From chemistry-request@server.ccl.net Tue May 13 07:53:29 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DBrSt32051 for ; Tue, 13 May 2003 07:53:28 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Tue, 13 May 2003 09:51:11 +0200 Message-ID: <001201c31924$e5ed7f50$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "elewars" , References: <3EBED228.3A272946@trentu.ca> Subject: Re: CCL:cartesians to z-mat and back Date: Tue, 13 May 2003 09:54:35 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Again I would like to mention Mol2Mol. It can convert Cartesian to Z-matrices with the following options: You can give the three starting atoms; The program steps along the atoms by star method or chain method or arbitrary manual numbering; Option to add MOPAC flags (*, 0, 1 or whatever you want) Option to use elemental symbols or atomic numbers; Option to select the dummy atom symbol; Option to add charges or not; Option to select left/right handed system; Option to create Gaussian format with symbolics; Option to select the number of decimals. Maybe the first option is the most important: In the case of the "chain" method the algorithm first tries to step along the longest chains of the molecule, and after them deals with the other atoms. In the case of the "star" method the program tries to include every atoms connected to the previous one before advancing: To read more about go to: http://web.interware.hu/frenzy/mol2mol select from the left menu bar Mol2Mol in a Nutshell, then Molfiles, then Z matrix /write Tamas Gunda --------------------------------- Prof. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "elewars" To: "Jan Labanowski" ; Sent: Monday, May 12, 2003 00:43 Subject: CCL:cartesians to z-mat and back > 2003 May 11 > > I might just add that > > As Jan Labanowski implies, writing an algorithm to convert a general set of > molecular Cartesians to a good Z-matrix is a problem in artificial intelligence > (the converse is trivial). > The dying (?) art of writing a Z-matrix is treated nicely and compactly, with > useful caveats, in _A Handbook of Computational Chemistry_, Tim Clark, Wiley, New > York, 1985; pp 102-119. > > E. Lewars > ====== > > > > > > Jan Labanowski wrote: > > > I love MOLDEN and use it often for my geometry conversions. It comes > > with the Z-matrix editor: > > > > http://www.cmbi.kun.nl/~schaft/molden/molden.html > > > > It should be stressed that conversion of cartesians to Z-matrix can only > > be a trivial task for molecules that are trees (i.e., do not contain cycles). > > When rings (or more complicated arrangements, like cages, say, cubane) are > > present, the well behaved Z-matrix should contain dummy atoms. You can try > > to understand the problem by build the Z-matrix in such a way > > that changing one parameter does not affect any other parameters. > > > > For example, the z-matrix for benzene ring has to involve a centroid (a dummy > > atom in the center of the ring) or otherwise, changing one torsion angles > > within the ring will change other torsion angles. With the centroid, and > > the rays going from it to the real atoms, you can build a Z-matrix which > > does not involve dependencies between parameters. > > > > Now... Can the software detect such situations automatically and deal with > > them. Sure... However, quite frankly, I did not see much of such > > packages around. It is not a trivial problem, and even for simple molecules > > with cycles, there are many ways to represent their geometry as a Z-matrix. > > And deciding which Z-matrix is better, is again not a trivial thing. While > > there are obviously objective measures, this is still an art, and the > > beauty of the Z-matrix is in the eye of the beholder. And while there are > > methods which make Z-matrix less important for unconstrained optimization > > of the whole molecule (e.g., redundant