From chemistry-request@server.ccl.net Mon Mar 11 09:24:58 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BEOv503578 for ; Mon, 11 Mar 2002 09:24:58 -0500 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id PAA04487; Mon, 11 Mar 2002 15:21:39 +0100 (MET) for Received: from ultr.vub.ac.be (ultr14.vub.ac.be [134.184.42.14]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id PAA27275; Mon, 11 Mar 2002 15:24:21 +0100 (MET) for Sender: lieven@ultr.vub.ac.be Message-ID: <3C8CBDCE.88F683AB@ultr.vub.ac.be> Date: Mon, 11 Mar 2002 15:23:10 +0100 From: Lieven Buts Organization: Vrije Universiteit Brussel (VUB) X-Mailer: Mozilla 4.78C-SGI [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: nl, nl-BE, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Lennar-Jones non-bonded parameters for manganese ions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to simulate a protein which contains a calcium (Ca2+) and a manganese(Mn2+) ion. All modelling programs and force fields that I have looked at include Lennard-Jones parameters for calcium ions, but not for managense. Does anyone have an idea where I could find these values, or whether it would be a reasonable approximation to use existing parameters for a similar ion instead? Thank you, Lieven Buts Department of Ultrastructure Brussel Free University From chemistry-request@server.ccl.net Mon Mar 11 04:58:42 2002 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2B9wf530208 for ; Mon, 11 Mar 2002 04:58:41 -0500 Message-ID: <20020311095803.18914.qmail@web12806.mail.yahoo.com> Received: from [203.87.132.164] by web12806.mail.yahoo.com via HTTP; Mon, 11 Mar 2002 01:58:03 PST Date: Mon, 11 Mar 2002 01:58:03 -0800 (PST) From: amor san juan Subject: AutoDock Tools segmentation core dumped To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii To all AutoDockers community: Pleasant day to all. I have a problem in compiling AutoDock Tools under RedHat 7. Registered message given is "segmentation fault:core dumped" after attempting to run adt1.5. Suggestions to be given is highly appreciated. Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? Try FREE Yahoo! Mail - the world's greatest free email! http://mail.yahoo.com/ From chemistry-request@server.ccl.net Mon Mar 11 09:45:01 2002 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BEj1503998 for ; Mon, 11 Mar 2002 09:45:01 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.35) for id 16kR29-0004fa-00; Mon, 11 Mar 2002 15:44:17 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.35) for id 16kR29-0007nn-00; Mon, 11 Mar 2002 15:44:17 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de (Unverified) Message-Id: Date: Mon, 11 Mar 2002 15:44:01 +0100 To: chemistry@ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: LAM-MPI vs. MPI-CH on LINUX (summary) Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2BEj1503999 A while ago I asked for experiences with LAM-MPI vs. MPICH on a LINUX cluster. I got few responses, all of which were in favour of LAM-MPI. The poor stability of MPI-CH was mentioned throughout, and there were strong statements indicating that LAM-MPI outperforms MPI-CH substantially. Since LAM-MPI is already on the installation medium in my LINUX distribution (SuSE), I just forget about MPICH for the moment. +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ From chemistry-request@server.ccl.net Mon Mar 11 09:58:56 2002 Received: from post.webmailer.de ([192.67.198.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BEwt504487 for ; Mon, 11 Mar 2002 09:58:55 -0500 Received: from fepa.biop.ox.ac.uk (fepa.biop.ox.ac.uk [163.1.16.72]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id PAA01699; Mon, 11 Mar 2002 15:56:56 +0100 (MET) Message-Id: <200203111456.PAA01699@post.webmailer.de> X-Mailer: exmh version 2.3.1 01/18/2001 (debian 2.3.1-1) with nmh-1.0.2 To: Lieven Buts cc: chemistry@ccl.net Subject: Re: CCL:Lennar-Jones non-bonded parameters for manganese ions In-reply-to: Your message of "Mon, 11 Mar 2002 15:23:10 +0100." <3C8CBDCE.88F683AB@ultr.vub.ac.be> X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Mon, 11 Mar 2002 14:56:56 +0000 From: Marc Baaden Dear Lieven, have a look at http://pharmacy.man.ac.uk/amber/ there is a reference and parameters concerning Ca and Mn ions. Cheers, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Mon Mar 11 10:09:38 2002 Received: from salmon.maths.tcd.ie (mmdf@[134.226.81.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2BF9b504937 for ; Mon, 11 Mar 2002 10:09:38 -0500 Received: from bell.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 11 Mar 2002 15:09:02 +0000 (GMT) Date: Mon, 11 Mar 2002 15:08:59 +0000 (GMT) From: Gemma Kinsella To: chemistry@ccl.net Subject: new atom types in force fields Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks, I am trying to add new atom types to amber/gromos/charmm force fields for a drug model. Is there an easy way (ie a utility program) to do this? Or can anybody give me some pointers as to how to go about it. Thanks, Gemma From chemistry-request@server.ccl.net Mon Mar 11 11:41:09 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BGf8507990 for ; Mon, 11 Mar 2002 11:41:09 -0500 Received: from ccc.uni-erlangen.de (temeraire.chemie.uni-erlangen.de [131.188.128.73]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id RAA25565 for ; Mon, 11 Mar 2002 17:40:33 +0100 (MET) Sender: Anselm.Horn@Organik.Uni-Erlangen.DE Message-ID: <3C8CD8D3.68281552@ccc.uni-erlangen.de> Date: Mon, 11 Mar 2002 17:18:27 +0100 From: Anselm Horn Organization: CCC X-Mailer: Mozilla 4.74 [en] (X11; U; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Free molecule editor under Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am looking for a free 3D-molecule editor/builder (not just viewer) under Linux/Unix. Input should be mouse-and-click-orientated (not just visualized Z-matrix-input), and ideally it should run without any additional installation effords (i.e. statically linked; C/C++/[Java]). At the moment, I am only aware of Pymol and GDIS. Are there any established alternatives ? My motivation is to offer our Windows-trained students some familiar input facility and visualization tool... I'll summarize the answers. Regards, Anselm -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | D-91025 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html _______________________________________________________________________ From chemistry-request@server.ccl.net Mon Mar 11 13:46:35 2002 Received: from postal.sdsc.edu (IDENT:1Edp6VjA3KcqR8ABLVjthFMlgB9lB0oH@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BIkZ511331 for ; Mon, 11 Mar 2002 13:46:35 -0500 Received: from koa.sdsc.edu (IDENT:GArxQGsBZQjd7tBBYnbAAi8Y7zp9dgeJ@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/server/32b1) with ESMTP id g2BIjwY17679; Mon, 11 Mar 2002 10:45:59 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id KAA39192; Mon, 11 Mar 2002 10:45:58 -0800 (PST) Date: Mon, 11 Mar 2002 10:45:57 -0800 From: Wibke Sudholt To: Anselm Horn cc: CCL Subject: Re: CCL:Free molecule editor under Linux In-Reply-To: <3C8CD8D3.68281552@ccc.uni-erlangen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, perhaps take a look at WebMO: http://www.webmo.net Kind regards, Wibke Sudholt University of California, San Diego USA On Mon, 11 Mar 2002, Anselm Horn wrote: > Dear CCLers, > > I am looking for a free 3D-molecule editor/builder (not just viewer) > under Linux/Unix. > Input should be mouse-and-click-orientated (not just visualized > Z-matrix-input), > and ideally it should run without any additional installation effords > (i.e. statically linked; C/C++/[Java]). > > At the moment, I am only aware of Pymol and GDIS. > Are there any established alternatives ? > > My motivation is to offer our Windows-trained students some familiar > input facility and visualization tool... > > I'll summarize the answers. > > > Regards, > > Anselm > > > > -- > _______________________________________________________________________ > Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de > ___ > / __| ___ Computer Chemie Centrum > | / ___ / __| > | | / __|| / Naegelsbachstrasse 25 > \ \__ | / | | D-91025 Erlangen > \___|| | \ \__ Deutschland / Germany > \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 > \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html > _______________________________________________________________________ > > > > > -= 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 Mon Mar 11 14:04:35 2002 Received: from ex1.ncsa.uiuc.edu ([141.142.2.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BJ4Z511911 for ; Mon, 11 Mar 2002 14:04:35 -0500 Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.2.8]) by ex1.ncsa.uiuc.edu (8.11.6/8.11.6) with ESMTP id g2BJ3xq17251; Mon, 11 Mar 2002 13:03:59 -0600 (CST) Received: from sudhakardell.ncsa.uiuc.edu (sudhakardell.ncsa.uiuc.edu [141.142.65.106]) by mx1.ncsa.uiuc.edu (8.11.6/8.11.6) with ESMTP id g2BJ3s003384; Mon, 11 Mar 2002 13:03:54 -0600 (CST) Message-Id: <5.1.0.14.2.20020311130111.0273ecf0@pop.ncsa.uiuc.edu> X-Sender: spamidig@pop.ncsa.uiuc.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 11 Mar 2002 13:05:12 -0600 To: Anselm Horn , CCL From: Sudhakar Pamidighantam Subject: Re: CCL:Free molecule editor under Linux In-Reply-To: <3C8CD8D3.68281552@ccc.uni-erlangen.de> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Please look at http://chemviz.ncsa.uiuc.edu/ under nanocad editor or http://chemviz.ncsa.uiuc.edu/cgi-bin/nanocad/nanocad.cgi You can register and get an account free. This applet will be included in a java based portal application to be distributed in the next few months. Sudhakar. At 05:18 PM 3/11/2002 +0100, Anselm Horn wrote: >Dear CCLers, > >I am looking for a free 3D-molecule editor/builder (not just viewer) >under Linux/Unix. >Input should be mouse-and-click-orientated (not just visualized >Z-matrix-input), >and ideally it should run without any additional installation effords >(i.e. statically linked; C/C++/[Java]). > >At the moment, I am only aware of Pymol and GDIS. >Are there any established alternatives ? > >My motivation is to offer our Windows-trained students some familiar >input facility and visualization tool... > >I'll summarize the answers. > > >Regards, > >Anselm > > > >-- >_______________________________________________________________________ >Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de > ___ > / __| ___ Computer Chemie Centrum >| / ___ / __| >| | / __|| / Naegelsbachstrasse 25 >\ \__ | / | | D-91025 Erlangen > \___|| | \ \__ Deutschland / Germany > \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 > \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html >_______________________________________________________________________ > > > > >-= 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 ---------------------------------------------------------------------------------------------------------- Sudhakar Pamidighantam, Ph. D. Ph:217-333-5831 Fax:217-244-2909 NCSA @ UIUC, 4147 Beckman Institute email: spamidig@ncsa.uiuc.edu 405 N Mathews Ave. Urbana, Illinois 61801 WWW: swarna.ncsa.uiuc.edu ----------------------------------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Mar 11 13:54:34 2002 Received: from mtiwmhc23.worldnet.att.net ([204.127.131.48]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BIsY511659 for ; Mon, 11 Mar 2002 13:54:34 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc23.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020311185353.BEKK10296.mtiwmhc23.worldnet.att.net@dopetec> for ; Mon, 11 Mar 2002 18:53:53 +0000 Message-ID: <00dc01c1c92f$2c624c50$529c178a@dopetec> From: "Donald Keidel" To: Subject: Biologically active molecule generation Date: Mon, 11 Mar 2002 11:01:37 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00D9_01C1C8EC.1D414B60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00D9_01C1C8EC.1D414B60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, Does anyone know of a program that will take a dimeric assymetric unit = and generate a hexameric complex. They biologically active form of this = complex is a hexamer, but I only have coordinates for a dimer. I tried = to XPAND using SGS operators. I would appreciate any advice and thanks = in advance to anyone for their help. Have a good day. Don --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_00D9_01C1C8EC.1D414B60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
 
Does anyone know of a program that will = take a=20 dimeric assymetric unit and generate a hexameric complex.  They=20 biologically active form of this complex is a hexamer, but I only have=20 coordinates for a dimer.  I tried to XPAND using SGS = operators.  I=20 would appreciate any advice and thanks in advance to anyone for their=20 help.  Have a good day.
 
Don
 
---------------------------------------------------
Donald = J.=20 Keidel
University of California, Riverside
Department of = Biochemistry and=20 Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= BR>
------=_NextPart_000_00D9_01C1C8EC.1D414B60-- From chemistry-request@server.ccl.net Mon Mar 11 14:44:36 2002 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BJia512881 for ; Mon, 11 Mar 2002 14:44:36 -0500 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GSTQUG00.A7D; Mon, 11 Mar 2002 14:44:40 -0500 Message-ID: <3C8D0903.9B05AF24@umbi.umd.edu> Date: Mon, 11 Mar 2002 14:44:03 -0500 From: "Michael K. Gilson" X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Name to structure conversion-- Summary of replies Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here is a summary of the replies I received regarding software to go from the name of a compound to a Molfile or SMILES string. Thanks to Stephen Bowlus, Jonathan Brecher, Laurent David and Carlos Faerman. Mike Gilson ================================================ ChemDraw Ultra will do this (assuming you can preprocess to remove the "R1=" part, and leave just the actual name string). Note that that specific example likely has a typo. It's probably intended to be "(N-methylcarbamoyl)methyl" Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com ============================================= From: Stephen Bowlus Take a look at the ACD offering. http://www.acdlabs.com/products/name_lab/rename/#top ============================================ > From Carlos Faerman: This is a very difficult problem since not everyone uses the IUPACnomenclature to name molecules, so drawing a molecule from a (non-IUPAC) name and then exporting it to a molfile or smiles is far > from simple. Check out ChemInnovation Software, Inc., San Diego, CA (www.cheminnovation.com ). They have two add-on's called Nomenclatorand NamExpert. The second option is AutoNom by Beilstein (Germany)(www.mdli.com). This product goes from structure to name and they might have a product to get a structure from a name. Chemical Abstracts Service offers a service which is as follows: You send a list of names for your molecules and they may send you back the coordinates (2D). The biggest problem is their fees ! It is worth exploring this additional option ============================================== > From Laurent David: For the name to structure conversion, we use ACD ChemSketch (www.acdlabs.com), it works quite well. From chemistry-request@server.ccl.net Mon Mar 11 15:26:12 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2BKQC513726 for ; Mon, 11 Mar 2002 15:26:12 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g2BKPc700209 for ; Mon, 11 Mar 2002 14:25:38 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g2BKPb907062 for ; Mon, 11 Mar 2002 14:25:37 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 11 Mar 2002 14:25:37 -0600 (CST) From: Jim Phillips To: chemistry@ccl.net Subject: NAMD 2.4 (Parallel MD) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.4 Release Announcement | | | +--------------------------------------------------------------------+ March 11, 2002 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.4 has several advantages over NAMD 2.3: - Greatly improved parallel scaling with particle mesh Ewald. - Locally enhanced sampling via multiple non-interacting images. - Alchemical free energy perturbation for mutation, ligands, etc. - GROMACS ASCII topology and coordinate input file compatibility. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software!