From chemistry-request@server.ccl.net Wed Oct 11 21:42:28 2000 Received: from linux2.ipc.pku.edu.cn (gao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA32645 for ; Wed, 11 Oct 2000 21:42:25 -0400 Received: from localhost (gao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id JAA25436 for ; Thu, 12 Oct 2000 09:50:00 +0800 Date: Thu, 12 Oct 2000 09:50:00 +0800 (CST) From: Gao Ying To: chemistry@ccl.net Subject: ANNOUNCE: LigBuilder v1.2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, We announce here that LigBuilder v1.0 is now available. You can download it free via anonymous FTP to ftp2.ipc.pku.edu.cn/pub/software/LigBuilder. LigBuilder is a multiple-purposed program written for structure-based drug design procedure. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them. In brief, main features of LigBuilder include: (1) The program analyzes the binding pocket of the target protein and derives the key interaction sites. A pharmacophore model is suggested and it could be applied to 3D database search for finding novel ligand molecules. (2) Molecules are constructed by using fragments as building blocks. Various kinds of structural manipulation are provided, such as growing, linking, and mutation. On-the-fly minimization of conformation is performed during the building-up procedure. While the target protein is kept rigid, flexibility of the ligand molecules is considered. (3) User can choose either growing strategy or linking strategy to develop ligand molecules. (4) Molecules are evolved by Genetic Algorithm. The fitness score of a molecule is evaluated by considering its chemical viability as well as binding affinity. (5) Chemical rules are adopted for evaluating "drug-likeness" of the resultant molecules. Chemical stability, synthesis feasibility, and toxicity can also be taken into account by defining "forbidden structure" libraries. (6) All the input and output molecules are presented in popular format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The program is very easy to use. LigBuilder is written in ANSI C++ and has been tested on UNIX and LINUX platforms. Running LigBuilder itself does not need any other software. However, you may need a graphical molecular modeling software to prepare the input files and check the resultant molecules. If you encounter any problem while downloading the program, please contact Ms. Ying Gao at gao@mdl.ipc.pku.edu.cn. If you are the old user of LigBuilder and have not received the encrypt key, please contact Ms. Ying Gao at gao@mdl.ipc.pku.edu.cn. Please forward this mail to anyone who may concern. With best wishes, Molecular Design Laboratory, Institute of Physical Chemistry Peking University, Beijing, China From chemistry-request@server.ccl.net Thu Oct 12 12:23:34 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04132 for ; Thu, 12 Oct 2000 12:23:34 -0400 Received: from dsmtp0.dion.ne.jp (dsmtp0.dion.ne.jp [210.172.64.79]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id MAA24309 for ; Thu, 12 Oct 2000 12:23:18 -0400 (EDT) Received: from b159504364 by dsmtp0.dion.ne.jp (8.9.3/3.7W-00031710) id BAA21040; Fri, 13 Oct 2000 01:23:11 +0900 (JST) Message-ID: <000501c03468$a0482660$dc25fbd2@b159504364> From: "Telkuni" To: Subject: Free MD program for Win95/98 Date: Fri, 13 Oct 2000 01:22:24 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi ! all, I am a novice of MD simulation. I'm looking for "free" and "for non-Bio" MD programs which are able to run on Win95/98. If anyone know such MD programs(and I wish they are also easy to use for beginners.) , please teach me. I would like to use them for "MD-learning". All responses I will be appreciated, and I will summarize them. Thanks in advance. --------------------------- Telkuni telmail@d4.dion.ne.jp From chemistry-request@server.ccl.net Thu Oct 12 04:51:32 2000 Received: from mailhost1.rdg.ac.uk (sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA01719 for ; Thu, 12 Oct 2000 04:51:32 -0400 Received: from indyp.chemistry ([134.225.168.35] helo=scsgind2) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {13je5E-0001rS-00} for CHEMISTRY@server.ccl.net; Thu, 12 Oct 2000 09:51:24 +0100 Received: from reading.ac.uk (localhost [127.0.0.1]) by scsgind2 (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA12791 for ; Thu, 12 Oct 2000 