internal coordinates in Gaussian), > > there is nothing better than a well behaved Z-matrix when doing partial > > optimizations of chosen geometrical features of the molecule(s), e.g., > > when studying transition states and reaction paths. > > > > Jan > > > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 > > Ohio Supercomputer Center | E-mail: jkl@ccl.net > > 1224 Kinnear Rd, | http://www.ccl.net/~jkl > > Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ > > > > > > -= 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 Tue May 13 08:24:38 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DCOVt00867 for ; Tue, 13 May 2003 08:24:33 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id UAA12742 for ; Tue, 13 May 2003 20:09:21 +0800 Message-Id: <200305131209.UAA12742@mx1.ustc.edu.cn> Date: Tue, 13 May 2003 20:11:23 +0800 From: 丁迅雷 Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: Help:Frozen calculation in g98 Organization: 中国科大选键化学实验室 X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; 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name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon508203777633_=====-- From chemistry-request@server.ccl.net Tue May 13 03:06:06 2003 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D765t09997 for ; Tue, 13 May 2003 03:06:05 -0400 Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with ESMTP id JAA01440; Tue, 13 May 2003 09:06:01 +0200 (MET DST) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.9.3/8.9.3) id JAA50568; Tue, 13 May 2003 09:06:00 +0200 (MESZ) Date: Tue, 13 May 2003 09:06:00 +0200 From: "Dr. Alexander Hofmann" To: Dmitry Rozmanov Cc: CCL Subject: Re: CCL:ab initio with periodic conditions Message-ID: <20030513090600.J408208@chemie.hu-berlin.de> Reply-To: ah@chemie.hu-berlin.de References: <008c01c3184c$56f56610$0203a8c0@goblin> <004701c318a7$c6e83e60$3e505882@pirx> <00be01c318b3$2591f180$0203a8c0@goblin> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <00be01c318b3$2591f180$0203a8c0@goblin>; from dima@xenon.spb.ru on Mon, May 12, 2003 at 10:20:20PM +0400 Hi Dimitry, there are a lot of these pseudopotential planewave DFT codes. They differ most probably in the pseudopotential implementation (accuracy & efficiency). Some typical examples are: CPMD (free of charge for public research) VASP (small cover fee) Abinit Fleur Siesta Campos (free of charge) and some more I do not know ... I know, that there is a commercial version of VASP for Windows systems (www.materialsdesign.com), but rather expensive. If you want to go to LCAO based stuff, try Crystal (HF, DFT, MP2 in development) Gaussian03 (HF, DFT, MP2 was announced but withdrawed again as I understand the website) For Gaussian, there is a Windows version available. My hint: Change to Linux, there are much more possibilities. And mostly cheaper! The desired program depends on your plans. If DFT is precise enough, use one of the pseudopotential codes. They are due to plane wave basis sets much more efficient. If you want to use MP2, well, ... Hope this helps Alex On Mon, May 12, 2003 at 10:20:20PM +0400, Dmitry Rozmanov wrote: > Thank you for the suggestion. Actually I know about CPMD, but still have not > tried it. I have no access to unix computer, only to windows ones. And could > not compile CPMD under windows. > > Though, I ran into AbInit code. Have you know anything about it? Is it > better or worse than CPMD? Is it the same thing as CPMD? > > Regards. > > ---Dmitry. -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Post: Unter den Linden 6 10099 Berlin Visitors: Brook-Taylor-Strasse 2 12489 Berlin ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From chemistry-request@server.ccl.net Tue May 13 03:53:37 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D7rbt11678 for ; Tue, 13 May 2003 03:53:37 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h4D7raru075365 