From chemistry-request@server.ccl.net Fri Nov 16 03:41:03 2001 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAG8f3B16950 for ; Fri, 16 Nov 2001 03:41:03 -0500 Received: from igc.phys.chem.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id fAG8eoP28445; Fri, 16 Nov 2001 09:40:50 +0100 (MET) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3BF4CC6D.818D3ABA@igc.phys.chem.ethz.ch> Date: Fri, 16 Nov 2001 09:21:01 +0100 From: Stefan Portmann X-Mailer: Mozilla 4.76 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: CCL CC: Hans Peter Luethi Subject: WATOC'02: Call for Contributions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science CALL FOR CONTRIBUTIONS Abstracts for oral or poster presentations can now be submitted through the WATOC'02 Webserver (http://www.watoc02.ch). There are 60 slots open for oral presentations. A special effort will be made to ensure optimal visibility for the posters. More information as well as electronic registration and accommodation booking are available at http://www.watoc02.ch. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Fri Nov 16 05:14:32 2001 Received: from bute.st-andrews.ac.uk (im17@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGAEWB18720 for ; Fri, 16 Nov 2001 05:14:32 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id KAA14433 for ; Fri, 16 Nov 2001 10:06:40 GMT Date: Fri, 16 Nov 2001 10:06:40 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: chemistry@ccl.net Subject: Velocity re-assignment Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I'm doing MD on my protein structure; in some recent work on simulation using MD at const. temp. I've seen people re-assign velocities every certain Intervals. I want to know excactly how to re-assign velocities periodically? Is it by changing the seed value randomly periodically? or they use another way to do that? What are the benefits for the simulation from velocity re-assignment? Doesn't this drift the trajectory everytime velocities being reassigned?? Is this good for simulation? I'd be appreciated if anyone calrify this point. I use Tripos software to do the simulation. Cheers, Ibrahim Name :Ibrahim M.Moustafa Mail address :Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk From chemistry-request@server.ccl.net Fri Nov 16 06:49:10 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGBnAB21175 for ; Fri, 16 Nov 2001 06:49:10 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id GAA15727; Fri, 16 Nov 2001 06:49:09 -0500 (EST) Date: Fri, 16 Nov 2001 06:49:09 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: jkl@ccl.net Subject: 02.06.02-05: 6th Int Conf on Chemical Structures, Netherlands Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 15 Nov 2001 22:35:29 -0800 From: Guenter Grethe To: CHMINF-L@LISTSERV.INDIANA.EDU Subject: 6th International Conference on Chemical Structures This important triannual conference will take place on June 2 - 6, 2002, at the beautiful conference center in Noordwijkerhout, The Netherlands. Please visit the conference's website at http://www.chemweb.com/docs/6iccs/6iccs.html. for the 'Call for Papers' and other details. Guenter Grethe Conference Chair Dr. Guenter Grethe Director, Scientific Applications Product Development, Research Group 14600 Catalina Street San Leandro, CA 94577 Tel.: (510) 357-2222, ext.1430 Fax: (510) 614-3616 e-mail: guenter@mdli.com http://www.mdli.com From chemistry-request@server.ccl.net Fri Nov 16 05:40:16 2001 Received: from web14907.mail.yahoo.com ([216.136.225.59]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAGAeGB19332 for ; Fri, 16 Nov 2001 05:40:16 -0500 Message-ID: <20011116104009.15912.qmail@web14907.mail.yahoo.com> Received: from [161.142.14.4] by web14907.mail.yahoo.com via HTTP; Fri, 16 Nov 2001 02:40:09 PST Date: Fri, 16 Nov 2001 02:40:09 -0800 (PST) From: Ng Pei Ling Subject: RE To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1619822193-1005907209=:13122" --0-1619822193-1005907209=:13122 Content-Type: text/plain; charset=us-ascii Dear friends : Can any body gives me the homepage address to download the latest versions of AMPAC? I want to assign the charges as teach in autodock manual. --------------------------------- Do You Yahoo!? Find the one for you at Yahoo! Personals. --0-1619822193-1005907209=:13122 Content-Type: text/html; charset=us-ascii

Dear friends :

 Can any body gives me the homepage address to download the latest versions of AMPAC? I want to assign the charges as teach in autodock manual.


Do You Yahoo!?
