From chemistry-request@ccl.net Wed Apr 13 02:27:44 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3D6RghL013131 for ; Wed, 13 Apr 2005 02:27:42 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3D6RgQt013130 for chemistry..at..ccl.net; Wed, 13 Apr 2005 02:27:42 -0400 Date: Wed, 13 Apr 2005 02:27:42 -0400 Message-Id: <200504130627.j3D6RgQt013130..at..server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request..at..ccl.net using -f From: "Jrg-Rdiger, , Hill" To: chemistry..at..ccl.net X-Web-Message-Number: 050411114108-13451 Subject: W:Algorithms to cut a surface from a crystal X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, I am trying to write some code which takes the unit cell of a crystal (both the cell vectors and the coordinates of the atoms) and creates a "cell" for a surface of the crystal (for a given set of Miller indices). I am having a little bit of a problem getting the coordinates of the atoms in the "surface cell" right. I thought that this should be a standard problem, but I can't find anything about a suitable algorithm for doing this neither on the Web nor in standard crystallography text books. If anybody has any pointers either to code or text books on this subject I would appreciate it. Best Regards, Jrg-Rdiger Hill From chemistry-request@ccl.net Wed Apr 13 06:39:47 2005 Received: from web30308.mail.mud.yahoo.com (web30308.mail.mud.yahoo.com [68.142.200.101]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3DAdhYJ023169 for ; Wed, 13 Apr 2005 06:39:44 -0400 Received: (qmail 57523 invoked by uid 60001); 13 Apr 2005 09:39:42 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=EnHsjo5gzh9JMKMv49nH1FkKmt6SkoyemPEjAW9RH5J4+DsakvMDlHbsDe/898U9wtkP36jrQc9TgCBRl1+nDKhzYRI7Xh0SMKu2ksqmtKIlpKjrmt72pkFKp7aZwYCb/AkhN8su3UrFaeru/vF4AZgZGOJXrlfIHyL5aolhBAU= ; Message-ID: <20050413093942.57521.qmail /a\ web30308.mail.mud.yahoo.com> Received: from [130.238.38.182] by web30308.mail.mud.yahoo.com via HTTP; Wed, 13 Apr 2005 02:39:42 PDT Date: Wed, 13 Apr 2005 02:39:42 -0700 (PDT) From: Yogesh Sabnis Subject: A suitable forcefield for sulfamides To: chemistry /a\ ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=2.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_YAHOO_RCVD autolearn=no version=3.0.1 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear all, I would like to know what would be a good forcefield to treat the sulfamides [N-S(O2)-N]. Essentially, a forcefield that has parameters for this kind of system. Any help is appreciated. Thank you. Kind regards, Yogesh ######################## Yogesh Sabnis, PhD BMC, Box 574, Avd Org. Farm. Kemi, Husargatan 3, Uppsala - 751 23 Sweden __________________________________ Do you Yahoo!? Make Yahoo! your home page http://www.yahoo.com/r/hs From chemistry-request@ccl.net Wed Apr 13 12:45:10 2005 Received: from opterone.unito.it (opterone.unito.it [130.192.119.88]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3DGj2oc003657 for ; Wed, 13 Apr 2005 12:45:03 -0400 Received: (from root@localhost) by opterone.unito.it (8.13.3/8.13.3) id j3DFb7mY019255; Wed, 13 Apr 2005 17:37:07 +0200 Received: from unito.it (chpc28.ch.unito.it [130.192.118.37]) by opterone.unito.it (8.13.3/8.13-unito) with ESMTP id j3DFb3Hc017954; Wed, 13 Apr 2005 17:37:04 +0200 Message-ID: <425D3C9E.56775BED +*+ unito.it> Date: Wed, 13 Apr 2005 17:37:02 +0200 From: Chimica Teorica X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "Jrg-Rdiger, , Hill" , chemistry +*+ ccl.net Subject: Re: CCL:W:Algorithms to cut a surface from a crystal References: <200504130627.j3D6RgQt013130 +*+ server.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-scanner: scanned by Inflex 1.0.12.7 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net "Jrg-Rdiger, , Hill" wrote: > > Hi, > I am trying to write some code which takes the unit cell of a crystal (both the cell vectors and the coordinates of the atoms) and creates a "cell" for a surface of the crystal (for a given set of Miller indices). I am having a little bit of a problem getting the coordinates of the atoms in the "surface cell" right. > I thought that this should be a standard problem, but I can't find anything about a suitable algorithm for doing this neither on the Web nor in standard crystallography text books. If anybody has any pointers either to code or text books on this subject I would appreciate it. > > Best