From chemistry-request@server.ccl.net Thu Jan 30 06:28:50 2003 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0UBSnP16035; Thu, 30 Jan 2003 06:28:49 -0500 To: Eugen Leitl Cc: chemistry@ccl.net, "Computational Chemistry List" , nano Subject: Re: CCL:[PyMOL] parallel em code (fwd) MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: rcompton@accelrys.com Date: Thu, 30 Jan 2003 11:28:48 +0000 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 01/30/2003 11:28:50 AM, Serialize complete at 01/30/2003 11:28:50 AM Content-Type: text/plain; charset="us-ascii" CHARMm can run as an MPI version on SGI64, LINUX or IBMSP Your local Accelrys representative should be able to help you out with this. See: http://www.accelrys.com/contact/contact.php Kind regards, Richard. _________________________________________ Mr Richard Compton Regional Director Accelrys Ltd. Office Tel. +44 1223 228 500 Web. http://www.accelrys.com Email. rcompton@accelrys.com Eugen Leitl Sent by: "Computational Chemistry List" 29/01/2003 20:13 To: cc: nano Subject: CCL:[PyMOL] parallel em code (fwd) ---------- Forwarded message ---------- Date: Wed, 29 Jan 2003 14:37:28 -0500 (EST) From: Nat Echols To: PyMOL list Subject: [PyMOL] parallel em code Hi-- This sounds a bit offtopic, but it's related to a project that would probably be built off of PyMOL. Does anyone have any experience with protein dynamics software that runs on clusters and performs energy minimization? I've seen all sorts of pure MD packages that run on clusters (GROMACS, NAMD, etc.) but all I want to do is adiabatic mapping. None of these programs seem to be designed for this. I've been using CNS for everything and as far as I know this does not come in an MPI-based flavor. I've seen reference to an MPI version of CHARMm, but I'm not sure how to get ahold of it (we have a Harvard CHARMm license, at least). thanks, Nat ---------------------------------------------------------------------------- Nathaniel Echols Programmer nat@bioinfo.mbb.yale.edu Gerstein Lab 203-589-6765 Yale University ---------------------------------------------------------------------------- ------------------------------------------------------- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jan 30 08:17:01 2003 Received: from alpha.cerm.unifi.it ([150.217.146.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0UDGuP18272 for ; Thu, 30 Jan 2003 08:17:01 -0500 Received: (qmail 25493 invoked by uid 204); 30 Jan 2003 12:55:16 -0000 Received: from unknown (HELO cerm.unifi.it) (127.0.0.1) by localhost with SMTP; 30 Jan 2003 12:55:16 -0000 Received: from 150.217.145.160 (SquirrelMail authenticated user sbaglia) by alpha.cerm.unifi.it with HTTP; Thu, 30 Jan 2003 13:55:16 +0100 (CET) Message-ID: <2088.150.217.145.160.1043931316.squirrel@alpha.cerm.unifi.it> Date: Thu, 30 Jan 2003 13:55:16 +0100 (CET) Subject: Virtual Combinatorial Libraries From: "Robert Sbaglia" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.10) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by AMaViS perl-11 Hi all, Was wondering if anyone knows of or can recommend a freeware program which can create virtual combinatorial libraries? Many thanks, Rob. -------------------------------------------------- Robert Sbaglia CERM Polo Scientifico Universita' degli Studi di Firenze 50019 Sesto Fiorentino (Florence) Italy PH: +39 055 457 4241 FAX: +39 055 457 4271 From chemistry-request@server.ccl.net Thu Jan 30 02:01:43 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0U71gP30662 for ; Thu, 30 Jan 2003 02:01:43 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h0U71RV13252 for ; Wed, 29 Jan 2003 23:01:27 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 7157; Wed, 29 Jan 2003 22:55:01 -0800 (PST) Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h0U71HC16853; Wed, 29 Jan 2003 23:01:17 -0800 (PST) Received: from quine.scripps.edu (gamow [137.131.252.67]) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id XAA26131; Wed, 29 Jan 2003 23:01:16 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Wed, 29 Jan 2003 23:01:06 -0800 Date: Wed, 29 Jan 2003 23:01:06 -0800 From: "David A. Case" To: Javier Cuervo Cc: chemistry@ccl.net Subject: Re: CCL:Force Field question Message-ID: <20030130070106.GB3840@scripps.