Find the one for you at Yahoo! Personals. --0-1619822193-1005907209=:13122-- From chemistry-request@server.ccl.net Fri Nov 16 08:19:05 2001 Received: from mhub15.lvs.dupont.com ([52.128.30.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGDJ4B23462 for ; Fri, 16 Nov 2001 08:19:04 -0500 Received: from mhub2.lvs.dupont.com by mhub15.lvs.dupont.com with ESMTP for chemistry@ccl.net; Fri, 16 Nov 2001 08:18:52 -0500 Received: from CDCLN05.LVS.DUPONT.COM by mhub2.lvs.dupont.com with ESMTP for chemistry@ccl.net; Fri, 16 Nov 2001 08:18:40 -0500 Subject: Program to convert spherical polar coordinates to XYZ coordinates To: chemistry@ccl.net From: "Ya-Jun Zheng" Date: Fri, 16 Nov 2001 08:20:51 -0500 Message-Id: X-MIMETrack: Serialize by Router on CDCLNMH1/DuPont_MHUB(Release 5.0.8 |June 18, 2001) at 11/16/2001 08:18:40 AM MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am looking for a simple program or script to convert spherical polar coordinates of a molecule to either XYZ or internal coordinates. Any help or suggestions will be appreciated. Thanks. Yajun From chemistry-request@server.ccl.net Fri Nov 16 08:38:26 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGDcPB23930 for ; Fri, 16 Nov 2001 08:38:26 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id IAA17734; Fri, 16 Nov 2001 08:38:24 -0500 (EST) Date: Fri, 16 Nov 2001 08:38:23 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: 02.05.31 SoftSimu2002 - Novel methods in soft matter simulations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT Date: Fri, 16 Nov 2001 14:33:31 +0200 (EET) From: Mikko Karttunen To: jkl@ccl.net Subject: SoftSimu2002 - Novel methods in soft matter simulations ======================================================= SoftSimu2002 - Novel methods in soft matter simulations ======================================================== WWW: http://www.lce.hut.fi/research/polymer/softsimu2002/ Email: softsimu2002@lce.hut.fi Location: Espoo/Helsinki, Finland Time: May 31 - June 6, 2002 Description: ----------- This Summer School concentrates on novel computer simulation techniques proposed for, and used in, studies of complex molecules and soft matter systems. Examples of these methods include the Dissipative Particle Dynamics, the Malevanets-Kapral method, and Smoothed Particle Hydrodynamics. Further topics of the Summer School include hybrid methods, phase filed methods, hydrodynamics, and electrostatics. A closely related topic of coarse-graining in time and space will be given plenty of attention during the school. Currently, there are no textbooks that cover these ideas & methods. This Summer School aims to fill that gap and to provide a good starting point for graduate students and young researchers who wish to apply them for large-scale studies of soft matter systems. Format of the School: -------------------- The School aims to provide the participants with a concise statistical mechanics description of the methods. This analytical approach is complemented with hands-on computer exercises whose role in the Summer School is important. Invited speakers: ----------------- Giovanni Ciccotti (Rome), Raymond Kapral (Toronto), Pep Espanol (Madrid), Florian Müller-Plathe (Mainz), Rob Groot (Vlaardingen) Ignacio Pagonabarraga (Barcelona), Andre Moreira (Santa Barbara), Chris Lowe (Delft), Eirik Flekkoy (Oslo), Aatto Laaksonen (Stockholm), Tapio Ala-Nissila (Helsinki) and Alexander Lyubartsev (Stockholm). ---------------------------------------------------------------- Mikko Karttunen -------------------------------------------------------------------- Dr. Mikko Karttunen, Biophysics/Lab of Computational Engineering, Helsinki U. of Tech., Finland. Web: www.lce.hut.fi/research/polymer/ -------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 16 09:25:32 2001 Received: from aspirine.u-strasbg.fr ([130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGEPVB24740 for ; Fri, 16 Nov 2001 09:25:32 -0500 Received: from hit1.pharma.u-strasbg.fr ([130.79.85.21]) by aspirine.u-strasbg.fr with ESMTP (1.37.109.24/16.2) id AA195346676; Fri, 16 Nov 2001 16:04:36 GMT Message-Id: <5.1.0.14.0.20011116152707.00aae8b0@aspirine.u-strasbg.fr> X-Sender: rognan@aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 16 Nov 2001 15:29:59 +0100 