From bakasov@ictp.trieste.it Thu Mar 6 05:27:28 1997 Received: from sol3.ictp.trieste.it for bakasov@ictp.trieste.it by www.ccl.net (8.8.3/950822.1) id FAA13146; Thu, 6 Mar 1997 05:25:50 -0500 (EST) Received: from localhost (bakasov@localhost) by sol3.ictp.trieste.it (8.6.9/8.6.9) with SMTP id LAA19150 for ; Thu, 6 Mar 1997 11:25:07 +0100 X-Authentication-Warning: sol3.ictp.trieste.it: bakasov owned process doing -bs Date: Thu, 6 Mar 1997 11:25:06 +0100 (MET) From: Bakasov Ayaz X-Sender: bakasov@sol3 To: chemistry@www.ccl.net Subject: G94/92: how it chooses "standard orientation" Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, anyone can tell how Gaussian94/92... chooses the so called "standard orientation"? 1) How it chooses the origin of the coordinate frame? 2) How it then chooses the orientation of axes? After one inputs a molecular geometry, Gaussian.. re-orients it somehow. How and why? Understanding the physical principles (if any) of Gaussian's "standard orientation" would be nice. At least one would know what to expect >from certain quantities like multipoles or moments of inertia. So far, I only found that the total dipole moment of nuclei roughly vanishes (at least in some cases) at Gaussian's standard orientation. Reading manual didn't help much. Explanations and references would be very appreciated. Regards, Ayaz Bakasov. From bantingl@cv.port.ac.uk Thu Mar 6 10:27:44 1997 Received: from cv.port.ac.uk for bantingl@cv.port.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA14507; Thu, 6 Mar 1997 09:38:28 -0500 (EST) From: Received: by cv.port.ac.uk (MX V4.2 VAX) id 5; Thu, 06 Mar 1997 14:33:51 GMT0 Date: Thu, 06 Mar 1997 14:33:51 GMT0 To: chemistry@www.ccl.net Message-ID: <009B0DC3.DF9947A0.5@cv.port.ac.uk> Subject: HYDRATED METAL IONS I HAVE A COLLEAGUE WORKING ON AN ION CONDUCTING CHANNEL AND IS REQUESTING INFO ON 'EFFECTIVE' HYDRATED ION SIZE. ANY TAKERS FOR A SUITABLE REFERENCE ? REGARDS, LEE. From dychen@cheyenne.bgsu.edu Thu Mar 6 15:27:35 1997 Received: from cheyenne.bgsu.edu for dychen@cheyenne.bgsu.edu by www.ccl.net (8.8.3/950822.1) id OAA16376; Thu, 6 Mar 1997 14:42:14 -0500 (EST) Received: by cheyenne.bgsu.edu (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA01205; Thu, 6 Mar 97 11:29:29 -0800 Date: Thu, 6 Mar 97 11:29:29 -0800 From: dychen@cheyenne.bgsu.edu (D. Y. Chen) Message-Id: <9703061929.AA01205@cheyenne.bgsu.edu> To: CHEMISTRY@www.ccl.net Subject: parameters for metals ion in quanta/charmm hello everyone, we are using quanta/charmm to build/calculate some organometallic ligands for the polypeptide binding studies. unfortunately, we don't have any parameters for the metal ions, mainly Ru and Co. we tried the scientific support of msi but have no luck at all (they told us the harvard list has no parameters for Ru and Co either). we desperately need helps from any of you who can offer us information of metal ions' charmm parameters. all responses are highly appreciated!! chen ps. we don't have cerius2 or insight2 for this kind of work. From fgonzale@lauca.usach.cl Thu Mar 6 18:27:46 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id RAA17638; Thu, 6 Mar 1997 17:32:00 -0500 (EST) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.7.4/8.7.3) with ESMTP id SAA00229 for ; Fri, 7 Mar 1997 18:35:22 -0300 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id TAA27092; Thu, 6 Mar 1997 19:40:24 -0300 Date: Thu, 6 Mar 1997 19:40:23 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: CHEMISTRY@www.ccl.net cc: fgonzale@lauca.usach.cl, lcontrer@lauca.usach.cl Subject: Water Box (MD) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! We are runnig a dynamic Calculation of a macroion with 8 positive charges in a water box, using PBC and a 30x30x30 cell, T=300 K, 50ps. We observe many water molecules going out from the box, during the process. We don't use any counterion. Is it normal that in the PBC condition, water molecules go out the cell? if not.... How can that be controlled? any help will be very much appreciated!! thanks! Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quimbio.usach.cl URL : http://quimbio.usach.cl/~danilo *************************************************************************x From online@mactech.com Thu Mar 6 19:27:34 1997 Received: from xenon.chem.ucla.edu for online@mactech.com by www.ccl.net (8.8.3/950822.1) id TAA18276; Thu, 6 Mar 1997 19:07:56 -0500 (EST) Received: from [128.97.76.42] ([128.97.76.42]) by xenon.chem.ucla.edu (8.6.9/8.6.9) with ESMTP id QAA23079 for ; Thu, 6 Mar 1997 16:12:32 -0800 X-Sender: nick@xenon.chem.ucla.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Mar 1997 16:07:57 -0800 To: CHEMISTRY@www.ccl.net From: "nick.c" Subject: CCL: PDB format Documented? Folks, Can someone point me to documentation in the literature regarding the PDB file format? I've noticed that several software products have slightly different "PDB" output formats for small molecules. I'm interested in getting more information on what the standard says... I'm just having trouble finding where that standard is documented :-) Pointers to HTTP sites, journal articles, or other places where the PDB standard is authoritatively described would be appreciated. Thanks, ____Nicholas C. DeMello, Ph.D.________________________________________ Online at MacTech Magazine, the Journal of Macintosh Programming http://www.MacTech.com/ _/ _/ _/ _/_/_/ _/ _/ Chemistry: Nick@chem.UCLA.edu _/_/ _/ _/ _/ _/ _/_/_/ MacTech: Online@MacTech.com _/ _/_/ _/ _/ _/ _/ http://www.chem.ucla.edu/~nick/ _/ _/ _/_/_/ _/ _/