From owner-chemistry@ccl.net Sun Aug 6 09:30:00 2006 From: "Michel Petitjean ptitjean+/-itodys.jussieu.fr" To: CCL Subject: CCL: [CCL]: Re: Negative surface areas ... Message-Id: <-32345-060806092735-31486-vRHBZVa3mYxwP2W6nQ/l7Q]|[server.ccl.net> X-Original-From: Michel Petitjean Date: Sun, 6 Aug 2006 15:27:24 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean,itodys.jussieu.fr] To: chemistry:ccl.net Subject: [CCL]: Re: Negative surface areas ... "Raghuraman Venkatapathy" [venkatap-.-yahoo.com] noticed: > ... While calculating the surface area... > I noticed that some of the atoms had a negative surface area... Well, having a set of intersecting spheres and adding a new one, the volume always increases (or remains constant) but the area may either increase or decrease, depending of the shape. (see more details in my 1994 paper cited on my web page) Michel Petitjean, Email: petitjean:itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean:ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html From owner-chemistry@ccl.net Sun Aug 6 10:24:01 2006 From: "Andreas Bender ab454[]cam.ac.uk" To: CCL Subject: CCL: SCI Graduate Modelling Symposium, London, 22 Sep 2006 Message-Id: <-32346-060806083533-28727-Sn8pi/0nunbLS8NzEJnLuQ===server.ccl.net> X-Original-From: Andreas Bender Content-Type: multipart/mixed; boundary="-1870870024-1714636915-1154863994=:12034" Date: 06 Aug 2006 12:33:14 +0100 Mime-Version: 1.0 Sent to CCL by: Andreas Bender [ab454*_*cam.ac.uk] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime^^docserver.cac.washington.edu for more info. ---1870870024-1714636915-1154863994=:12034 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Graduate Modelling Symposium, London, 22 Sep 2006 --- MODELLING THE PROPERTIES AND BEHAVIOUR OF MOLECULES --- Call for Posters, Registration Open Dear CCL'ers, We are pleased to announce the first meeting for graduate students in computer-aided drug design, cheminformatics and molecular modelling organized by the BioActive Sciences Group of the SCI. The focus of this conference is firstly to showcase the research of PhD students from an international arena and secondly to act as a forum for interaction among graduate students, academics and industrial delegates who are attending the conference. The scientific programme is arranged around three themes - methods, applications and case studies. There will be 10 presentations plus a poster session. Any student attending this event is invited to submit a poster abstract (maximum length 300 words) to nicole.honeyghan^^soci.org. The event will take place at the SCI HQ in London, Belgrave Square, on 22 September 2006. The official part of the programme will last > from 9am-5pm, and we will conclude with a visit to a local pub - so don't book your return trip too early. For further information and registration please visit the following website: http://www.soci.org/SCI/events/details.jsp?eventID=EV890 Best wishes and looking forward to seeing you in London! Andreas -- Andreas Kieron Patrick Bender - http://www.andreasbender.de Postdoctoral Fellow (Lead Discovery Informatics, LDI) Novartis Institutes for BioMedical Research, Cambridge/MA ---1870870024-1714636915-1154863994=:12034 Content-type: text/html; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body

Hi Andreas,

I've just been sent the link to the meeting page, it is http://www.soci.org/SCI/events/details.jsp?eventID=EV890 if you could put it on the CCL again that would be fantastic. I've just gotten in touch with the lady who runs the MGMS website so hopefully they will put a link on there too.

See you soon mate,

Matt

---1870870024-1714636915-1154863994=:12034-- From owner-chemistry@ccl.net Sun Aug 6 10:59:00 2006 From: "Andreas Bender ab454{:}cam.ac.uk" To: CCL Subject: CCL: Call for Participation: CompLife'06, Cambridge/UK, 27-29 Sep 2006 Message-Id: <-32347-060806102549-23305-aweAOphyO5j3RI+wHstGfA(a)server.ccl.net> X-Original-From: Andreas Bender Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 06 Aug 2006 15:25:39 +0100 Mime-Version: 1.0 Sent to CCL by: Andreas Bender [ab454:-:cam.ac.uk] Dear CCL'ers, We are very glad to invite you to the 2nd International Symposium on Computational Life Science which will be held in Cambridge from 27-29 September 2006. Please find further information below, and we are looking forward to seeing you in Cambridge! Best wishes, Andreas ------------------------------------------------------------- -- CALL FOR PARTICIPATION: CompLife '06 -- -- The 2nd Int'l Symposium on Computational Life Science -- -- -- -- FINAL PROGRAM NOW ONLINE AT www.CompLife.org -- -- (Early Bird Registration until 15-August 2006) -- ------------------------------------------------------------- -- Cambridge, United Kingdom, on September 27 - 29, 2006 -- ------------------------------------------------------------- The focus of the symposium is on computational methods for the modeling, analysis and exploration of all aspects of life sciences, ranging from effects on the molecular level to complex interactions networks. Of prime importance for this truly interdisciplinary event will be the integration of the three disciplines Computer Science, Biology, and Chemistry. The detailed program can be found at http://www.inf.uni-konstanz.de/complife06/program.html This year there will also be a special session on free life science software on the first day of the conference, see http://www.inf.uni-konstanz.de/complife06/freesoft.html If you are only interested in parts of the programm, day passes are also available. Register for the conference here, http://www.inf.uni-konstanz.de/complife06/registration.html We are looking forward to seeing you in Cambridge! -- Computational Life Sciences '06 Cambridge/UK, 27-29 September 2006: Visit http://www.complife.org for more information! Andreas Bender - http://www.andreasbender.de Novartis Institutes for BioMedical Research, Cambridge/MA From owner-chemistry@ccl.net Sun Aug 6 22:50:01 2006 From: "Gregory Tawa gtawa^-^hotmail.com" To: CCL Subject: CCL: TINKER pdbxyz routine Message-Id: <-32348-060806171752-22466-sPFEEi2AzN259x+gsXAKzg_-_server.ccl.net> X-Original-From: "Gregory Tawa" Date: Sun, 6 Aug 2006 17:17:52 -0400 Sent to CCL by: "Gregory Tawa" [gtawa#,#hotmail.com] To all Recently I have been looking at the TINKER modeling package (J. Ponder group). I have been using it to calculate protein-protein interaction energies just fine. Lately however I have tried to calculate ligand-protein interaction energies. The first step is to use the pdbxyz routine to convert a pdb file (containing a ligand-protein complex) into a TINKER xyz file. The problem is that when using pdbxyz to do the conversion, the ligand drops out. In fact all HETATM fields drop out. In the end I get an xyz file with just the protein. Am I missing something? Or do I have to develop some kind of work around to fix this problem. Does anyone have a solution to this problem? Thanx Greg