To: chemistry@ccl.net From: Didier Rognan Subject: virtual library of protein 3D structures Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCLrs I am looking for a virtual library of proteins 3D structures that would be the most representative of the the Protein Data Bank. Has anyone already compiled such a database ? Thanks for your answer ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherches - CNRS Laboratoire de Pharmacochimie de la Communication Cellulaire UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 35 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan@pharma.u-strasbg.fr From chemistry-request@server.ccl.net Fri Nov 16 14:04:45 2001 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGJ4iB31452 for ; Fri, 16 Nov 2001 14:04:44 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id LAA24452 for ; Fri, 16 Nov 2001 11:04:37 -0800 (PST) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1.mdli.com via smap (V2.1) id xma024448; Fri, 16 Nov 01 11:04:34 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id LAA11891; Fri, 16 Nov 2001 11:04:33 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2653.19) id ; Fri, 16 Nov 2001 11:06:31 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE50922F54F@shepherd.mdli.com> From: Bob Snyder To: "'List Server, CCL'" Cc: Guenter Grethe , Bob Snyder Subject: 6th International Conference on Chemical Structures Date: Fri, 16 Nov 2001 11:06:15 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" This important triannual conference will take place on June 2 - 6, 2002, at the beautiful conference center in Noordwijkerhout, The Netherlands. Please visit the conference's website at http://www.chemweb.com/docs/6iccs/6iccs.html. for the 'Call for Papers' and other details. Guenter Grethe Conference Chair Dr. Guenter Grethe Director, Scientific Applications Product Development, Research Group 14600 Catalina Street San Leandro, CA 94577 Tel.: (510) 357-2222, ext. 1430 Fax: (510) 614-3616 e-mail: guenter@mdli.com http://www.mdli.com From chemistry-request@server.ccl.net Fri Nov 16 14:16:33 2001 Received: from sina.iums.ac.ir ([194.225.184.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGJG1B31823 for ; Fri, 16 Nov 2001 14:16:11 -0500 Received: from amshome.iums.ac.ir ([194.225.184.136]) by sina.iums.ac.ir (8.9.2/8.9.2) with ESMTP id WAA16771 for ; Fri, 16 Nov 2001 22:46:33 +0330 (IST) Message-Id: <5.0.2.1.2.20011116222033.00b67bf8@sina.iums.ac.ir> X-Sender: armin@sina.iums.ac.ir X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Fri, 16 Nov 2001 22:40:01 +0330 To: chemistry@ccl.net From: "Armin M. Sobhani" Subject: Re: CCL:Program to convert spherical polar coordinates to XYZ coordinates In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Zheng, Here is a simple algorithm in C semantics that simply does the trick in both ways. It is very easy to rewrite them as two separate functions: Polar coordinate (latitude, longitude, distance) to Euclidean coordinate (X, Y, Z): x = cos(latitude) * sin(longitude); y = sin(latitude); z = cos(latitude) * cos(longitude); Euclidean coordinate (X, Y, Z) to Polar coordinate (latitude, longitude, distance): distance = sqrt(x*x + y*y + z*z); x /= distance; y /= distance; z /= distance; xz_dist = sqrt(x*x + z*z); latitude = atan2(xz_dist, y) * RADIANS; longitude = atan2(x, z) * RADIANS; Good luck, Armin At 08:20 AM 2001/11/16 -0500, you wrote: >Hi, > >I am looking for a simple program or script to convert spherical polar >coordinates of a molecule to either XYZ or internal coordinates. Any help >or suggestions will be appreciated. Thanks. Yajun From chemistry-request@server.ccl.net Fri Nov 16 14:18:47 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAGJIlB31874 for ; Fri, 16 Nov 2001 14:18:47 -0500 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id NAA18226 for ; Fri, 16 Nov 2001 13:15:24 -0600 (CST) Date: Fri, 16 Nov 2001 13:15:24 -0600 (CST) From: Vemparala Satyavani To: chemistry@ccl.net Subject: peptide nano tubes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Can anyone tell me where i can find the PDB files for some cyclic peptide sequences? Iam actually looking for the sequence: cyclo[-(D-Ala-Glu-D-Ala-Gln)2-] if i cannot find a PDB file, how can i construct such a sequence? Thanks vani