received: from localhost (bra369@localhost) by tigger.pp.molsci.csiro.au (8.9.3+Sun/8.9.3) with SMTP id WAA00673 for ; Tue, 23 Jan 2001 22:43:47 +1100 (EST) Date: Tue, 23 Jan 2001 22:43:47 +1100 (EST) From: Kim Branson To: chemistry@ccl.net Subject: virtual combinatorial library generation In-Reply-To: <003201c084e0$f3214b00$33ac0441@sttln1.wa.home.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'm looking for software to aid in the generation of virtual combinatorial databases for virtual screening processes. cheers kim ______________________________________________________________________ Mr Kim Branson Phd Student Structral Biology Walter and Elisa Hall Institute Royal Parade, Parkville, Melbourne, Victoria Ph 61 03 9662 7136 Email kim.branson@bioresi.com.au ______________________________________________________________________ From chemistry-request@server.ccl.net Tue Jan 23 09:53:44 2001 Received: from server.ttpharma.com ([206.74.77.186]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0NEred15448 for ; Tue, 23 Jan 2001 09:53:44 -0500 Received: from jerome ([192.168.4.24]) by server.ttpharma.com (8.9.3/8.8.7) with SMTP id IAA07532; Tue, 23 Jan 2001 08:58:29 -0600 From: "Jerome Baudry" To: Cc: "'Nilesh Banavali'" Subject: RE: WHAM programs for 1D PMF Date: Tue, 23 Jan 2001 09:58:22 -0500 Message-ID: <001501c0854c$ef1ae5e0$1804a8c0@ttpharma.com> 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 CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 In-Reply-To: Hi Nilesh You can ask Benoit Roux ( benoit.roux@med.cornell.edu ) or Serge Crouzy(crouzy@blavet.ceng.cea.fr) for their WHAM code. It's actually a 2D WHAM, but it's very easy to turn it into 1D. As for possible differences in the results, I would first check the default values for all the WHAM parameters. In particular, the number of iterations of the WHAM equations was found to significantly affect the convergence of the results (see following paper by Crouzy et al.). Also, in the case of a periodic degree of freedom, like e.g. a dihedral angle, the final results would be changed if you correct the hysteresis (by, for instance, replicating times series at the ends of the reaction coordinate, or by imposing equality of the PMF values at both ends of the reaction coordinate during the WHAM iterations) You can have a look at a paper that addresses these issues: Efficient calculation of 2-dimensional adiabatic and free energy maps: Application to the isomerization of the C13=C14 and C15=N16 bonds in the retinal of bacteriorhodopsin. Serge Crouzy, Jerome Baudry, Jeremy C. Smith and Benoit Roux. J. Comp. Chem. 20,15 (1999) 1644-1658. Justing Gullingsrud ( justin@ks.uiuc.edu ) and colleagues in the Schulten group compared WHAM results with other procedures, in the particular case of nonequilibrium SMD simulations. The authors of the paper could also have a WHAM code available: Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Journal of Computational Physics, 151:190--211, 1999. ( see this paper at: http://www.ks.uiuc.edu/Publications/Papers/abstract.cgi?tbcode=GULL99 ) Cheers for WHAM !!!! Jerome ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On > Behalf Of Nilesh Banavali > Sent: Monday, January 22, 2001 7:27 PM > To: chemistry@ccl.net > Subject: CCL:WHAM programs for 1D PMF > > > > Hi CCLers, > > Are there any stand-alone Weighted Histogram Analysis Method (WHAM) > programs available out there to calculate a one-dimensional > potential of mean force (PMF) given sampled values of a given reaction > coordinate obtained by a set of constrained MD simulations. The > program that I currently have access to is the one written by > Bockzo and > Brooks. The purpose of this inquiry is for me to personally understand > empirically if the PMF calculated by different programs are > different for > the same set of coordinate values and if so why. I guess they should > theoretically be the same, however, any help provided is > greatly appreciated. I will summarize the responses. > > Thanks, > > Nilesh. > -------------------------------------------------------------- > ----------- > NILESH BANAVALI > GRADUATE STUDENT > UNIVERSITY OF MARYLAND, BALTIMORE > -------------------------------------------------------------- > ----------- > > > > > -= 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 Jan 23 13:14:29 2001 Received: from goliath.cnchost.com (goliath.cnchost.com [207.155.252.47]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0NIETd16249 for ; Tue, 23 Jan 2001 13:14:29 -0500 Received: from guillermo (c1121593-a.stcla1.sfba.home.com [24.15.219.11]) by goliath.cnchost.com id NAA17043; Tue, 23 Jan 2001 13:14:21 -0500 (EST) [ConcentricHost SMTP Relay 1.10] Errors-To: Reply-To: From: "Dr. Guillermo A. Morales" To: "Kim Branson" , Subject: RE: virtual combinatorial library generation Date: Tue, 23 Jan 2001 10:13:59 -0800 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) Importance: Normal In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, I have a compilation of companies that provide/develop software for combinatorial library generation at my site CombiChemLab.com (http://www.combichemlab.com) You can find it going to the Software listing in the CombiChem section. I hope this helps. Guillermo Morales ----- 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 Kim Branson Sent: Tuesday, January 23, 2001 3:44 AM To: chemistry@ccl.net Subject: CCL:virtual combinatorial library generation Hi all, I'm looking for software to aid in the generation of virtual combinatorial databases for virtual screening processes. cheers kim ______________________________________________________________________ Mr Kim Branson Phd Student Structral Biology Walter and Elisa Hall Institute Royal Parade, Parkville, Melbourne, Victoria Ph 61 03 9662 7136 Email kim.branson@bioresi.com.au ______________________________________________________________________ -= 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 Jan 23 14:46:08 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0NJk8d16805 for ; Tue, 23 Jan 2001 14:46:08 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA26817 for ; Tue, 23 Jan 2001 14:46:09 -0500 (EST) Date: Tue, 23 Jan 2001 14:46:08 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: 01.07.23 Int. Conf: Appl. Stat. Phys.-ASTATPHYS 2001 in Cancun, MX Message-ID: From: Yosadara Ruiz-Morales To: jkl@ccl.net Subject: 01.07.23 Int. Conf: Appl. Stat. Phys.-ASTATPHYS 2001 in Cancun, Mexico First International Conference on Applied Statistical Physics: Molecular Engineering (ASTATPHYS-MEX- 2001) July 23-27, 2001 in Cancun, Mexico SECOND ANNOUNCEMENT Dear Colleague: It is my pleasure to invite you to attend/or contribute with an oral or poster presentation to the "First International Conference on Applied Statistical Physics: Molecular Engineering (ASTATPHYS-MEX- 2001)", which will be held in Cancun, Mexico on July 23-27, 2001. The aim of the Conference is to gather applied and basic scientists interested in the design and understanding of nano-structures, nano- circuits and gene-delivery. Applications to catalysis, electronics and gene-therapy are particularly sought. The Conference topics will be: molecular catalysis, nano-tubes and fullerenes, nano-structures, nano-circuits microlithography, supramolecular materials, polymers, gene-delivery, self assembling, confined complex fluids, ionic channels, dynamics of confined fluids, phase transitions and layered materials. The application forms, registration fees, accommodation, and more and complete information about the conference can be found in our web page: http://www.aspm2001.com.mx The following colleagues have, in principle, accepted to give an Invited Lecture in ASTATPHYS-MEX-2001: M. Boudart, Stanford U.; M. El-Sayed, Georgia Inst. of Technology; B. Korgel, U. of Texas; R. L. Whetten, Georgia Inst. of Technology; P. Jena, Virginia Commonwealth U.; W. M. Gelbart, UCLA; N.S. Templeton, Baylor College of Chemistry; M.E. Davis, Caltech, and D. Henderson, Brigham Young U, R. A. van Santen, Eindhoven University of Technology, Netherlands. The excellent facilities of the Marriott Casamagna and the Sheraton and Westin Hotels in Cancun together with the turquoise-blue beaches of the Mexican Caribbean will offer an excellent natural frame to all of the conference activities. If you have any question please contact: Dr. Felipe Guevara fguevara@imp.mx Conference assistant Sincerely yours, Dr. Marcelo Lozada-Cassou Conference Chairman Director Molecular Simulation Program, Mexican Petroleum Institute and Physics Professor, Universidad Autonoma Metropolitana INTERNATIONAL SCIENTIFIC COMMITTEE: Gustavo Chapela, IMP, Miguel Jose Yacaman, University of Texas, at Austin, Jose Luis Gazquez, UAM, Mexico, Ferid Rachdi, Montpellier University, France , Rudi Podgornik, NIH, USA, Lorenzo Martinez, IMP, Mexico, Christian Holm, Max Planck Inst., FRG, Juan Murgich, IVIC, Venezuela, Isaac Hernandez- CINVESTAV, Mexico, George Jackson, Imperial College of Science&Technology, UK, Douglas Henderson, B.Y.U, USA, Magdaleno Medina Noyola, UASLP, Mexico, Miguel Rubi, University of Barcelona, Spain, Jose Manuel Dominguez, IMP, Mexico, Andres Alfonso Gutierrez, CNR, Mexico, Leo Degreve, Universidade de Sao Paulo, Brazil, Nikola Batina, UAM, Mexico, Mariano López de Haro, UNAM, Mexico, Jesus Dorantes, UASLP, Mexico, Carlos Lira, IMP, Mexico, Jose Segobia, CINVESTAV, Mexico, Enrique Gonzalez Tovar, UAM, Mexico, Alberto Robledo, UNAM, México, Felipe Guevara, IMP, México, Claudio Mota, UFRJ, Brazil, Roque Hidalgo, Universidad de Granada, Spain. The support of the Mexican Petroleum Institute, Metropolitan Autonomous University, Consejo Nacional para la Ciencia y la Tecnología (CONACYT), Silicon Graphics Incorporated (SGI), México is gratefully acknowledged.