From chemistry-request@server.ccl.net Mon Aug 5 10:05:08 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g75E58l01743 for ; Mon, 5 Aug 2002 10:05:08 -0400 Received: from attglobal.net (slip-32-101-203-209.in.us.prserv.net[32.101.203.209]) by prserv.net (out4) with SMTP id <20020805140507204040fkm6e>; Mon, 5 Aug 2002 14:05:08 +0000 Message-ID: <3D4E40BB.5CF98653@attglobal.net> Date: Mon, 05 Aug 2002 09:09:15 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PIMM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Can anyone point me to a source for Lindner's PIMM code? The contactb e-mail address from the PIMM webpage seems to be nolonger valid. Thanks ! John McKelvey From chemistry-request@server.ccl.net Mon Aug 5 06:43:02 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g75Ah2l27453 for ; Mon, 5 Aug 2002 06:43:02 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g75AQoh13823 for ; Mon, 5 Aug 2002 12:26:50 +0200 Message-ID: <3D4E56B5.6070507@pharma.u-strasbg.fr> Date: Mon, 05 Aug 2002 12:43:01 +0200 From: Antoine Logean Reply-To: alogean@aspirine.u-strasbg.fr Organization: CNRS - ULP - ETHZ User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr-FR; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: fr-fr, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: molecular similarity Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all, Imagine a chemist come to you ( you, the strange person who does strange things with computers ! - the organic chemists have really a primitive view of our work ! any way it is an other story ) with two molecules on a paper and he want to know the "similarity" between the two molecules (for which we have no idea of the receptor 3D structure). Imagine you do not want to investigate more as 10 hours (a day) to the thing. What would you do ? Until know I just build the two 3D molecular models (20 minutes). So I have still 9 hours and 40 minutes for the thing. (minus 10 minutes for this mail). What can I do ? I plan to : 1) first fit the two molecules (two glycolypids). If this task until now was trivial (I mainly work with protein) I realize that for two organic compounds with not necessary the same scaffold, it is not an easy job ! I will use FlexS. But I would prefer to use a free program. Do you have any suggestions ? (most programs I know are good to handle proteins but not organic compounds.) 2) after fitting I will measure : the polar and apolar surface, the solvation energy, the number of H donnor/acceptor and the molecular volume. Perhaps if I have time I will make a dynamic with Amber to have an idea of the "rigidity" of the two molecules. I am sure that "old dinosaurs" in the modeling field can give me good hints in order to spend 10 hours and not 10 days on a project that has 1 chance over 1000 to be realized. Thank you Antoine From chemistry-request@server.ccl.net Mon Aug 5 07:50:37 2002 Received: from relay2.uni-heidelberg.de ([129.206.210.211]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g75Bobl29434 for ; Mon, 5 Aug 2002 07:50:37 -0400 Received: from ix.urz.uni-heidelberg.de (mail.urz.uni-heidelberg.de [129.206.119.234]) by relay2.uni-heidelberg.de (8.12.4/8.12.4) with ESMTP id g75BoL2T003570 for ; Mon, 5 Aug 2002 13:50:21 +0200 (MET DST) Received: from aixterm6.urz.uni-heidelberg.de (ft7@aixterm6.urz.uni-heidelberg.de [129.206.119.46]) by ix.urz.uni-heidelberg.de (8.8.8/8.8.8) with ESMTP id NAA20140 for ; Mon, 5 Aug 2002 13:50:21 +0200 Received: (from ft7@localhost) by aixterm6.urz.uni-heidelberg.de (AIX4.2/UCB 8.7/8.7) id NAA27192; Mon, 5 Aug 2002 13:50:18 +0200 (METDST) Date: Mon, 5 Aug 2002 13:50:18 +0200 (METDST) From: Rainer Remenyi X-X-Sender: ft7@aixterm6.urz.uni-heidelberg.de To: chemistry@ccl.net Subject: CCL: Force Field development, DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am doing force field developement by exploring DFT Potential Energy Surfaces and I got the following comment on this: "No one DFT method is capable of simultaneously reproducing energies and geometries." Any comments, references etc. are interesting for me. I will give a summary, of course. Best Regards, Rainer Remenyi Anorganisch-Chemisches Institut Im Neuenheimer Feld 270 69120 Heidelberg Germany phone ++ 49 6221 54 8653 fax ++ 49 6221 54 6617 From chemistry-request@server.ccl.net Sun Aug 4 23:13:55 2002 Received: from gordon.chem.wayne.edu ([141.217.26.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g753Dsl29732 for ; Sun, 4 Aug 2002 23:13:54 -0400 Received: from localhost (tyan@localhost) by gordon.chem.wayne.edu (8.10.2+Sun/8.10.2) with ESMTP id g753Dp414190 for ; Sun, 4 Aug 2002 23:13:51 -0400 (EDT) Date: Sun, 4 Aug 2002 23:13:51 -0400 (EDT) From: Tianying Yan To: chemistry@ccl.net Subject: Questions of MOPAC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Deal cclers, I am a Ph.D. student in computational chemistry and am new in using semi-empirical package MOPAC version 7.0. Here I have several questions and hopefully get help from experts like you: 1. In MOPAC7.0, is there a rigid scan method, just doing the same work as the 'scan' keywork in Gaussian 9x, for scanning the PES of A + B interactions? or is there any other alternative way to do it? It is too tedious to change the input .dat file every time for every single point calculations. 2. If I want to evaluate A + B vdW interaction at certain A-B distant as well as configuration using MOPAC7.0, is the following equation correct? E(A-B vdW) = Escf(A-B) - Escf(A) - Escf(B) Also, is there any correction to account for basis set superposition error (BSSE) in MOPAC 7.0? 3. If I want to use MOPAC to evaluate reaction energy, A + B -> C + D, is the following equation correct? Reaction Energy = Escf(C) + Escf(D) - Escf(A) - Escf(B) + ZPE(C) + ZPE(D) - ZPE(A) - ZPE(B) 4. As indicated in MOPAC 7.0 Manual, "Escf (defined as Heat of formation), force constants and normal mode vibrations are all related to the values at 25 degree C." (cited directly from the Manual), the above values in Q.2 and Q.3 (supposed it is correct) are related to 25 degree C. Here comes another question, is there any convienent way to convert them to 0 or any other degree in Kelvin? In above questions, I implicitly consider using PM3 method, while I believe these questions can be also applied to other semi-empirical methods (MNDO, MINDO/3 and AM1) included in MOPAC7.0. Any suggestion will be much more than welcome! Regards, Tianying Tianying Yan Institute for scientific computing Department of Chemistry Wayne State University Detroit, MI 48202