Regards, > Jrg-Rdiger Hill > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY +*+ ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST +*+ ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ The program CRYSTAL allows cutting of a slab (periodic in 2D) parallel to a given crystallographic plane. See http://www.crystal.unito.it => tutorials => Surfaces and adsorption CRYSTAL support team Torino From chemistry-request@ccl.net Wed Apr 13 17:23:09 2005 Received: from mail.monmouth.edu (mail.monmouth.edu [192.100.64.12]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3DLN7ED013372 for ; Wed, 13 Apr 2005 17:23:08 -0400 Received: from monmouth.edu (MU14162.backbone.monmouth.edu [10.1.1.63]) by mail.monmouth.edu (8.12.11/8.12.11) with ESMTP id j3DLMwfl018903; Wed, 13 Apr 2005 17:22:58 -0400 Message-ID: <425D8DB2.3040002[at]monmouth.edu> Date: Wed, 13 Apr 2005 17:22:58 -0400 From: Robert Topper Organization: Chemistry, Med Tech and Physics, Monmouth University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: Participate in ECCC10 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Colleagues, The 10th Electronic Computational Chemistry Conference is underway at http://eccc.monmouth.edu. We have over 50 excellent presentations this year. Registration and participation are free. This week is the Interactive Week and authoes are "standing by" their presentations to answer your questions. Please come and participate! Robert -- Robert Q. Topper Chair and Associate Professor Department of Chemistry, Medical Technology and Physics Monmouth University 400 Cedar Avenue West Long Branch, NJ 07764-1898 (732)571-4418 (voice);(732)263-5213 (fax) rtopper[at]monmouth.edu Check out ECCC10 in April 2005! Registration is free! http://eccc.monmouth.edu From chemistry-request@ccl.net Wed Apr 13 15:07:37 2005 Received: from astro.systems.pipex.net (astro.systems.pipex.net [62.241.163.6]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3DJ7VYG007956 for ; Wed, 13 Apr 2005 15:07:32 -0400 Received: from [127.0.0.1] (81-178-7-82.dsl.pipex.com [81.178.7.82]) by astro.systems.pipex.net (Postfix) with ESMTP id 4F88BE000303; Wed, 13 Apr 2005 19:01:21 +0100 (BST) Message-ID: <425D5D74.3090102~at~strath.ac.uk> Date: Wed, 13 Apr 2005 18:57:08 +0100 From: "Dr. Peter Bladon" Reply-To: cbas25~at~strath.ac.uk User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Jrg-Rdiger, , Hill" , CHEMISTRY~at~ccl.net Subject: Re: CCL:W:Algorithms to cut a surface from a crystal References: <200504130627.j3D6RgQt013130~at~server.ccl.net> In-Reply-To: <200504130627.j3D6RgQt013130~at~server.ccl.net> Content-Type: multipart/alternative; boundary="------------060609020109080305000900" X-Spam-Status: No, score=1.3 required=5.0 tests=FROM_ENDS_IN_NUMS,HTML_20_30, HTML_FONT_BIG,HTML_MESSAGE,HTML_TITLE_EMPTY autolearn=no version=3.0.1 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a multi-part message in MIME format. --------------060609020109080305000900 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Perhaps Interchem-PC does what you want See http://www.interprobe.co.uk/inter/interprobe.html It allows the creation of nests of unit cells, and allows the operator to orient the display, so that the "crystal" is viewed in a direction normal to the plane defined by Miller indices, or in a direction parallel to this plane. With parallel viewing, it is them possible to "slice" the crystal parallel to the plane, using one (top) or two (top and bottom) slices. This will give a wafer of controllable thickness, at least in the cases of ionic crystals. Whether the process has any validity with the generality of molecular crystals is open to question; but being performed in silico there are minimal hazards due to toxic waste!! If you go to the download site you can get an executable version of the program as well as the appropriate Fortran-90 code. Yours sincerely Peter Bladon ------------------------------------------ Original message Jrg-Rdiger, , Hill wrote: >Hi, >I am trying to write some code which takes the unit cell of a crystal (both the cell vectors and the coordinates of the atoms) and creates a "cell" for a surface of the crystal (for a given set of Miller indices). I am having a little bit of a problem getting the coordinates of the atoms in the "surface cell" right. >I thought that this should be a standard problem, but I can't find anything