From chemistry-request@ccl.net Wed May 12 21:05:15 2004 Received: from www4.ctimail.com (www4.ctimail.com [203.186.94.49]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4D253kh029208 for >ccl.net>; Wed, 12 May 2004 21:05:09 -0500 Received: (from cgiuser@localhost) by www4.ctimail.com (8.10.1/8.10.1) id i4D27Dc22910; Thu, 13 May 2004 10:07:13 +0800 (HKT) Date: Thu, 13 May 2004 10:07:13 +0800 (HKT) Message-Id: <200405130207.i4D27Dc22910<>www4.ctimail.com> X-Authentication-Warning: www4.ctimail.com: cgiuser set sender to skpang<>ctimail.com using -f From: skpang<>ctimail.com To: chemistry<>ccl.net Subject: Which are the files in NWChem 4.5 CD for installing NWChem Cc: X-Spam-Status: No, hits=0.5 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Have you any experienced to install NWChem? I just receive the NWChem 4.5 CD. There are many files in this CD. I do not know which files are suitable. My operation system is RedHat Fedora Core. My computer is pentium 4 2.4Gc. Which are the files in CD for this system? Thank you for your attention! Patrick my e-mail address : skpang<>ctimail.com From chemistry-request@ccl.net Wed May 12 16:15:33 2004 Received: from CLEMSON.EDU (mail.clemson.edu [130.127.28.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4CLFVkh016390 for ; Wed, 12 May 2004 16:15:32 -0500 Received: from venus.clemson.edu (rhodes153dhcp156.ces.clemson.edu [130.127.153.156]) by CLEMSON.EDU (8.12.11/8.12.8) with ESMTP id i4CLHiYw009575 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Wed, 12 May 2004 17:17:44 -0400 (EDT) Message-Id: <5.2.1.1.2.20040512171100.02f4cce0(at)mail.clemson.edu> X-Sender: sun(at)mail.clemson.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Wed, 12 May 2004 17:17:02 -0400 To: chemistry(at)ccl.net From: "Yu Sun (Denis)" Subject: view CHARMM trajectory Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Scanned-By: MIMEDefang 2.42 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, everybody, Could someone suggest me how to view CHARMM trajectory file ? I tried to use VMD but it failed. I intended to post this message to CHARMM forum but I cannot find the "post new message button " today as before. Thanks, Yu -------------------------------------------------- Error message from VMD: Info) Using plugin psf for structure file C:/Documents and Settings/Denis/My Doc uments/sim_experiments/12-MAY-04/2ech.psf Info) Analyzing structure ... Info) Atoms: 713 Info) Residues: 49 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 1 Nucleic: 0 ERROR) Error reading optional structure information from coordinate file C:/Docu ments and Settings/Denis/My Documents/sim_experiments/12-MAY-04/2ech_run.cor ERROR) Will ignore structure information in this file. Info) Using plugin cor for coordinates from file C:/Documents and Settings/Denis /My Documents/sim_experiments/12-MAY-04/2ech_run.cor ERROR) Incorrect number of atoms (0) in ERROR) coordinate file C:/Documents and Settings/Denis/My Documents/sim_experime nts/12-MAY-04/2ech_run.cor Info) Finished with coordinate file C:/Documents and Settings/Denis/My Documents /sim_experiments/12-MAY-04/2ech_run.cor. From chemistry-request@ccl.net Thu May 13 06:01:29 2004 Received: from socrate.unime.it (pharma.unime.it [192.167.106.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DB1Rkh024412 for ; Thu, 13 May 2004 06:01:28 -0500 Received: from bunker (mlbarreca.unime.it [192.167.106.131]) by socrate.unime.it (8.12.8/8.12.8) with ESMTP id i4DB3ewN013165; Thu, 13 May 2004 13:03:41 +0200 From: "maria letizia barreca" To: "'Yu Sun \(Denis\)'" Cc: Subject: R: view CHARMM trajectory Date: Thu, 13 May 2004 13:03:43 +0200 Message-ID: <000001c438d9$f6802b30$836aa7c0@bunker> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal In-Reply-To: <5.2.1.1.2.20040512171100.02f4cce0.