09:51:27 -0100 (BST) Sender: dave@reading.ac.uk Message-ID: <39E597AF.B9BC1EAF@reading.ac.uk> Date: Thu, 12 Oct 2000 09:51:27 -0100 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Summary of replies to Simplified DFT reference Content-Type: text/plain; charset=iso-8859-1 X-MIME-Autoconverted: from 8bit to quoted-printable by scsgind2 id JAA12791 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA01720 Dear CCLers, Thank you to all (named below) that repsonded to my question. The answers fell between two camps; one went for - 'Structural Chemistry and Biology' eds A. Rich and N. Davidson. W.H. Freeman (San Francisco) 753-760 (1968) while the other group went for- "Lecture Notes in Quantum Chemistry II", edited by B. O. Roos, Springer-Verlag (1994) but it was pointed out that this statement was made in a spectroscopy(?) conference in 1965 (before I was born, I'm affraid). I have checked the former reference and it does indeed contain the same sort of arguements as above, but from the stand-point of proving the theorem not to be incorrect. I haven't been able to lay my hands on the second reference yet and, as stated previously, was too young to attend the said conference. I am deeply indebted to - Laurence Cuffe, Thomas Bligaard Pedersen, Claudia Stückl, Thomas Gray, Pradipta Bandyopadhyay, Marcel Swart, Petra from Duesseldorf, Wolfgang Roth and Chris Page. I hope I haven't missed out anyone and that you will forgive me not replying to each of you individually. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 12 16:55:02 2000 Received: from daphne.aspentec.com ([208.201.90.48]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05369 for ; Thu, 12 Oct 2000 16:55:02 -0400 Received: by daphne.aspentech.com with Internet Mail Service (5.5.2650.21) id <4X1DX6Y6>; Thu, 12 Oct 2000 16:53:55 -0400 Message-ID: <958946B36E5AD211888C0008C7A4E9CC0381D0DE@cadbury.aspentec.com> From: Paul Mathias To: "'Dave Price'" , Comp Chem Mailing List Subject: RE: Summary of replies to Simplified DFT reference Date: Thu, 12 Oct 2000 15:33:52 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id QAA05370 -----Original Message----- From: Dave Price [mailto:d.w.price@reading.ac.uk] Sent: Thursday, October 12, 2000 6:51 AM To: Comp Chem Mailing List Subject: CCL:Summary of replies to Simplified DFT reference Dear CCLers, Thank you to all (named below) that repsonded to my question. The answers fell between two camps; one went for - 'Structural Chemistry and Biology' eds A. Rich and N. Davidson. W.H. Freeman (San Francisco) 753-760 (1968) while the other group went for- "Lecture Notes in Quantum Chemistry II", edited by B. O. Roos, Springer-Verlag (1994) but it was pointed out that this statement was made in a spectroscopy(?) conference in 1965 (before I was born, I'm affraid). I have checked the former reference and it does indeed contain the same sort of arguements as above, but from the stand-point of proving the theorem not to be incorrect. I haven't been able to lay my hands on the second reference yet and, as stated previously, was too young to attend the said conference. I am deeply indebted to - Laurence Cuffe, Thomas Bligaard Pedersen, Claudia Stückl, Thomas Gray, Pradipta Bandyopadhyay, Marcel Swart, Petra from Duesseldorf, Wolfgang Roth and Chris Page. I hope I haven't missed out anyone and that you will forgive me not replying to each of you individually. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 12 21:41:21 2000 Received: from hotmail.com (f87.law9.hotmail.com [64.4.9.87]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA06292 for ; Thu, 12 Oct 2000 21:41:20 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 12 Oct 2000 18:39:17 -0700 Received: from 128.192.2.199 by lw9fd.law9.hotmail.msn.com with HTTP; Fri, 13 Oct 2000 01:39:17 GMT X-Originating-IP: [128.192.2.199] From: "jose conceicao" To: CHEMISTRY@ccl.net Subject: Tin and Germanium with B3LYP/LANL2DZ ? Date: Thu, 12 Oct 2000 21:39:17 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 13 Oct 2000 01:39:17.0367 (UTC) FILETIME=[666FD070:01C034B6] Hi everyone Hope someone out there could prove me with a couple of references discussing the reliability and accuracy of B3LYP/LANL2DZ method for Germanium / Tin compounds. Thanks in advance. Jo _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com.