about a suitable algorithm for doing this neither on the Web nor in standard crystallography text books. If anybody has any pointers either to code or text books on this subject I would appreciate it. > >Best Regards, >Jrg-Rdiger Hill > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > --------------060609020109080305000900 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Perhaps Interchem-PC does what you want See http://www.interprobe.co.uk/inter/interprobe.html It allows the creation of nests of unit cells, and allows the operator to orient the display, so that the "crystal" is viewed in a direction normal to the plane defined by Miller indices, or in a direction parallel to this plane. With parallel viewing, it is them possible to "slice" the crystal parallel to the plane, using one (top) or two (top and bottom) slices. This will give a wafer of controllable thickness, at least in the cases of ionic crystals. Whether the process has any validity with the generality of molecular crystals is open to question; but being performed in silico there are minimal hazards due to toxic waste!! If you go to the download site you can get an executable version of the program as well as the appropriate Fortran-90 code. Yours sincerely Peter Bladon ------------------------------------------ Original message Jrg-Rdiger, , Hill wrote:

Hi,
I am trying to write some code which takes the unit cell of a crystal (both the cell vectors and the coordinates of the atoms) and creates a "cell" for a surface of the crystal (for a given set of Miller indices). I am having a little bit of a problem getting the coordinates of the atoms in the "surface cell" right.
I thought that this should be a standard problem, but I can't find anything about a suitable algorithm for doing this neither on the Web nor in standard crystallography text books. If anybody has any pointers either to code or text books on this subject I would appreciate it.

Best Regards,
Jrg-Rdiger Hill

 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

--------------060609020109080305000900-- From chemistry-request@ccl.net Wed Apr 13 20:18:50 2005 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3E0IiMA021256 for ; Wed, 13 Apr 2005 20:18:44 -0400 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.13.3/8.12.8) with SMTP id j3DMlOSe042205 for ; Wed, 13 Apr 2005 15:47:28 -0700 (PDT) (envelope-from announce(at)schrodinger.com) From: Schrodinger Announcements To: CCL Subject: Schrodinger Online Seminars Date: Wed, 13 Apr 2005 18:47:14 -0400 Message-ID: <0413105184714.1@SVETLA> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Schrodinger is pleased to announce a series of webcast seminars. The seminars will cover a wide range of applications as well as the latest in technology development. The upcoming series will begin on April 21st. To learn more, and to see the full abstracts, please visit our web site http://www.schrodinger.com/Announce/Workshop/seminars.html for further details. The seminars and their topics include: Date/Time Seminar --------- ------------------------------------------------------------ 4/21/2005 Combining quantum chemistry and classical physics modeling: 1 PM EDT Using mixed QM/MM methods to obtain an atomically detailed view of biochemical and biophysical processes Presented by: Professor Victor Guallar School of Medicine and Center for Computational Biology, Washington University at St. Louis 4/28/2005 Phase: A new engine for pharmacophore perception, QSAR model 1 PM EDT development, and 3D database screening Presented by: Dr. Steve Dixon Phase Product Manager, Schrodinger 5/5/2005 Understanding the mechanism of squalene synthase: 1 PM EDT Prediction of ligand binding modes Presented by: Dr. Jason Perry Applications Scientist, Schrodinger 5/12/2005 Jaguar and QSite: A high-level overview of QM tools' 1 PM EDT capabilities, highlighting latest new features Presented by: Dr. Dale Braden QM Product Manager, Schrodinger 5/19/2005 Schrodinger induced fit docking: Methodology and results 1 PM EDT Presented by: Dr. Woody Sherman Applications Scientist, Schrodinger The seminars will run for one hour, including time for questions and answers. The number of connections is limited, so please register early http://www.schrodinger.com/Announce/Workshop/seminars.html to ensure your participation. Sincerely, Mike Campbell Schrodinger Seminar Coordinator