-at-.mail.clemson.edu> X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4939.300 X-pharma-MailScanner-Information: Please contact the ISP for more information X-pharma-MailScanner: Found to be clean X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Yu, you can try with VEGA http://users.unimi.it/ddl/ or gOpenMol http://www.csc.fi/gopenmol/ Cheers, Letizia Maria Letizia Barreca, Ph.D. Dipartimento Farmaco-Chimico Universita'degli Studi di Messina Viale Annunziata 98168 MESSINA ITALY Phone: +39 090 6766464 Fax: +39 090 355613 email: barrecal.-at-.pharma.unime.it -----Messaggio originale----- Da: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net] Per conto di Yu Sun (Denis) Inviato: mercoledi 12 maggio 2004 23.17 A: chemistry.-at-.ccl.net Oggetto: CCL:view CHARMM trajectory Hi, everybody, Could someone suggest me how to view CHARMM trajectory file ? I tried to use VMD but it failed. I intended to post this message to CHARMM forum but I cannot find the "post new message button " today as before. Thanks, Yu -------------------------------------------------- Error message from VMD: Info) Using plugin psf for structure file C:/Documents and Settings/Denis/My Doc uments/sim_experiments/12-MAY-04/2ech.psf Info) Analyzing structure ... Info) Atoms: 713 Info) Residues: 49 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 1 Nucleic: 0 ERROR) Error reading optional structure information from coordinate file C:/Docu ments and Settings/Denis/My Documents/sim_experiments/12-MAY-04/2ech_run.cor ERROR) Will ignore structure information in this file. Info) Using plugin cor for coordinates from file C:/Documents and Settings/Denis /My Documents/sim_experiments/12-MAY-04/2ech_run.cor ERROR) Incorrect number of atoms (0) in ERROR) coordinate file C:/Documents and Settings/Denis/My Documents/sim_experime nts/12-MAY-04/2ech_run.cor Info) Finished with coordinate file C:/Documents and Settings/Denis/My Documents /sim_experiments/12-MAY-04/2ech_run.cor. -= 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.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow.-at-.nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu May 13 04:47:51 2004 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4D9lmkh020299 for ; Thu, 13 May 2004 04:47:49 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id A2F08129; Thu, 13 May 2004 11:50:06 +0200 (MST) Received: from mx3.informatik.uni-tuebingen.de ([134.2.12.26]) by localhost (mx5 [134.2.12.32]) (amavisd-new, port 10024) with ESMTP id 11922-05; Thu, 13 May 2004 11:50:05 +0200 (DFT) Received: from [134.2.9.133] (anywhere [134.2.9.133]) by mx3.informatik.uni-tuebingen.de (Postfix) with ESMTP id A6C62134; Thu, 13 May 2004 11:50:04 +0200 (MST) Message-ID: <40A344CC.3040502~at~uni-tuebingen.de> Date: Thu, 13 May 2004 11:50:04 +0200 From: Andreas Kerzmann User-Agent: Mozilla Thunderbird 0.6 (Windows/20040502) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Sei-Hwan Kim Cc: CHEMISTRY~at~ccl.net Subject: Re: CCL:The pi-pi stacking of hetero-aromatic ring References: <00e001c437c3$618edec0$8ecba8c0@insilico> In-Reply-To: <00e001c437c3$618edec0$8ecba8c0@insilico> X-Enigmail-Version: 0.83.6.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new (McAfee AntiVirus) at informatik.uni-tuebingen.de X-Spam-Status: No, hits=1.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Sei-Hwan Kim wrote: > Dear CCLers > > I am looking for a reference to the pi-pi stacking of hetero-aromatic ring. > ( face to edge, offset, face to face ) There is one review covering this topic amongst others: Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed Engl. 2003 Mar 17;42(11):1210-50. Review. PMID: 12645054 [PubMed - in process] Best regards, Andreas -- Andreas Kerzmann phone +49-7071-29-70461 Wilhelm-Schickard-Institut T|bingen fax +49-7071-29-5152 andreas.kerzmann~at~uni-tuebingen.de From chemistry-request@ccl.net Thu May 13 09:19:15 2004 Received: from