From chemistry-request@server.ccl.net Wed Sep 26 02:16:42 2001 Received: from mx1.ustc.edu.cn ([61.132.182.1]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8Q6Gf120359 for ; Wed, 26 Sep 2001 02:16:41 -0400 Received: from mail.ustc.edu.cn (mail.ustc.edu.cn [202.38.64.10]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id PAA29572 for ; Wed, 26 Sep 2001 15:13:47 -0800 Received: (qmail 6547 invoked by uid 6193); 26 Sep 2001 06:01:31 -0000 Date: Wed, 26 Sep 2001 14:01:31 +0800 (CST) From: benny X-X-Sender: To: Subject: G3 problem? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi,ccl members When I used G3 method to do calculation on CH4, It was error terminated. The information is: Sphere: Did not find three 2-fold axes Error termination via Lnk1e in /usr/g98/l202.exe. Please tell how to solve it, thanks. Best Wishes! ------------------------------------------------ Kesheng Song 323-137, East Campus, Department of Chemistry, University of Science and Technology of China Hefei, 230026, Anhui, P. R. of China Telephone Number: 0551-3632834(dorm) 3606640(lab) Email Address : kssong@mail.ustc.edu.cn ------------------------------------------------ From chemistry-request@server.ccl.net Wed Sep 26 10:01:05 2001 Received: from research.dfci.harvard.edu ([155.52.50.28]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8QE15103410 for ; Wed, 26 Sep 2001 10:01:05 -0400 Received: from [155.52.18.51] (account reche HELO research.dfci.harvard.edu) by research.dfci.harvard.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP-TLS id 540429 for chemistry@ccl.net; Wed, 26 Sep 2001 09:58:51 -0400 Sender: par@ccl.net Message-ID: <3BB1DFC7.3B482F3A@research.dfci.harvard.edu> Date: Wed, 26 Sep 2001 10:01:43 -0400 From: Pedro A Reche Gallardo Reply-To: reche@research.dfci.harvard.edu Organization: Dana-Farber Cancer Institute X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: protein interfaces Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All, I am looking for a program that will take a pdb file of protein complex and identify and list the residue atoms of the interface that interacts together with type of interaction (salt bridge, h-bonds, vdw). Any idea if that program exists? Comments and/or suggestions for doing this thing using any free software will also be welcomed. regards, Pedro *************************************************************************** PEDRO a. RECHE gallardo, pHD TL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: reche@research.dfci.harvard.edu Harvard Medical School, EM: reche@mifoundation.org 44 Binney Street, D610C, URL: http://www.reche.org Boston, MA 02115 *************************************************************************** From chemistry-request@server.ccl.net Wed Sep 26 10:30:52 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8QEUn105102 for ; Wed, 26 Sep 2001 10:30:49 -0400 Received: from ppp-212.56.193.139.mldnet.com (ppp-212.56.193.139.mldnet.com [212.56.193.139]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id RAA16590 for ; Wed, 26 Sep 2001 17:30:41 +0300 Date: Wed, 26 Sep 2001 17:36:02 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <6771025.20010926173602@yahoo.com> To: CHEMISTRY@ccl.net Subject: semiempirical methods coparison MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CHEMISTRY, While reading article on application of semiempirical and ab initio calculations of heterocyclic compounds dated 1979, I find a reference to paper Clark D.T. Int.J.Sulf.Chem., 1972, Vol.C7, p.11. This paper was referred as "detailed and vivid overview of different techniques". Could anybody point me out more recent paper, which includes ZINDO/S or INDO/1S, PM3 and other methods developed _after_ 1972? I will summarize all informative answers. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Wed Sep 26 12:21:31 2001 Received: from alcides.host4u.net ([216.71.64.98]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8QGLV107539 for ; Wed, 26 Sep 2001 12:21:31 -0400 Received: from saturn.simbiosys.ca (cr808583-b.shprd1.on.wave.home.com [24.43.18.40]) by alcides.host4u.net (8.11.6/8.11.6) with ESMTP id f8QGFen01278 for ; Wed, 26 Sep 2001 11:15:40 -0500 Received: from simbiosys.ca (jupiter.simbiosys.ca [192.168.213.6]) by saturn.simbiosys.ca (Postfix) with ESMTP id E3DD91B1A for ; Wed, 26 Sep 2001 12:21:29 -0400 (EDT) Sender: aniko@simbiosys.ca Message-ID: <3BB20089.C4D80933@simbiosys.ca> Date: Wed, 26 Sep 2001 12:21:29 -0400 From: Aniko Simon Organization: SimBioSys Inc. X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-20mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: New version of SPROUT - de-novo design software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SimBioSys Inc. is pleased to announce the release of SPROUT version 4.0. This version provides great speed improvements by the use of distributed and parallel computing (SGI and Linux clusters) SPROUT is an effective tool for the design of drug-like, biologically active molecules. It is an interactive system that can assist in several stages of the structure-based rational drug design process. The system is modularized and offers automatic methods for solving a number of problems in drug design. Powerfully, the user maintains control and is able to guide and modify each module for maximum versatility. SPROUT is the only de novo ligand design tool guaranteed to find all solutions within the constraints defined by the input parameters. FUNCTIONS: * Detection of potential binding pockets. * Identification of favourable interaction regions for various forces, including: hydrogen bonding, hydrophobic, metal ion and covalent bonding interactions. * Docking of functional groups to the target sites. * Building novel chemical structures by fragment joining to fulfill the chemical and steric constraints of the binding site. * Scoring, sorting and clustering of the results. For further information please visit our website http://www.simbiosys.ca/ -- Aniko Simon, Ph.D. aniko@simbiosys.ca From chemistry-request@server.ccl.net Wed Sep 26 13:05:57 2001 Received: from oxygen.chem.nthu.edu.tw (postfix@[140.114.45.223]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8QH5u108412 for ; Wed, 26 Sep 2001 13:05:57 -0400 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 23B6C288FE; Thu, 27 Sep 2001 01:05:50 +0800 (CST) Date: Thu, 27 Sep 2001 01:05:50 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: Re: CCL:undefined fstat for G98 [SUMMARY] Message-ID: <20010927010550.A23668@OXYGEN.chem.nthu.edu.tw> References: <20010924050240.B21240@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20010924050240.B21240@OXYGEN.chem.nthu.edu.tw>; from chem@oxygen.chem.nthu.edu.tw on Mon, Sep 24, 2001 at 05:02:40AM +0800 My original question follows: On Mon, Sep 24, 2001 at 05:02:40AM +0800, chem@oxygen.chem.nthu.edu.tw wrote: > Dear CCLers > > While I tried to run G98 RevA.7 on Slackware Linux 8.0, the following > undefined message appears, > > g98: error while loading shared libraries: /tmp/pgig98/g98/util.so: undefined > symbol: fstat > > I suspect that this is due to the change to glibc-2.2.3 on Slackware > Linux 8.0. Does anyone have some idea to solve this problem? Thanks a lot > in advance. Thanks to Dr. Darko Basis for forwarding of a previous message. But for my case, there are two ways to solve the problem. 1. Not to use the blas-f2c.a library. The undefined 'fstat' was imposed from that library. This symbol should exist somewhere in the system library. But I guess Slackware 8.0 made some change about the fortran/g77, thus causing the missing of that reference while linking. If performance is considered, the ATLAS library is an alternative to the BLAS library. But pay attention to the release note of the ATLAS library before compiling it. Some Linux distributions need other gcc compiler than their default gcc. 2. Compile Gaussian on an older system (for me, Slackware 7.0) and transfer the binary to the new system. -- Jen-Shiang Kenny Yu // jsyu@Platinum.chem.nthu.edu.tw Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN