From chemistry-request@server.ccl.net Fri Feb 8 02:53:54 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g187rrc07539 for ; Fri, 8 Feb 2002 02:53:53 -0500 Received: from unisi.it (ccmaol1.chim.unisi.it [192.167.123.206]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KE0XM57U88000F9X@unisi.it> for chemistry@ccl.net; Fri, 08 Feb 2002 08:53:32 +0100 (MET) Date: Fri, 08 Feb 2002 08:50:05 +0100 From: Nicolas Ferre Subject: Re: CCL:QM program calculating forces exerted on point charges? Sender: ferre@unisi.it To: Hannes Loeffler Cc: chemistry@ccl.net Message-id: <3C63832D.3D434099@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en References: <87wuxpi3r8.fsf@uibk.ac.at> Hi Hannes, In fact, point charges can be considered (from the computational point of vue) as "quantum atoms without basis functions (centered on the corresponding nuclei) and with a partial atomic charge". It's what I coded into G98 and it works well. You just have to put to your code (in a fortran-like scheme): IF QUANTUM THEN DO AS USUAL ELSE SKIP BASIS FUNCTIONS DEFINITION CHARGE = CHARGEMM INSTEAD OF Z ENDIF That's enough. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Feb 7 22:43:59 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g183hxc15257 for ; Thu, 7 Feb 2002 22:43:59 -0500 Received: from dhcp457.sd.accelrys.com ([172.30.201.203] helo=water) by mh1-cam.cam.accelrys.com with smtp (Exim 3.12 #1 (Debian)) id 16Z1ws-0005hy-00 for ; Fri, 08 Feb 2002 03:43:42 +0000 Message-ID: <01ad01c1b052$ccbd00f0$cbc91eac@water> From: "Tien Luu" To: Subject: Accelrys Life Science Training in San Diego Date: Fri, 8 Feb 2002 03:38:15 -0000 Organization: Accelrys 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 5.50.4522.1200 X-Mimeole: Produced By Microsoft MimeOLE V5.50.4522.1200 Accelrys Inc. will be holding two workshops involving the Cerius2 user interface at the San Diego Supercomputer Center, San Diego, CA. The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on March 26-27. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. On March 28-29, the "Library Design and Analysis Workshop" will be held. This course will cover the basics of combinatorial library design, from initial library specification through to library analysis techniques. Various approaches to library subsetting will be described, including methods to select chemically diverse subsets from a virtual library, as well as techniques for lead explosion, after initial SAR data has been determined. Other topics covered will include methods for library-library comparison and several approaches to hole-filling of an existing library. Familiarity with the Cerius2 environment is required for attendance to this workshop. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Tien Luu +44 1223-402-895 Jeffrey L. Nauss +1 858-799-5555 From chemistry-request@server.ccl.net Fri Feb 8 10:14:26 2002 Received: from mserv3.dl.ac.uk (IDENT:root@[148.79.80.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g18FEPc16725 for ; Fri, 8 Feb 2002 10:14:25 -0500 Received: from tcsg7.dl.ac.uk (tcsg7.dl.ac.uk [193.62.112.46]) by mserv3.dl.ac.uk (8.11.6/8.11.6/[ref postmaster@dl.ac.uk]) with ESMTP id g18FE2Q24965; Fri, 8 Feb 2002 15:14:02 GMT Received: from dl.ac.uk (localhost [127.0.0.1]) by tcsg7.dl.ac.uk (SGI-8.9.3/8.9.3) with ESMTP id PAA97547; Fri, 8 Feb 2002 15:11:44 GMT Sender: P.Sherwood@dl.ac.uk Message-ID: <3C63EAAE.8391C98A@dl.ac.uk> Date: Fri, 08 Feb 2002 15:11:42 +0000 From: Paul Sherwood X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Hannes Loeffler CC: chemistry@ccl.net Subject: QM program calculating forces exerted on point charges? References: <87wuxpi3r8.fsf@uibk.ac.at> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hannes, > Now I wonder if there are any QM programs which output these additional > gradients by default (or probably by user request). Since many QM programs > already allow the calculation of energy/gradients with point charges, would it > be difficult to enhance the program to compute these additional gradient? GAMESS-UK (www.dl.ac.uk/CFS) uses the simple and general approach of treating the point charges as atoms without basis functions, and therefore generates the forces by default. The disadvantage is that for a large number of point charges the memory requirement is greater than it should be. There is also a switch controlling whether the interactions between the point charges are included/excluded from this calculation. We have also implemented a variant in which the point charges can be "blurred" using Gaussian functions. Incidentally, GAMESS-UK also has an interface to CHARMM. Paul Sherwood -- ====================================================================== Dr Paul Sherwood, email: p.sherwood@daresbury.ac.uk CLRC Daresbury Lab, tel: +44-1925-603553 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.clrc.ac.uk ====================================================================== From chemistry-request@server.ccl.net Fri Feb 8 19:27:47 2002 Received: from auth01.cs.net (root@[204.252.76.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g190Rlc30139 for ; Fri, 8 Feb 2002 19:27:47 -0500 Received: from cs.net (wksta111.cyberlearning.org [206.67.155.111]) by auth01.cs.net (8.10.2/8.10.2) with SMTP id g190RVa05916 for ; Fri, 8 Feb 2002 19:27:34 -0500 (EST) From: To: chemistry@server.ccl.net Subject: COMPUTER AND IT TRAINING SCHOLARSHIPS FOR FACULTY, TEACHERS, STUDENTS AND STAFF Date: Sun, 3 Feb 2002 19:24:14 Message-Id: <709.445682.864225@cs.net> Reply-To: digitaldivide@cyberlearning.org Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" COMPUTER AND IT TRAINING SCHOLARSHIPS FOR FACULTY, TEACHERS, STUDENTS AND STAFF Dear Faculty/Teacher/Student/Staff, National Education Foundation (NEF) CyberLearning, a non-profit organization dedicated to bridging the Digital Divide since 1994, is offering tuition-free on-line training in Information Technology to the first 2,000 applicants. 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