av2-2-sn3.vrr.skanova.net (av2-2-sn3.vrr.skanova.net [81.228.9.108]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DEJEkh002338 for >ccl.net>; Thu, 13 May 2004 09:19:14 -0500 Received: by av2-2-sn3.vrr.skanova.net (Postfix, from userid 502) id 2FE4437E8D; Thu, 13 May 2004 16:21:33 +0200 (CEST) Received: from smtp1-2-sn3.vrr.skanova.net (smtp1-2-sn3.vrr.skanova.net [81.228.9.178]) by av2-2-sn3.vrr.skanova.net (Postfix) with ESMTP id 190F137E44; Thu, 13 May 2004 16:21:33 +0200 (CEST) Received: from [192.168.0.100] (h93n1fls32o916.telia.com [213.65.165.93]) by smtp1-2-sn3.vrr.skanova.net (Postfix) with ESMTP id AC44F38003; Thu, 13 May 2004 16:21:27 +0200 (CEST) Mime-Version: 1.0 X-Sender: u42123287<>m1.421.telia.com Message-Id: Date: Thu, 13 May 2004 16:17:44 +0200 To: Sei-Hwan Kim >cwp.co.kr> From: Per-Ola Norrby >kemi.dtu.dk> Subject: CCL:The pi-pi stacking of hetero-aromatic ring Cc: CHEMISTRY<>ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Sei-Hwan Kim wrote: >Dear CCLers > >I am looking for a reference to the pi-pi stacking of hetero-aromatic ring. > ( face to edge, offset, face to face ) I'd like to comment on a serious misnomer here. The interaction between two aromatic rings is frequently called pi-pi stacking, which implies an attractive interaction between the pi-clouds. In the wast majority of experimental cases, there is no such attraction, two negative pi-clouds repel each other! Only in the case of strong lowering of a LUMO and/or raising of a HOMO does two pi-faces attract each other (like in oxidized donor stacks, or possibly in the case of nitrobenzene with aniline). It was shown a few decades ago (by Liljefors and Pettersson) that the attractive interactions of two benzene rings with each other (face to edge or offset) can be represented by simple electrostatic effects. The hydrogens are slightly positive, the carbons slightly negative (about 0.15, a C-H dipole of 0.6 D). In all stable situations, the hydrogens of one ring are situated over the face of another ring. Inclusion of this effect is the reason why most current molecular mechanics programs give good results for aromatic interaction. See, for example, Houk's computational study of the Wilcox torsional balance a few years ago. Thus, I'd propose reserving the term "pi-pi stacking" for the very rare cases where two very different aromatic rings are in a perfect face to face arrangement, and use the more correct "CH-pi interaction" for the more common cases of benzene-like molecules interacting with each other. /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon<>kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@ccl.net Thu May 13 09:04:00 2004 Received: from CLEMSON.EDU (mail.clemson.edu [130.127.28.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DE3xkh001527 for ; Thu, 13 May 2004 09:03:59 -0500 Received: from venus.clemson.edu (rhodes153dhcp156.ces.clemson.edu [130.127.153.156]) by CLEMSON.EDU (8.12.11/8.12.8) with ESMTP id i4DE6G2c023025 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Thu, 13 May 2004 10:06:17 -0400 (EDT) Message-Id: <5.2.1.1.2.20040513095445.023b2df8=at=mail.clemson.edu> X-Sender: sun=at=mail.clemson.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Thu, 13 May 2004 10:05:25 -0400 To: chemistry=at=ccl.net From: "Yu Sun (Denis)" Subject: view CHARMM trajectory problem : number of atom number not match In-Reply-To: <5.2.1.1.2.20040512171100.02f4cce0=at=mail.clemson.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Scanned-By: MIMEDefang 2.42 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Thank you all for recommend me gOpenMol. I successfully use it to view the trajectory file in the demo and for one of my trajectory file. However, when comes to another trajectory file (not standard protein or DNA molecules), after import the coordinates, I encounter error : "Number of atoms in the file does not match" when I try to open the trajectory file. I think it is nothing to do with gOpenmol but comes from charmm program. Anyone using charmm has same problem before ? Thanks for your help. Yu At 05:17 PM 5/12/2004 -0400, Yu Sun (Denis) wrote: >Hi, everybody, > >Could someone suggest me how to view CHARMM trajectory file ? I tried to >use VMD but it failed. I intended to post this message to CHARMM forum but >I cannot find the "post new message button " today as before. > > >Thanks, > >Yu > > From chemistry-request@ccl.net Thu May 13 09:47:10 2004 Received: from CLEMSON.EDU (mail.clemson.edu [130.127.28.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DEl9kh003666 for ; Thu, 13 May 2004 09:47:09 -0500 Received: from venus.clemson.edu (rhodes153dhcp156.ces.clemson.edu [130.127.153.156]) by CLEMSON.EDU (8.12.11/8.12.8) with ESMTP id i4DEnRDZ020340 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Thu, 13 May 2004 10:49:27 -0400 (EDT) Message-Id: <5.2.1.1.2.20040513104507.023bf750(at)mail.clemson.edu> X-Sender: sun(at)mail.clemson.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Thu, 13 May 2004 10:48:43 -0400 To: chemistry(at)ccl.net From: "Yu Sun (Denis)" Subject: view CHARMM trajectory-problem solved Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Scanned-By: MIMEDefang 2.42 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I found in my own defined RTF file I did not add "END" at the end of the file. After adding it and run the CHARMM again. I was able to view the trajectory file in VMD or gOpenMol. Thank you all for your suggestions Yu At 05:17 PM 5/12/2004 -0400, Yu Sun (Denis) wrote: >Hi, everybody, > >Could someone suggest me how to view CHARMM trajectory file ? I tried to >use VMD but it failed. I intended to post this message to CHARMM forum but >I cannot find the "post new message button " today as before. > > >Thanks, > >Yu > From chemistry-request@ccl.net Thu May 13 19:01:24 2004 Received: from calmail-cr.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4E01Nkh028920 for ; Thu, 13 May 2004 19:01:23 -0500 Received: from [128.32.198.91] (account shaji:at:calmail.berkeley.edu HELO berkeley.edu) by calmail-cr.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP id 27807201 for CHEMISTRY:at:ccl.net; Thu, 13 May 2004 17:03:39 -0700 Message-ID: <40A40CDB.2060306:at:berkeley.edu> Date: Thu, 13 May 2004 17:03:39 -0700 From: Shaji Chempath User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY:at:ccl.net Subject: Slab Calculations References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, Could you please tell me what are the commonly used programs for calculating the structures of surfaces with DFT level theory. I have seen that CPMD, VASP, NWCHEM, and CRYSTAL03 are capable of doing such calculations, but I have not used any of those. Specifically I want to study the adsorption of small molecules on different surfaces of ZrO2 crystals. I will have to use pseudopotentials for Zr. If anybody can recommend me some softwares that will do the job that will be great. I promise to post a summary of available softwares and their limitations. I notice that Gaussian (G03) has periodic (PBC) caluclations. If anybody has experience with this and can share it with me that will be great. Thanks a lot, Shaji From chemistry-request@ccl.net Thu May 13 17:27:51 2004 Received: from mx1.tripos.com (mx1.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DMRpkh025750 for >ccl.net>; Thu, 13 May 2004 17:27:51 -0500 Message-ID: >mailhost.tripos.com> From: "John Begemann" >tripos.com> To: >ccl.net> Date: Thu, 13 May 2004 17:30:10 -0500 Subject: CCL: Workshop: Virtual Screening with FlexX MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Thread-Index: AcQ5OdoQ5dYkLkh8QQSbz4Vp440u7w== X-eShield-AntiVirus: Passed X-eShield-AntiVirus-Message: Scanned by http://www.bluecoat.com/eShield X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net "Virtual Screening Workshop" August 18-20, 2004 This event is an intense two-day workshop designed by scientific experts at BioSolveIT and Tripos to provide hands-on training to customers interested in effectively utilizing their FlexX suite of in-silico discovery tools. This training course is designed to uncover the benefits that the FlexX suite of virtual screening tools can bring to your molecular modeling and computational chemistry programs. Scientists from both companies will train participants of this docking workshop using the latest software releases. This course will provide a mixture of lectures, workshops and discussions. Space for this scientific training session is limited, so please register early. For further details see: http://www.tripos.com/flexxworkshop/flexxworkshopagenda.html. Alternatively contact Tripos at (mailto:contact_us<>tripos.com) or BioSolveIT at (mailto:workshop<>biosolveit.de) From chemistry-request@ccl.net Thu May 13 12:45:58 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DHjvkh013310 for ; Thu, 13 May 2004 12:45:57 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4DHmHqB012357 for ; Thu, 13 May 2004 13:48:17 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4DHmEd3012298; Thu, 13 May 2004 13:48:14 -0400 Date: Thu, 13 May 2004 13:42:59 -0400 From: Rick Venable To: "Yu Sun (Denis)" cc: chemistry=at=ccl.net Subject: Re: CCL:view CHARMM trajectory In-Reply-To: <5.2.1.1.2.20040512171100.02f4cce0=at=mail.clemson.edu> Message-ID: References: <5.2.1.1.2.20040512171100.02f4cce0=at=mail.clemson.edu> ReplyTo: Rick_Venable=at=nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 12 May 2004, Yu Sun (Denis) wrote: > Could someone suggest me how to view CHARMM trajectory file ? I tried > to use VMD but it failed. I intended to post this message to CHARMM > forum but I cannot find the "post new message button " today as > before. I note that you've fixed the error in your custom RTF and solved your immediate problem. I would just like to add: [1] There is a 'Post' button at the top of the page when viewing a list of posts in one of the CHARMM Forums at www.charmm.org, but you must be a registered user in order to post a message. You may not see the 'Post' button if you haven't registered. [2] For those comfortable with a CLI*, one can view trajectories in CHARMM directly via the X11 graphics; I also use the graphics to produce POV-Ray format files, either for nice single images, or as a first step to making an MPEG animation of a CHARMM trajectory. * CLI = Command Line Interface, i.e. no mouse interaction Regards, =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable=at=nih.gov ALT email: rvenable=at=speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Thu May 13 12:17:52 2004 Received: from smtp.csc.fi (smtp.csc.fi [193.166.0.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DHHpkh011859 for ; Thu, 13 May 2004 12:17:51 -0500 Received: from laaksonen (vpn-165.csc.fi [193.166.2.165]) by smtp.csc.fi (CSC-Sendmail) with ESMTP id i4DHK2Cl022928; Thu, 13 May 2004 20:20:02 +0300 Message-Id: <200405131720.i4DHK2Cl022928*at*smtp.csc.fi> From: "Leif Laaksonen" To: "'Yu Sun \(Denis\)'" , Subject: RE: view CHARMM trajectory problem : number of atom number not match Date: Thu, 13 May 2004 20:20:35 +0300 Organization: CSC, the Finnish IT Center for Science MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 In-Reply-To: <5.2.1.1.2.20040513095445.023b2df8*at*mail.clemson.edu> Thread-Index: AcQ5CpVFdHiBeannSTKb5GXXTHhidAAA4lMQ X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Yu! The problem is that the number of atoms in your trajectory file does not match the number of atoms in your coordinate file! Stupid or not but gOpenMol expects to find the same number of MOVING atoms in the trajectory and coordinate