From chemistry-request@server.ccl.net Wed Mar 15 02:32:22 2000 Received: from mail.anrb.ru ([62.76.11.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA25901 for ; Wed, 15 Mar 2000 02:31:53 -0500 Received: from mail.anrb.ru ([62.76.11.199]) by mail.anrb.ru (8.9.3/8.9.3) with SMTP id MAA18356 for ; Wed, 15 Mar 2000 12:40:33 +0500 Date: Wed, 15 Mar 2000 12:36:44 +0500 From: "Ilfir R. Ramazanov" X-Mailer: The Bat! (v1.036) S/N 0 Reply-To: "Ilfir R. Ramazanov" Organization: Institute of Petrochemistry and Catalysis,Ufa,Russia Priority: Normal Message-ID: <13525.000315@anrb.ru> To: chemistry@ccl.net Subject: Mopac --> Spartan Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, I'm interested in a Mopac file conversion to Spartan. Is there any program to do it? Best regards, Ilfir R. Ramazanov, Ph.D., Laboratory of Catalytic Synthesis Institute of Petrochemistry and Catalysis, pr. Oktyabrya, 141, Ufa, 450075, Russia. mailto:elf@anrb.ru Visit my homepage and find some QC software http://members.tripod.com/~ChemELF Visit our lab web page http://organomet.cjb.net 15.03.2000 12:32 From chemistry-request@server.ccl.net Wed Mar 15 03:34:03 2000 Received: from oulu.fi (root@ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA26215 for ; Wed, 15 Mar 2000 03:34:02 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id KAA19809 for ; Wed, 15 Mar 2000 10:33:53 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id KAA17000576 for ; Wed, 15 Mar 2000 10:33:53 +0200 (EET) Date: Wed, 15 Mar 2000 10:33:52 +0200 From: Atte Sillanpaa X-Sender: asillanp@paju.oulu.fi To: chemistry@ccl.net Subject: free energy of activation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCLers, I'm trying to calculate the free energy of activation for a process where there is no minimum on the potential energy surface (PES). The (ethene polymerisation termination) reaction begins with a beta elimination from an alkyl group to the metal center. This forms a fairly unstable metal hydride and a hapto2-alkene. The PES for scanning the alkene away from the metal increases monotonically approaching the separated products value. The free energy of separated products is readily calculated, and is naturally much lower relative to PE. However, as the alkene recedes from the metal it gradually gains the translational and rotational degrees of freedom and its free energy drops, but there is a maximum at some point. The question is that if I calculate the free energy with the harmonic approximation at some (ambigious) constrained geometry (distance from the metal) is it of any approximate value for the free energy of activation? Is there some other method for calculating the free energy of activation in this kind of PES? Thanks for the bandwidth, and I will summarise, Atte atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 Oulun Yliopisto FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Wed Mar 15 06:19:13 2000 Received: from sirppi.helsinki.fi (salho@sirppi.helsinki.fi [128.214.205.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA26983 for ; Wed, 15 Mar 2000 06:19:12 -0500 Received: from localhost (salho@localhost) by sirppi.helsinki.fi (8.8.8-spammers-bug-off/8.8.0) with ESMTP id NAA02710 for ; Wed, 15 Mar 2000 13:19:01 +0200 (EET) X-Authentication-Warning: sirppi.helsinki.fi: salho owned process doing -bs Date: Wed, 15 Mar 2000 13:19:00 +0200 (EET) From: Susanna P Alho Sender: salho@cc.helsinki.fi To: chemistry@ccl.net Subject: units: hd Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Last week I asked a question about constraining torsions when docking a flixible ligand to protein using AutoDock 3.0. I haven't got any replies yet. (Unfortunately). Now I have another question about a unit symbol hd. I don't know what unit it is. I came across with it when I was trying to define an energy barrier in AutoDock using command 'barrier 10 000' and the output file told me that the energybarrier was set to 10000hd. What is this energy unit hd? I was looking for an explanation in the internet and I found out that it means hogshead, which is a volume unit. I don't think that's the case here. In addition to this issue, any kind of information about constraining torsion using AutoDock would probably help me in my research project (for pro graduation work). Thank you. Susanna Alho, Pharmacy student Department of Pharmaceutical Chemistry University of Helsinki, Finland e-mail: Susanna.Alho@helsinki.fi From chemistry-request@server.ccl.net Wed Mar 15 03:28:11 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA26176 for ; Wed, 15 Mar 2000 03:28:10 -0500 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id JAA03806; Wed, 15 Mar 2000 09:28:18 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14543.18850.682935.222573@yogi.pc1.uni-duesseldorf.de> Date: Wed, 15 Mar 2000 09:28:18 +0100 (CET) From: Jochen Küpper To: Huajun Fan Cc: CHEMISTRY@ccl.net Subject: CCL:call in Fortran code In-Reply-To: <38CEB5F3.EBB975B5@mail.chem.tamu.edu> References: <38CEB5F3.EBB975B5@mail.chem.tamu.edu> X-Mailer: VM 6.72 under 21.1 (patch 9) "Canyonlands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA26177 Huajun Fan writes: > I wonder if the fortran code can call a excutable file, instead of a > source code. If so, how can I do it? Any advice will be highly > appreciated. The completely non-portable solution I use is to call system from the C library ;-O ( `man system` :-) You can do this by providing a f77_system_ (or so) by yourself, or use cfortran.h, ... . Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.Jochen-Kuepper.de From chemistry-request@server.ccl.net Wed Mar 15 04:55:00 2000 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA26673 for ; Wed, 15 Mar 2000 04:54:43 -0500 From: scott.l.owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id JAA27018; Wed, 15 Mar 2000 09:54:58 GMT Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma026988; Wed, 15 Mar 00 09:54:51 GMT Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Wed, 15 Mar 2000 09:59:36 +0000 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA02438 for ; Wed, 15 Mar 2000 09:53:19 GMT Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002568A3.003658E4 ; Wed, 15 Mar 2000 09:53:37 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-Id: <002568A3.0035BEE9.00@BNotesMTA1.sell.bnfl.com> Date: Wed, 15 Mar 2000 09:53:52 +0000 Subject: Source code for MC with Ewald sum MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline I am trying to get hold of source code for performing Monte Carlo simulations on molecular/ionic periodic systems which includes an implementation of Ewald, if anyone has or knows of such a source code (in some flavour of C or FORTRAN) then could you get in touch with me. We need to be able to edit the routines to include some non-standard MC procedures. Thanks in anticipation. Will summarise if there are sufficient replies to warrant it! Scott Owens slo1@bnfl.com From chemistry-request@server.ccl.net Wed Mar 15 04:59:47 2000 Received: from shardagate.mahindrabt.com (root@[206.102.1.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA26694 for ; Wed, 15 Mar 2000 04:59:44 -0500 Received: (from uucp@localhost) by shardagate.mahindrabt.com (8.9.3/8.8.6) id RAA17769 for ; Wed, 15 Mar 2000 17:03:14 +0530 Received: from UNKNOWN(10.5.0.15), claiming to be "intranet.sharda.mahindrabt.com" via SMTP by shardagate, id smtpdAJIw6Z; Wed Mar 15 17:03:09 2000 Received: from mahindrabt.com ([10.5.2.39]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id PAA03183 for ; Wed, 15 Mar 2000 15:28:20 +0530 Message-ID: <38CF5EEC.27C4742D@mahindrabt.com> Date: Wed, 15 Mar 2000 15:29:08 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dreiding validation suite Content-Type: multipart/mixed; boundary="------------57AAD758BAD1A938E3C39B70" This is a multi-part message in MIME format. --------------57AAD758BAD1A938E3C39B70 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Can some one send me references, pointers for validation of Dreiding Force Field method by W. A. Goddard? Thanks in advance. Sudhir --------------57AAD758BAD1A938E3C39B70 Content-Type: text/x-vcard; charset=us-ascii; name="sudhirk.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Sudhir A. Kulkarni Content-Disposition: attachment; filename="sudhirk.vcf" begin:vcard n:Kulkarni;Dr. Sudhir A. tel;work:Mahindra British Telecom Limited x-mozilla-html:FALSE org:Mahindra British Telecom Limited adr:;;;;;; version:2.1 email;internet:sudhirk@MahindraBT.com x-mozilla-cpt:;27792 fn:Dr. Sudhir A. Kulkarni end:vcard --------------57AAD758BAD1A938E3C39B70-- From chemistry-request@server.ccl.net Wed Mar 15 06:10:24 2000 Received: from syntem.eerie.fr (syntem.site-eerie.ema.fr [146.19.248.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA26940 for ; Wed, 15 Mar 2000 06:10:22 -0500 Received: from syntem.eerie.fr (eva.eerie.fr [146.19.248.34]) by syntem.eerie.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA66929 for ; Wed, 15 Mar 2000 12:09:54 +0100 (MET) Sender: elie@syntem.eerie.fr Message-ID: <38CF6FA5.E76F7425@syntem.eerie.fr> Date: Wed, 15 Mar 2000 12:10:29 +0100 From: Elie Giraud Organization: syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: fr, en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Variable selection References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I'm looking for a recent review (after 1997) on variable selection in 2D and 3D QSAR. I will appreciate if someone can point me some papers or books that review such technics. Thanks in advance, Elie. Elie Giraud Synt:em Junior Research Scientist Parc Scientifique G.Besse Pharmaco Informatics 30000 Nimes email: egiraud@syntem.eerie.fr France Tel: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Discover New Drugs, Discover Synt:em http://www.syntem.com From chemistry-request@server.ccl.net Wed Mar 15 08:28:32 2000 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA28658 for ; Wed, 15 Mar 2000 08:28:31 -0500 Received: from pat.biochem.