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i On Wed, Jan 29, 2003, Javier Cuervo wrote: > > We are thinking in obtain a program for doing energy calculation of > proteins. We would like to be able of have the energy profile given as a > "contribution per atom" to the total energy, and this contribution split > in the differents terms (van Der Walls, electrostatic,H-bond, etc). > > We are considering AMBER as an option but we don't now if this package has > this feature (or if there is any program that can do what we want). > The concept of a "contribution per atom" is a bit foreign to molecular mechanics. It is possible (and sometimes useful) to define such a thing, but it requires pretty artificial assigning of (say) an angle energy among the three atoms involved, or a dihedral term among the four atoms involved. And such a decomposition is even more strained for polarizable force fields, or for Ewald techniques (where the "reciprocal" energy is not easily expressed in a pairwise format.) For classical force fields, Amber allows you to decompose systems into arbitrary groups, and can perform analyses of interactions among these, including a "contribution per group" term that sums to the total energy. In principle, each group could be a single atom, although I suspect it would be pretty unwieldy to do this for any sizeable molecule. The program is really designed more to produce "interaction energies between groups", rather than "contributions per group". So, it's probably possible, but not really what the program was designed for. Maybe other CCL=ers will have alternate suggestions. ..hope this helps....dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Thu Jan 30 10:31:53 2003 Received: from mail.nnit.dk ([152.73.7.111]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0UFVrP22008 for ; Thu, 30 Jan 2003 10:31:53 -0500 Received: from localhost (localhost.novonordisk.com [127.0.0.1]) by localhost.novonordisk.com (Postfix) with ESMTP id 507281500A5 for ; Thu, 30 Jan 2003 16:31:53 +0100 (CET) Received: from mail9m-int.novo.dk (mail9m-int.novo.dk [10.1.13.98]) by mail9m-ext.novo.dk (Postfix) with ESMTP id A17CD1501ED for ; Thu, 30 Jan 2003 16:31:52 +0100 (CET) Received: from exdkhub06.novo.dk (exdkhub06.novo.dk [10.1.8.216]) by mail9m-int.novo.dk (Postfix) with ESMTP id 6F5EB148093 for ; Thu, 30 Jan 2003 16:31:50 +0100 (CET) Received: by exdkhub06.novo.dk with Internet Mail Service (5.5.2653.19) id ; Thu, 30 Jan 2003 16:31:50 +0100 Message-ID: <76F96CFE2AA2114C886B028A065A7FC40F82B9@exdkba020.novo.dk> From: "LEDM (Leonardo De Maria)" To: "'CHEMISTRY@ccl.net'" Subject: Any GNU-GPL Homology Modelling software? Date: Thu, 30 Jan 2003 16:31:47 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2C874.B36E42A0" X-Virus-Scanned: AMaViS/novo-catpipe (uvscan: v4.1.60/v4245. iscan: v3.1/v6.150-1001/451/47758. ), processed in 0.592784 s. This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C2C874.B36E42A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi everybody, are there any GNU-GPL Homology Modelling sotwares out there? Bye, Leonardo De Maria, Ph.D. Research Scientist Novozymes A/S Sm=F8rmosevej 25 2880 Bagsv=E6rd Denmark Phone: +45 44421890 Fax: +45 44980246 e.mail: ledm@novozymes.com ------_=_NextPart_001_01C2C874.B36E42A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Any GNU-GPL Homology Modelling software?

Hi everybody,

are there any GNU-GPL Homology = Modelling sotwares out there?

Bye,

Leonardo De Maria, Ph.D.
Research Scientist
Novozymes A/S
Sm=F8rmosevej 25
2880 Bagsv=E6rd
Denmark

Phone:  +45 44421890
Fax:      = +45 44980246

e.mail: ledm@novozymes.com


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