file. The molecular topology is built from the coordinate file and if the number of atoms doesn't match gOpenMol has problems with the topology. Regards, -leif laaksonen > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request*at*ccl.net] On Behalf Of Yu Sun (Denis) > Sent: Thursday, May 13, 2004 5:05 PM > To: chemistry*at*ccl.net > Subject: CCL:view CHARMM trajectory problem : number of atom > number not match > > Thank you all for recommend me gOpenMol. > > I successfully use it to view the trajectory file in the demo > and for one > of my trajectory file. However, when comes to another > trajectory file (not > standard protein or DNA molecules), after import the coordinates, I > encounter error : "Number of atoms in the file does not > match" when I > try to open the trajectory file. I think it is nothing to do > with gOpenmol > but comes from charmm program. Anyone using charmm has same > problem before ? > > Thanks for your help. > > Yu > > > At 05:17 PM 5/12/2004 -0400, Yu Sun (Denis) wrote: > >Hi, everybody, > > > >Could someone suggest me how to view CHARMM trajectory file > ? I tried to > >use VMD but it failed. I intended to post this message to > CHARMM forum but > >I cannot find the "post new message button " today as before. > > > > > >Thanks, > > > >Yu > > > > > > > > > -= 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*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu May 13 17:46:25 2004 Received: from iqe1.ethz.ch (iqe1-hptf.ethz.ch [129.132.22.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DMkNkh026288 for ; Thu, 13 May 2004 17:46:24 -0500 Received: from 129.94.6.28 (iqe1 [129.132.22.196]) by iqe1.ethz.ch (8.9.3/8.9.3) with SMTP id AAA29765; Fri, 14 May 2004 00:48:37 +0200 (MET DST) Message-Id: <200405132248.AAA29765*at*iqe1.ethz.ch> To: arashid*at*phys.unsw.edu.au Cc: CHEMISTRY*at*ccl.net From: arashid*at*iqe.phys.ethz.ch Subject: Fwd: CCL:The pi-pi stacking of hetero-aromatic ring Date: Thu, 13 May 2004 22:48:40 +0000 X-Mailer: Endymion MailMan v2.0 X-Spam-Status: No, hits=0.8 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Forwarded Message: > To: Sei-Hwan Kim > From: Per-Ola Norrby > Subject: CCL:The pi-pi stacking of hetero-aromatic ring > Date: Thu, 13 May 2004 16:17:44 +0200 > ----- 
Sei-Hwan Kim wrote:

>Dear CCLers
>
>I am looking for a reference to the  pi-pi stacking of hetero-aromatic ring.
>  ( face to edge, offset, face to face )

	I'd like to comment on a serious misnomer here.  The 
interaction between two aromatic rings is frequently called pi-pi 
stacking, which implies an attractive interaction between the 
pi-clouds.  In the wast majority of experimental cases, there is no 
such attraction, two negative pi-clouds repel each other!  Only in 
the case of strong lowering of a LUMO and/or raising of a HOMO does 
two pi-faces attract each other (like in oxidized donor stacks, or 
possibly in the case of nitrobenzene with aniline).  It was shown a 
few decades ago (by Liljefors and Pettersson) that the attractive 
interactions of two benzene rings with each other (face to edge or 
offset) can be represented by simple electrostatic effects.  The 
hydrogens are slightly positive, the carbons slightly negative (about 
0.15, a C-H dipole of 0.6 D).  In all stable situations, the 
hydrogens of one ring are situated over the face of another ring. 
Inclusion of this effect is the reason why most current molecular 
mechanics programs give good results for aromatic interaction.  See, 
for example, Houk's computational study of the Wilcox torsional 
balance a few years ago.

	Thus, I'd propose reserving the term "pi-pi stacking" for the 
very rare cases where two very different aromatic rings are in a 
perfect face to face arrangement, and use the more correct "CH-pi 
interaction" for the more common cases of benzene-like molecules 
interacting with each other.

