From chemistry-request@server.ccl.net Sat Apr 6 03:58:59 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g368wxp09716 for ; Sat, 6 Apr 2002 03:58:59 -0500 Message-ID: <20020406085845.19246.qmail@web12804.mail.yahoo.com> Received: from [203.87.132.164] by web12804.mail.yahoo.com via HTTP; Sat, 06 Apr 2002 00:58:45 PST Date: Sat, 6 Apr 2002 00:58:45 -0800 (PST) From: amor san juan Subject: Asking for comments/suggestions To: sergio@proinformatix.com Cc: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sir: I would like to ask your view in my understanding about working on AutoDock3.0 with AutoDockTools (ADT). 1. In AutoGpf program of ADT, I read pdb macromolecule then saved as pdbqs file. Is this already the file I needed prior converting to macro.gpf file? 2. I understand that ADT is a graphical user interface for file preparation, execution of Autogrid & AutoDock and analysis. As a neophyte in docking experiment, I'm confused to what will be the role of my compiled AutoDock3.0. It seems for me that all the AutoDock3.0 programs is embedded already in ADT. 3.I used chemsketch5.0 in drawing ligands. I save it as mol file format then converted to mol2 using Babel. However, when i opened this file by ADT the structural model shown at Molecular Viewer differs from what I originately drawn in chemsketch5.0 i.e. non-polar Hydrogens merge to polar atoms forming bonds. How can I correct this? Please help me. Amor San Juan University of the Philippines __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Sat Apr 6 09:52:34 2002 Received: from mail.salve.edu ([12.154.160.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g36EqXp13611 for ; Sat, 6 Apr 2002 09:52:34 -0500 Received: from salve5.salve.edu (salve5.salve.edu [12.154.160.58]) by mail.salve.edu (8.9.3 (MessagingDirect 1.0.4)/8.9.3) with SMTP id JAA12659 for ; Sat, 6 Apr 2002 09:56:28 -0500 Date: Sat, 6 Apr 2002 09:25:42 -0500 (EST) From: Ascanio DiPippo To: chemistry@ccl.net Subject: Princeton meeting 12 April 2002 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Colleagues, i inadvertently deleted the message concerning the(a) meeting on April 12, 2002 at princeton U. The time is 6-9 P.M. but the rest was quickly deleted. Could some one, please, resend me the notice ? Thank you. A.G. DiPippo From chemistry-request@server.ccl.net Sat Apr 6 13:26:07 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g36IQ7p15237 for ; Sat, 6 Apr 2002 13:26:07 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g36IQ3322007; Sat, 6 Apr 2002 13:26:03 -0500 (EST) Date: Sat, 6 Apr 2002 13:26:01 -0500 (EST) From: Jan Labanowski To: Ascanio DiPippo cc: chemistry@ccl.net Subject: Re: Princeton meeting 12 (17 ?) April 2002 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII All messages to CCL are archived, though there is a one day delay before you can see them (it will be corrected soon, hopefully...). Just go to: http://www.ccl.net and choose List Archive under Resources. Jan I am not sure if this is the meeting you are talking about: > From chemistry-request@server.ccl.net Fri Apr 5 15:09:36 2002 > Message-ID: <3CAE053A.3403E216@3dp.com> > Date: Fri, 05 Apr 2002 15:12:42 -0500 > From: Ed Jaeger > To: chemistry@ccl.net > Subject: MACC Meeting on April 17th in Princeton > > I ask CCL's indulgence for the broadcast nature of this meeting notice > of local interest. > > The Mid-Atlantic Computational Chemistry discussion group > will be holding its next meeting on April 17th from 6-9 P.M. > > Professor Curt Breneman of Renssalear Polytechnic Institute > will be speaking on "New Developments in Molecular Property > Descriptors, Machine Learning and Computational ADME" > > The schedule is: Social Hour 6-7 P.M. > Seminar 7-8 > > The venue is Kresge Auditorium (Room 120 Frick) at Princeton University. > > For R.S.V.P. and information please email to jaeger@3dp.com > > -- > Ed Jaeger 3-Dimensional Pharmaceuticals, Inc. ph:610-458-6052 > jaeger@3dp.com 665 Stockton Drive, Exton, PA 19341 fx:610-458-8249 > On Sat, 6 Apr 2002, Ascanio DiPippo wrote: > Colleagues, > i inadvertently deleted the message concerning the(a) meeting on > April 12, 2002 at princeton U. The time is 6-9 P.M. but the rest was > quickly deleted. Could some one, please, resend me the notice ? > Thank you. > A.G. DiPippo > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Sat Apr 6 13:52:16 2002 Received: from web20604.mail.yahoo.com ([216.136.226.162]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g36IqGp15763 for ; Sat, 6 Apr 2002 13:52:16 -0500 Message-ID: <20020406185202.28911.qmail@web20604.mail.yahoo.com> Received: from [64.130.222.245] by web20604.mail.yahoo.com via HTTP; Sat, 06 Apr 2002 10:52:02 PST Date: Sat, 6 Apr 2002 10:52:02 -0800 (PST) From: Sengen Sun Subject: Mechanism of Cycloadditions To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii In response to a recent preprint paper by Dr. Ian Miller, I posted some comments there ( http://preprint.chemweb.com/orgchem/0203001). I’d like to emphasize a critical issue here. The critical issue is the assumption that “electrons remain in stationary wave functions throughout the reaction”. Many many publications of elegant mathematical treatments, rules and theorems have been implicitly or explicitly based on such an assumption for the last decades. If this assumption is false, all those mathematical treatments, rules and theorems founded on this assumption are invalid. I don’t see this assumption to be true based on the electrons’ fundamental nature of uncertainty. There is no way you can track a portion of two electrons along a reaction path as we can do in classical systems. Those rules and theorems may be seen as the classical thinking of the nonclassical systems. This assumption can not be seen as a reasonable mathematical approximation, but is an issue of conceptual correctness or wrongness about the non-classical systems. As mentioned in Miller’s paper, the force vector is the first derivative of the potential energy. The ubiquity of force in any chemical reactions is supported by the vigorous mathematical logic. Why do we then use the phrase “classical concept” to describe force? The force field is a collective effect of a set of electrons and nuclei. Ignoring the collective effect has led to a tremendous complexity of chemical concepts. In a simple case of benzene, I don’t think that its effective force field in a chemical reaction can be described based on its two resonance structures. Any comments? Sengen __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Sat Apr 6 20:29:47 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g371Tlp20189 for ; Sat, 6 Apr 2002 20:29:47 -0500 Received: from wiracocha (wiracocha.ee.sc.edu [129.252.22.166]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2655.55) id H3SVS6SM; Sat, 6 Apr 2002 20:29:39 -0500 Message-ID: <004901c1ddd2$e8b548f0$a616fc81@ee.sc.edu> From: "Hernan P Figueroa" To: References: <5.0.2.1.2.20020331143030.00b5f0e8@sina.iums.ac.ir> Subject: CCL: DNA theoretical models Date: Sat, 6 Apr 2002 20:23:46 -0500 Organization: University of South Carolina MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear CCL group I am interested in characterize DNA molecules, I would like to obtain Hamiltonian matrices, DOS, and another related properties. Could anybody of you can advice me what kind of software I can use? Do you know if Cerius has examples for DNA molecules? I appreciate your help Thanks Hernan Figueroa Dept of Electrical Engineering University of South Carolina Phone: (803) 777-0392 SWGN 3A13 figueroh@engr.sc.edu