for ; Tue, 13 May 2003 09:53:36 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h4D7rarj339035; Tue, 13 May 2003 09:53:36 +0200 (MEST) Date: Tue, 13 May 2003 09:53:36 +0200 (MEST) From: Michel Petitjean Message-Id: <200305130753.h4D7rarj339035@ds10.itodys.jussieu.fr> To: chemistry@ccl.net Subject: CCL:Re: How to calculate molecular volume X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CCL Subject: CCL:Re: How to calculate molecular volume The ASV freeware computes analytically surfaces and volumes of any union of spheres. The precision is near the machine real*8 precision, and thus the volumes values may be used for numerical calculations of gradients. The reliability is good, since the method handles all topological situations for the set of spheres, including those which are never encountered in chemistry. If your input set contains some uncertainty, you can automatically generate perturbated inputs and see the effects on the analytical values. If you need real*16 precision, I can recompile for you the f77 source, provided that this is on a platform enabling it (e.g. the IBM autodblpad compiler option). The freeaware ASV includes also a Monte-Carlo calculation of surfaces and volumes (with precision calculus), which is useful if you need a short computing time for large sets, and provided that a limited precision suffice, such as for empirical correlations. See programmes, documentation, and ref. of the method on: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV The rectangular grid containing the molecule may be approximated > from the xmin,xmax, ymin,ymax, zmin,zmax via random rotations. Before doing that, since the parallelepiped box is convex, you can first extract the extremal points which the RADI freeware, which computes also the minimal sphere containing your set of points. See programmes, documentation and reference on: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html =?gb2312?q?Jinsong=20Zhao?= wrote: >Dear all, > >I hope to know if there is any program or routine >could calculate the molecular volume with high >precision and reliability, moreover, to figure out the >length, width and high of the grid that contain the >molecule.=20 > >Any comments, suggestion are welcome! > >Thanks for essential responses! > >Best regards, > >Jinsong From chemistry-request@server.ccl.net Tue May 13 02:05:15 2003 Received: from ns.cwp.co.kr ([210.109.76.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D65Et08149 for ; Tue, 13 May 2003 02:05:14 -0400 Received: from virtual ([172.24.15.115]) by ns.cwp.co.kr (8.9.3 (PHNE_25184)/8.9.3) with SMTP id PAA05976 for ; Tue, 13 May 2003 15:05:36 +0900 (KST) Message-ID: <001401c31915$8b394620$fd2ffea9@cri2.cwp.co.kr> From: "Sean" To: Subject: CCL:3D generation problem! Date: Tue, 13 May 2003 15:04:41 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C31960.FAEB8640" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C31960.FAEB8640 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 RGVhciBDQ0xlciENCg0KSSBkcmF3IDJEIHN0cnVjdHVyZSBvZiB0aGUgNiw2IG1lYmVyIHJpbmcg Y29udGFpbmcgY2hpcmFsIGNlbnRlciB3aXJoIGlzaXMvZHJhdygyLjQpLg0KYW5kIHRoZW4sIEkg Y2FuIG5vdCBjb252ZXJ0IHRvIDNEIHN0cnVjdHVyZSBjb3JyZWN0bHkuIHNvbXRpbWVzIGNoaXJh bCBjZW50ZXIgaXMgY2hhbmdlZCAoUiB0byBTIG9yICBTIHRvIFIgKSB3aGVuIEkgZ2VuZXJhdGUg dGhlICAzRCBzdHJ1Y3R1cmUuIA0KRG8geW91IGhhdmUgYW55IGlkZWEgb3Igc29sdXRpb24/IA0K DQpTZWFuDQogDQpzZWloa2ltQGN3cC5jby5rciANCiA= ------=_NextPart_000_0011_01C31960.FAEB8640 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI4MDAuMTEwNiIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwv SEVBRD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgZmFjZT1BcmlhbCBzaXpl PTI+RGVhciBDQ0xlciE8L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9QXJpYWwgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgZmFjZT1BcmlhbCBzaXplPTI+SSBkcmF3 