	/Per-Ola
-- 
Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon*at*kemi.dtu.dk  tel +45-45252123,  fax +45-45933968


-= 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*at*ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net 
HOME Page: http://www.ccl.net  | Jobs Page: http://www.ccl.net/jobs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow*at*nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
From chemistry-request@ccl.net Thu May 13 11:36:58 2004 Received: from www4.ctimail.com (www4.ctimail.com [203.186.94.49]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DGaukh009349 for ; Thu, 13 May 2004 11:36:57 -0500 Received: (from cgiuser@localhost) by www4.ctimail.com (8.10.1/8.10.1) id i4DGdCe23631; Fri, 14 May 2004 00:39:12 +0800 (HKT) Date: Fri, 14 May 2004 00:39:12 +0800 (HKT) Message-Id: <200405131639.i4DGdCe23631~at~www4.ctimail.com> X-Authentication-Warning: www4.ctimail.com: cgiuser set sender to skpang~at~ctimail.com using -f From: skpang~at~ctimail.com To: chemistry~at~ccl.net Subject: total potential in ECP Cc: X-Spam-Status: No, hits=0.5 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, According to Hay ECP and Wadt (LanL2DZ), the total potential (effective core potential) is U(r) = UL(r) + {summation of [Ul(r)-UL(r)] from l=0 to L-1} x Pl Is the basis sets (LanL2DZ) for 1 row transition elements : Gaussian funcitons for f potential + (Gaussian functions for s-f + Gaussian function for p-f + Gaussian functions for d-f) + Gaussian function for 3s orbitals + Gaussian function for 3p orbitals + Gaussian function for 3d orbitals? The Pl = 1. Right? Best regards, Patrick My e-mail is skpang~at~ctimail.com From chemistry-request@ccl.net Thu May 13 13:08:55 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4DI8skh014132 for ; Thu, 13 May 2004 13:08:54 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id B404A48290; Thu, 13 May 2004 14:10:24 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 25312-03; Thu, 13 May 2004 14:10:23 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 27285481A2; Thu, 13 May 2004 14:10:23 -0400 (EDT) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: The pi-pi stacking of hetero-aromatic ring Date: Thu, 13 May 2004 14:10:23 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD63~at~srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: The pi-pi stacking of hetero-aromatic ring Thread-Index: AcQ5DUVzt0PYMY/pTiygSAix4g1BYgABlgJw From: "Shobe, David" To: "Per-Ola Norrby" , "Sei-Hwan Kim" Cc: X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4DI8tkh014136 But I wonder, would pi-pi stacking (using Per-Ola's definition) be more common in heterocyclic rings where there would be positively and negatively charged atoms in the ring? I'm sure this has been studied extensively in purines and pyrimidines at least. Does pyridine dimerize in the manner of benzene, or do the two molecules pi-stack with oppositely directed dipoles? --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request~at~ccl.net]On Behalf Of Per-Ola Norrby Sent: Thursday, May 13, 2004 10:18 AM To: Sei-Hwan Kim Cc: CHEMISTRY~at~ccl.net Subject: CCL:The pi-pi stacking of hetero-aromatic ring Sei-Hwan Kim wrote: >Dear CCLers > >I am looking for a reference to the pi-pi stacking of hetero-aromatic ring. > ( face to edge, offset, face to face ) I'd like to comment on a serious misnomer here. The interaction between two aromatic rings is frequently called pi-pi stacking, which implies an attractive interaction between the pi-clouds. In the wast majority of experimental cases, there is no such attraction, two negative pi-clouds repel each other! Only in the case of strong lowering of a LUMO and/or raising of a HOMO does two pi-faces attract each other (like in oxidized donor stacks, or possibly in the case of nitrobenzene with aniline). It was shown a few decades ago (by Liljefors and Pettersson) that the attractive interactions of two benzene rings with each other (face to edge or offset) can be represented by simple electrostatic effects. The hydrogens are slightly positive, the carbons slightly negative (about 0.15, a C-H dipole of 0.6 D). In all stable situations, the hydrogens of one ring are situated over the face of another ring. Inclusion of this effect is the reason why most current molecular mechanics programs give good results for aromatic interaction. See, for example, Houk's computational study of the Wilcox torsional balance a few years ago. Thus, I'd propose reserving the term "pi-pi stacking" for the very rare cases where two very different aromatic rings are in a perfect face to face arrangement, and use the more correct "CH-pi interaction" for the more common cases of benzene-like molecules interacting with each other. /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon~at~kemi.dtu.dk tel +45-45252123, fax +45-45933968 -= 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~at~ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+