From chemistry-request@server.ccl.net Mon Sep 24 09:27:57 2001 Received: from gatekeeper2.novartis.com ([194.191.169.74]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8ODRq100942 for ; Mon, 24 Sep 2001 09:27:55 -0400 Received: from mta3.is.chbs (mta3.novartis.com [192.37.33.14]) by gatekeeper2.novartis.com (8.11.0/8.11.0) with ESMTP id f8ODRfZ28941 for ; Mon, 24 Sep 2001 15:27:42 +0200 (MET DST) Received: from NVCHBS-S0121.is.chbs (nvchbs-s0121.is.chbs [192.37.33.41]) by mta3.is.chbs (8.11.0/8.11.0) with ESMTP id f8ODQHF00805 for ; Mon, 24 Sep 2001 15:26:17 +0200 (MET DST) Subject: covalent bond lenghts To: chemistry@ccl.net From: maria.brandl@pharma.novartis.com Date: Mon, 24 Sep 2001 15:27:25 +0200 Message-ID: X-MIMETrack: Serialize by Router on CHBSMN12/N1/Novartis(Release 5.0.8 |June 18, 2001) at 09/24/2001 03:27:40 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Dear CCL - folks, does anybody know where to get comprehensive tabulated information on standard geometries (bond lengths, angles) of chemical groups ? Cheers, Maria From chemistry-request@server.ccl.net Mon Sep 24 05:54:25 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 f8O9sO129570 for ; Mon, 24 Sep 2001 05:54:25 -0400 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 4BFF4218EC; Mon, 24 Sep 2001 17:54:23 +0800 (CST) Date: Mon, 24 Sep 2001 17:54:23 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Cc: chem@oxygen.chem.nthu.edu.tw Subject: Re: CCL:undefined fstat for G98 Message-ID: <20010924175423.A25622@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: ; from dbabic@rudjer.irb.hr on Mon, Sep 24, 2001 at 11:24:02AM +0200 The opinion from Dr. Doug Fox is correct. fstat is supposed to reside in /lib/ld-linux.so.2, which is symbolic link to /lib/ld-2.x.x.so. For me, the older system (Slackware 7.0) uses glibc-2.1.2, so I can find fstat in ld-2.1.2.so using the "nm -s" command. However, for Slackware 8.0 which utilizes glibc-2.2.3, fstat no longer resides in ld-2.2.3.so. The replacement I suspect in the new shared lib is fstat64, which supports long file (>2GB). But installing an older share library on the system cannot solve the problem. It may survive Gaussian 98, but on the contrary it will make other programs which reference the newer share library fail with undefined reference. IMHO, we need some way else to resolve this because I believe any updated releases of Linux distributions will go for the new glibc. -- Jen-Shiang Kenny Yu // jsyu@Platinum.chem.nthu.edu.tw Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN > Hi, Dear Listers, > > Several days ago, I posted a qustion about g98 on Redhat 7.1: > > > I compile g98 on Redhat 7.1 with pgf77 version 3.1 and get following > warnings: > util.so: the use of `tmpnam' is dangerous, better use `mkstemp' > /home/scratch/test/pgi/linux86/lib/libpgftnrtl.a(cnfg.o): In function > `__fio_scratch_name': > cnfg.o(.text+0x33): the use of `tempnam' is dangerous, better use `mkstemp'. > > The compilation finished anyway, but when I ran g98, > following error appeared: > > g98: error while loading shared libraries: /home/scratch/test/g98/util.so: > undefined symbol: fstat > Nothing appeared in output file at all. > > > > I received several warm replies from Dr. Doug Fox, Dr. Darko Babic, > > > From Dr. Doug Fox: > > fstat is a standard system utility and should be resolved out of runtime > libraries provided with RedHat. This error suggests RedHat has either > a) made very substantial changes to the structure of these libraries or > b) you omitted some of the runtime library packages when you installed > Linux. > > This lives in libc on my 6.2 machine so check to see if you have an > older version of libc you can install. From chemistry-request@server.ccl.net Mon Sep 24 11:00:51 2001 Received: from mail.virginia.edu ([128.143.2.9]) by server.ccl.net (8.11.2/8.11.0) with SMTP id f8OF0o103843 for ; Mon, 24 Sep 2001 11:00:50 -0400 Received: from unix.mail.virginia.edu by mail.virginia.edu id aa20085; 24 Sep 2001 11:00 EDT Received: from patch2 (d-128-44-24.bootp.Virginia.EDU [128.143.44.24]) by unix.mail.Virginia.EDU (8.9.3/8.9.3) with SMTP id LAA78432 for ; Mon, 24 Sep 2001 11:00:46 -0400 Message-Id: <3.0.6.32.20010924110702.00a7b4c0@unix.mail.virginia.edu> X-Sender: ps2t@unix.mail.virginia.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 24 Sep 2001 11:07:02 -0400 To: chemistry@ccl.net From: Pornthep Sompornpisut Subject: Q:Molecular visualization software for Pocket PC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleage, Does anyone know if there is any molecular modeling software that can run on Pocket PC or Handheld PDA? Thep ======================================================================= Pornthep Sompornpisut, Ph.D Postdoctoral Fellow Molecular Physiology & Biological Physics Department School of Medicine University of Virginia Tel: 804-924-5473 Fax: 804-982-1616 Email:ps2t@virginia.edu ======================================================================= From chemistry-request@server.ccl.net Mon Sep 24 14:54:44 2001 Received: from unq.edu.ar ([200.49.110.238]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8OIqk111531 for ; Mon, 24 Sep 2001 14:54:42 -0400 Received: from pii400win95.unq.edu.ar [200.49.110.145] by unq.edu.ar [200.49.110.238] with SMTP (MDaemon.PRO.v4.0.0.R) for ; Mon, 24 Sep 2001 15:49:03 -0300 Message-Id: <5.1.0.14.0.20010924153719.00a2a5e0@mail.unq.edu.ar> X-Sender: mlema@mail.unq.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 24 Sep 2001 15:42:28 -0300 To: chemistry@ccl.net From: =?iso-8859-1?Q?Mart=EDn?= Lema Subject: Temperature trouble Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-MDRemoteIP: 200.49.110.145 X-Return-Path: mlema@unq.edu.ar X-MDaemon-Deliver-To: chemistry@ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8OIsi111582 Dear CCLs: In my MD simulations, I start heating up the system using Berendsenīs algorithm and when it reaches 300 K I switch to Andersenīs. The thing is the average temperature of the system then stabilizes around 294 K. The system is a myoglobin of 2134 atoms (including hydrogens), implicitly solvated using the SASA algorithm and using the CHARMM27 parameter set. I have tried different collision frequencies for the thermostat, longer times, longer cutoffs, etc, but I canīt find the origin of this discrepancy. Collision values of 0 (which means no application of the thermostat) and 166 (which means velocity is reassigned for every atom in every step) renders the system at 300 K, but it is not the case for more reasonable values in the range 0.02 - 5. The trouble persist when performing the simulation in vacuo or using other solvation algorithms. Does someone figures out where the trouble is? clues are welcome at mlema@unq.edu.ar. Useful responses will be summarized. Martin Lema National University of Quilmes Argentina .