IDJEIHN0cnVjdHVyZSBvZiB0aGUgNiw2IG1lYmVyIA0KcmluZyZuYnNwO2NvbnRhaW5nIGNoaXJh bCBjZW50ZXIgd2lyaCBpc2lzL2RyYXcoMi40KS48L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZh Y2U9QXJpYWwgc2l6ZT0yPmFuZCB0aGVuLCBJIGNhbiBub3QgY29udmVydCB0byAzRCBzdHJ1Y3R1 cmUgDQpjb3JyZWN0bHkuJm5ic3A7c29tdGltZXMgY2hpcmFsIGNlbnRlciBpcyBjaGFuZ2VkIChS IHRvIFMmbmJzcDtvciAmbmJzcDtTIHRvIA0KUiZuYnNwOykgd2hlbiZuYnNwO0kgZ2VuZXJhdGUm bmJzcDt0aGUgJm5ic3A7M0Qgc3RydWN0dXJlLiA8L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZh Y2U9QXJpYWwgc2l6ZT0yPkRvJm5ic3A7eW91IGhhdmUgYW55IGlkZWEgb3IgDQpzb2x1dGlvbj88 L0ZPTlQ+Jm5ic3A7PC9ESVY+DQo8RElWPiZuYnNwOzwvRElWPg0KPERJVj48Rk9OVCBmYWNlPUFy aWFsIHNpemU9Mj5TZWFuPC9GT05UPjwvRElWPg0KPERJVj4mbmJzcDs8L0RJVj4NCjxESVY+PEZP TlQgZmFjZT1BcmlhbCBzaXplPTI+PEEgDQpocmVmPSJtYWlsdG86c2VpaGtpbUBjd3AuY28ua3Ii PnNlaWhraW1AY3dwLmNvLmtyPC9BPjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+Jm5ic3A7PC9E SVY+PC9CT0RZPjwvSFRNTD4NCg== ------=_NextPart_000_0011_01C31960.FAEB8640-- From chemistry-request@server.ccl.net Tue May 13 02:22:13 2003 Received: from mail.shcnc.ac.cn ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D6MBt08787 for ; 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Tue, 13 May 2003 10:34:37 -0400 Received: from rygar.gpcc.itd.umich.edu (rygar.gpcc.itd.umich.edu [141.211.2.202]) by donkeykong.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id KAA20500 for ; Tue, 13 May 2003 10:34:34 -0400 (EDT) Received: from localhost (brupalf@localhost) by rygar.gpcc.itd.umich.edu (8.9.3/5.1-client) with ESMTP id KAA19991 for ; Tue, 13 May 2003 10:34:33 -0400 (EDT) Precedence: first-class Date: Tue, 13 May 2003 10:34:33 -0400 (EDT) From: Bruce Allan Palfey X-X-Sender: brupalf@rygar.gpcc.itd.umich.edu To: CHEMISTRY@ccl.net Subject: Anaglyph stereo display Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone recommend a fee (or cheap) program for looking at proteins that can render the molecules using anaglyph (i.e., red/blue) stereo? Bruce Palfey Department of Biological Chemistry University of Michigan Ann Arbor, MI 48109-0606 From chemistry-request@server.ccl.net Tue May 13 10:59:01 2003 Received: from opal.saintmarys.edu ([147.53.6.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DEx1t07579 for ; Tue, 13 May 2003 10:59:01 -0400 Received: from saintmarys.edu (pbays-tmp.saintmarys.edu [147.53.80.81]) by opal.saintmarys.edu (8.12.8/8.12.8) with ESMTP id h4DEx1mV021232 for ; Tue, 13 May 2003 09:59:01 -0500 (EST) Date: Tue, 13 May 2003 09:59:18 -0500 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: Fwd: PDB viewing and Mac OSX From: Philip Bays To: chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: <78F8937D-8553-11D7-BD21-0003937E291E@saintmarys.edu> X-Mailer: Apple Mail (2.552) > > Does any one know of a plugin that can be used with a browser under > Mac OSX that will allow one to view 3-D chemical structures.? I am > thinking of a Chime-like plug-in, but MDL has no plans for OSX or > Linux. I am familiar with iMol but have been unable to install it as > a helper ap. > > > Phil Bays > > J. Philip Bays > Department of Chemistry and Physics > Saint Mary's College > Notre Dame IN 46556 > pbays@saintmarys.edu > > From chemistry-request@server.ccl.net Tue May 13 11:34:06 2003 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DFY5t08958 for ; Tue, 13 May 2003 11:34:05 -0400 Received: from ac12 by wn1.sci.kun.nl via ac12.sci.kun.nl [131.174.179.19] with ESMTP id h4DFY4rG017000 (8.12.9/3.57); Tue, 13 May 2003 17:34:05 +0200 (MEST) Content-Type: text/plain; charset="iso-8859-1" From: "E.L. Willighagen" Reply-To: egonw@sci.kun.nl To: Philip Bays , chemistry@ccl.net Subject: Re: CCL:Fwd: PDB viewing and Mac OSX Date: Tue, 13 May 2003 17:34:04 +0200 User-Agent: KMail/1.4.2 References: <78F8937D-8553-11D7-BD21-0003937E291E@saintmarys.edu> In-Reply-To: <78F8937D-8553-11D7-BD21-0003937E291E@saintmarys.edu> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200305131734.04254.egonw@sci.kun.nl> On Tuesday 13 May 2003 16:59, Philip Bays wrote: > > Does any one know of a plugin that can be used with a browser under > > Mac OSX that will allow one to view 3-D chemical structures.? I am > > thinking of a Chime-like plug-in, but MDL has no plans for OSX or > > Linux. I am familiar with iMol but have been unable to install it as > > a helper ap. Have a look at Jmol: jmol.sourceforge.net. It's applet does most browsers/platforms, including MacOSX. The soon-to-be-released version 6 has interesting scripting facilities which allows HTML pages to interact with the applet. kind regards, Egon Willighagen From chemistry-request@server.ccl.net Tue May 13 09:53:02 2003 Received: from sal.ahpcrc.org ([144.34.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DDr2t04949 for ; Tue, 13 May 2003 09:53:02 -0400 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h4DDr1b16110 for ; Tue, 13 May 2003 08:53:01 -0500 Received: from ahpcrc.org (GULL.dhcp.famu.ahpcrc.org [144.34.131.114]) by mycroft.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h4DDqtt09747 for ; Tue, 13 May 2003 08:52:55 -0500 Message-ID: <3EC0F8B7.71C2D3B@ahpcrc.org> Date: Tue, 13 May 2003 09:52:55 -0400 From: Genzo Tanaka X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: SIGNAL: Floating point exception (invalid floating point operation) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Floating point exception errors occurred at an very early stage of a Gaussian 98 DFT optimization on Cray T3E to a transition state for transition structures found by the PM3 in Gaussian and DFT by Jaguar. It seems to me that the error is related to dividing by zero due to the coplanarity of four atoms for initial (transition state) structures (by PM3 and Jaguar DFT). Does anyone have any idea to avoid this kind of error? My route section looks like the following: #P B3LYP/6-31G* opt=(modredundant,TS,noeigen,CalcFC) nosymm GFINPUT IOP(6/7=3) I also added scf=qc and also tried to check frequencies by freq instead of opt, but both resulted the same error. Thanks in advance. Genzo Tanaka From chemistry-request@server.ccl.net Tue May 13 13:08:41 2003 Received: from MMSSERVER ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DH8ft12040 for ; Tue, 13 May 2003 13:08:41 -0400 Received: from 10.3.1.165 by MMSSERVER with ESMTP (CHLA SMTP Relay (MMS v5.5.0)); Tue, 13 May 2003 10:10:28 -0700 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Tue, 13 May 2003 10:08:23 -0700 Message-ID: <73564B8DE398D61180500008C75D7E494389B3@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Threshold values Date: Tue, 13 May 2003 10:08:21 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 12DFF88E9226-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit Dear All, I am in a urgent need to unserstand the threshold values of global score function, interatomic distances, electrostatic values and hydrophobic values for a successful docking , please help!! Thanks, Jaya From chemistry-request@server.ccl.net Tue May 13 13:13:56 2003 Received: from MMSSERVER ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DHDut12205 for ; Tue, 13 May 2003 13:13:56 -0400 Received: from 10.3.1.165 by MMSSERVER with ESMTP (CHLA SMTP Relay (MMS v5.5.0)); Tue, 13 May 2003 10:15:41 -0700 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Tue, 13 May 2003 10:13:36 -0700 Message-ID: <73564B8DE398D61180500008C75D7E494389B4@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Bigger Date: Tue, 13 May 2003 10:13:29 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 12DFF7B79324-02-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit Dear All, The docking software BiGGER in the top of solution manager window shows a graphical representation of the solutions provided and the corresponding scores to it. Can somebody help me to undersatnd how to select and understand the best solution ? Thanks, Jaya From chemistry-request@server.ccl.net Tue May 13 11:48:52 2003 Received: from polaris.scs.uiuc.edu ([130.126.225.41]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DFmqt09709 for ; Tue, 13 May 2003 11:48:52 -0400 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by polaris.scs.uiuc.edu (8.12.9/8.12.8) with SMTP id h4DFmqED3999719; Tue, 13 May 2003 10:48:52 -0500 (CDT) Reply-To: From: "Jerome Baudry" To: "'Bruce Allan Palfey'" , Subject: RE: Anaglyph stereo display Date: Tue, 13 May 2003 10:45:40 -0500 Message-ID: <001701c31966$b53369f0$efe27e82@leonidas> 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 CWS, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: VMD (http://www.ks.uiuc.edu/Research/vmd/) as an anaglyph rendering option. I nerver used anaglyph within VMD myself so I can't comment on its rendering. NAMD2 is free. ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager Computer Applications & Network Services School of Chemical Sciences University of Illinois at Urbana-Champaign > -----Original Message----- > From: Computational Chemistry List > Can anyone recommend a fee (or cheap) program for looking at > proteins that > can render the molecules using anaglyph (i.e., red/blue) stereo? > > Bruce Palfey From chemistry-request@server.ccl.net Tue May 13 12:40:47 2003 Received: from dqo.qo.ub.es ([161.116.74.251]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DGekt11244 for ; Tue, 13 May 2003 12:40:46 -0400 Received: from qo.ub.es (unknown [161.116.74.156]) by dqo.qo.ub.es (Postfix) with ESMTP id 2598A5C350; Tue, 13 May 2003 20:21:31 +0200 (CEST) Message-ID: <3EC1200B.1000302@qo.ub.es> Date: Tue, 13 May 2003 18:40:43 +0200 From: Oriol Pineda User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Bruce Allan Palfey Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Anaglyph stereo display References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I think that SwissPDB Viewer can do it, and it can be downloaded for free from http://us.expasy.org/spdbv/ Luck! Bruce Allan Palfey wrote: >Can anyone recommend a fee (or cheap) program for looking at proteins that >can render the molecules using anaglyph (i.e., red/blue) stereo? > >Bruce Palfey >Department of Biological Chemistry >University of Michigan >Ann Arbor, MI 48109-0606 > > >-= 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 Tue May 13 15:39:04 2003 Received: from hotmail.com ([64.4.11.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4DJd4t17877 for ; Tue, 13 May 2003 15:39:04 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 13 May 2003 12:39:04 -0700 Received: from 138.73.24.40 by by7fd.bay7.hotmail.msn.com with HTTP; Tue, 13 May 2003 19:39:04 GMT X-Originating-IP: [138.73.24.40] X-Originating-Email: [jdthlr@hotmail.com] From: "john thaler" To: chemistry@ccl.net Subject: I Need Help: Warning message Gaussian98 Date: Tue, 13 May 2003 16:39:04 -0300 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 13 May 2003 19:39:04.0126 (UTC) FILETIME=[4F7B35E0:01C31987] I was running a frequency calculation in Gaussian98 on a molecule similar to the sugar in the DNA backbone and it returned these errors around the place where it reports the Zero point Calculation. I was wondering if anybody knows what these errors means and how I can fix them or maybe even ignore them? 1. THIS MOLECULE IS AN ASYMMETRIC TOP. ROTATIONAL SYMMETRY NUMBER 1. WARNING-- ASSUMPTION OF CLASSICAL BEHAVIOR FOR ROTATION MAY CAUSE SIGNIFICANT ERROR 2. WARNING-- EXPLICIT CONSIDERATION OF 15 DEGREES OF FREEDOM AS VIBRATIONS MAY CAUSE SIGNIFICANT ERROR John Thaler - jdthlr@hotmail.com _________________________________________________________________ The new MSN 8: advanced junk mail protection and 2 months FREE* http://join.msn.com/?page=features/junkmail