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Wed, 15 Mar 2000 13:27:51 +0000 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id NAA11685 for ; Wed, 15 Mar 2000 13:28:14 GMT Date: Wed, 15 Mar 2000 13:28:13 +0000 ("GMT) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: DOCK very repulsive van der Waals energies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Has anyone, working with DOCK4.0, encountered the problem that it is sometimes necessary to scale down the van der Waals contribution to the intermolecular energy, to get reasonable results? Is this mainly a problem of short distances between non-polar hydrogens and other atoms, and is there a way I can trace it? My other problem is that I remember reading about this scaling factor in a paper, which unfortunately I lost, and I have no information anymore on the authors, journal or title! If anyone knows what I'm talking about and has the reference I would appreciate it, if they could forward it to me. Many thanks in advance Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> Ignorance -of others- is bliss <<< From chemistry-request@server.ccl.net Wed Mar 15 11:25:25 2000 Received: from ecstasy.ksu.ru (ecstasy.ksu.ru [193.232.252.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA29535 for ; Wed, 15 Mar 2000 11:25:19 -0500 X-Pass-Through: Kazan State University network Received: from chem-50.ksu.ru (chem-50.ksu.ru [194.85.240.132]) by ecstasy.ksu.ru (8.9.3/8.9.3) with ESMTP id TAA09738; Wed, 15 Mar 2000 19:13:42 +0300 (MSK) Date: Wed, 15 Mar 2000 19:13:32 +0300 From: gshamov X-Mailer: The Bat! (v1.34a) UNREG / CD5BF9353B3B7091 Reply-To: gshamov Organization: ksu X-Priority: 3 (Normal) Message-ID: <4801.000315@ksu.ru> To: chemistry , Ulrike Salzner Subject: Re: CCL:linux In-reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Ulrike, Friday, March 10, 2000, 8:51:08 AM, you wrote: US> Hi Linux fans, US> I am experimenting with linux in Pentium computers. The main goal is US> using Gaussian. But I am running into various problems. I have installed US> Red Hat 6.1 on one computer and WinLinux on another. In both cases Linux US> does not seem to have a driver for my VGA card: S3 Trio 3D/2X. Has US> anybody found a driver for this card? There is no _drivers_ in linux at all. U need the X-server ! And old X-servers from Xfreee86 (3.3.4 or 3.3.3)shipped with RedHat doze not supporting your card. U must download new version of Xfree, 3.3.6 or greater, from http://www.xfree86.org/ and upgrade your system. Next, run XF86Setup and select X_SVGA server for your S3Trio3d/2x. US> WinLinux (from www.winlinux.net) boots with the above card but gives the US> error "PCI ..... at IRQ 0, which is unlikely to work". So I could not US> connect to the net. Next I tried a "cold boot" which is in the trouble US> shooting utility. This forces a configuration for an unkown card. US> Afterwards networking is possible but the display is very bad (uni color US> in netscape). If u know exactly, what network card u have, u should try to recompile linux kernel with related options enabled. US> Having reached this this point, I installed compilers and libraries for US> G98. Unfortunately "bldg98" is written for the C-shell and WinLinux comes US> only with "bash". I am afraid that rewriting the skripts will create US> problems without end. Therefore I would like to find out whether the US> C-shell can be added to WinLinux. There is tcsh shell in RedHat6.1 distribution, and i think tcsh must be in WinLinux too! U must just install it using rpm, gnorpm or something! Best regards, gshamov mailto:gshamov@ksu.ru From chemistry-request@server.ccl.net Wed Mar 15 09:57:21 2000 Received: from simulux.us.es (rafapa@simulux.us.es [150.214.145.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA29154 for ; Wed, 15 Mar 2000 09:57:15 -0500 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.9.3/Debian/GNU) with ESMTP id QAA01152; Wed, 15 Mar 2000 16:06:49 GMT Date: Wed, 15 Mar 2000 16:06:49 +0000 (/etc/localtime) From: Rafael Rodriguez Pappalardo To: scott.l.owens@bnfl.com cc: CHEMISTRY@ccl.net Subject: Re: CCL:Source code for MC with Ewald sum In-Reply-To: <002568A3.0035BEE9.00@BNotesMTA1.sell.bnfl.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 15 Mar 2000 scott.l.owens@bnfl.com wrote: > I am trying to get hold of source code for performing Monte Carlo > simulations on molecular/ionic periodic systems which includes an > implementation of Ewald, if anyone has or knows of such a source code (in > some flavour of C or FORTRAN) then could you get in touch with me. We need > to be able to edit the routines to include some non-standard MC procedures. > > Thanks in anticipation. Will summarise if there are sufficient replies to > warrant it! > > Scott Owens > slo1@bnfl.com > Check ftp://ftp.dl.ac.uk/ccp5/. There are several codes. Maybe some of them fullfill your requierements. Sincerely, Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es