From chemistry-request@server.ccl.net Thu Sep 16 00:19:09 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA00219 for ; Thu, 16 Sep 1999 00:19:09 -0400 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id AAA16142 for ; Thu, 16 Sep 1999 00:12:58 -0400 (EDT) Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id XAA13763 for ; Wed, 15 Sep 1999 23:13:00 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id XAA01520 for ; Wed, 15 Sep 1999 23:13:00 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Wed, 15 Sep 1999 23:13:00 -0500 (CDT) From: Jim Phillips To: chemistry@www.ccl.net Subject: ANNOUNCE: NAMD 2.1b1 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.1b1 Release Announcement | | | +--------------------------------------------------------------------+ September 15, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD 2.1b1 is more stable than NAMD 2.0 and adds several new features: - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. Mail any questions or comments to namd@ks.uiuc.edu. From chemistry-request@server.ccl.net Thu Sep 16 10:46:43 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03386 for ; Thu, 16 Sep 1999 10:46:43 -0400 Received: from ccshst01 (wtian@ccshst01.cs.uoguelph.ca [131.104.96.81] (may be forged)) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id KAA18841 for ; Thu, 16 Sep 1999 10:40:28 -0400 (EDT) Date: Thu, 16 Sep 1999 10:40:27 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: CHEMISTRY@ccl.net Subject: Additional information on NLO with DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Additional information of DFT on NLO: Dr. Bartlett had a talk on ACS national meetings this summer: DFT on NLO: failure or success? However, I don't know ACES has such subroutine to do NLO by DFT. Wei Quan From chemistry-request@server.ccl.net Thu Sep 16 12:41:05 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA03841 for ; Thu, 16 Sep 1999 12:41:05 -0400 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id MAA29606 for ; Thu, 16 Sep 1999 12:34:47 -0400 (EDT) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862567EE.005A8636 ; Thu, 16 Sep 1999 11:28:45 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: CHEMISTRY@www.ccl.net Message-ID: <862567EE.005A8093.00@unomail.unomaha.edu> Date: Thu, 16 Sep 1999 11:28:28 -0500 Subject: Summary; Experiments using MM Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline I only received one response to my original post (which is re-stated below). The book Ray mention is available at amazon.com for ca. $60. >Dear CCLers, > >In developing a molecular modeling course, I am looking for experiments that >will expand on molecular mechanics calculations into the biochemistry area. >Specifically, after two labs of introduction to force fields and the components >that determine energy, minimization, etc., I'd like to have a lab that displays >how molecular mechanics is used to predict guest/host interactions of a protein >or DNA sequence. We will be purchasing MacroMol as our primary molecular >mechanics package. What I am looking for are articles involving a simple >example of relatively large biomolecules and their interactions with each other. >Other possible topics could involve the following: >1) display of molecular dynamics, i.e. the conformations possible to a protein >at room temp and how one particular conformation may be responsible for >biological activity >2) intercalation of a molecule into the base stacking of DNA >3) the effects of amino acid sequence on the conformation of a protein >4) docking of a ligand into an active site. > >My use of molecular modeling is mainly quantum calculation on small organic >compounds, thus these topics are a bit foreign to me. Any J. Chem. Ed. articles >would be ideal. > >Thanks for your time, I be sure to summarize the responses. > >Douglas E. Stack >Assistant Professor >Department of Chemistry >University of Nebraska at Omaha >Omaha, NE 68182-0109 >(402) 554-3647 >(402) 544-3888 (fax) >destack@unomaha.edu > > Doug, Take a look at the book "Molecular Mechanics Across Chemistry", by Tony Rappe' and Carla Casewit, published by University Science Books. It has numerous examples from the literature of the kind of thing you describe, which easily could be turned into experiments for a modeling course. Ray Ray Fort Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine E-mail: rcfort@maine.maine.edu Orono, ME 04469 Web: oldblue.umeche.maine.edu/fort.html Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Wed Sep 15 17:27:27 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA31441 for ; Wed, 15 Sep 1999 17:27:27 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id RAA27567 for ; Wed, 15 Sep 1999 17:21:25 -0400 (EDT) Received: from pellan.CERCA.UMontreal.CA (pellan.CERCA.UMontreal.CA [132.204.150.49]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id RAA04020 for ; Wed, 15 Sep 1999 17:21:24 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id RAA06822 for chemistry@ccl.net; Wed, 15 Sep 1999 17:21:24 -0400 (EDT) Message-Id: <199909152121.RAA06822@pellan.CERCA.UMontreal.CA> Subject: HIV-1 PR and H2O To: chemistry@ccl.net Date: Wed, 15 Sep 1999 17:21:24 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers I wish to extend my thanks to those people who replied to my questions: 1) ab inito, 2) HIV-Pr However, it seems that the word "confuse" has a different meaning in French canadian as compared to English. I hope by using this terminology I did not brought some unfortunate interpretation with regards to landmark works. Soon there will be the 2nd International Conference on Protease Inhibitors: http://www.ufbi.ufl.edu/conferences/icpi Not Everyone will have the opportunity to attend this very important conference. HIV-Pr is a member of the aspartic proteinases family. Because it turned out that due to the low resolution the data for the HIV-PR crystal structure could not indicate the exact position of a possible water molecule bound to the Asp25/Asp25', I posted my question to the CCL. There are many theoretical studies which address the question where to place the water molecule within the catalytic site of aspartyl proteases, as for example the important work made by Beveridge and Heywood. Thus, in my opinion if we are looking for the exact position of this water molecule I interpret it as: there is no experimental evidence of where this particular water molecule is situated in the free enzyme. Why it is so important? because it is crucial for accurately describing the enzyme catalytic mechanism. Now I have touched the idea "catalytic mechanism". Again, I am confronted with various solutions: a GA/GB involving a water molecule, a direct nucleophilic attack without water molecule etc. On the other hand, there are HIV/inhibitor complexes with a water molecule close to the Asp25/Asp25' dyad and there are some without it. There is experimental evidence that the HIV-1/PR Asp25/Asp25' dyad may be monoprotonated, diprotonated or unprotonated depending on the inhibitor complexed with the enzyme. What I would really like to know is the following; Is there any experimental evidence that show unconditionnally that a water molecule is bound to the Asp25/Asp25' dyad in the FREE enzyme (HIV-PR). If no, is it possible that the low resolution of the data may represent another type of ion say (NH4+, etc.) Sincerely, Suzanne Sirois From chemistry-request@server.ccl.net Wed Sep 15 20:21:16 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA32025 for ; Wed, 15 Sep 1999 20:21:16 -0400 Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id UAA13264 for ; Wed, 15 Sep 1999 20:15:08 -0400 (EDT) Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by alchemy.yonsei.ac.kr (8.8.8H2/8.8.8) with ESMTP id JAA24450; Thu, 16 Sep 1999 09:14:14 +0900 (KST) Date: Thu, 16 Sep 1999 09:14:14 +0900 (KST) From: Kim Hanjo To: "Fulton CR (Charles)" cc: "'CCL'" Subject: Re: CCL:chemisty on linux In-Reply-To: <47F7EAA0389AD011840500805FEAB9C60376E27F@sctms01.sct.ucarb.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, SAL(Scientific Applications on Linux) homepage. http://bioinfo.kaist.ac.kr/sal This is the mirror page in Korea. I don't know any other mirrors, but this page might have links of many mirrors. +-----+ Kim Hanjo +----------------------------------------+ | ------------- | | Ph.D candidate student | | Bioorganic & Medicinal Chemistry Lab. | | Department of Chemistry | | Yonsei University, Seoul 120-749, Korea | | ================================================ | | E-mail : lordmiss@alchemy.yonsei.ac.kr | | artemia@nownuri.net | | PCS : 016-720-2691 | | Fax : 82-2-364-7050 | +----------------------------------------------------------+ From chemistry-request@server.ccl.net Wed Sep 15 23:33:33 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA00046 for ; Wed, 15 Sep 1999 23:33:33 -0400 Received: from spdmraaa.compuserve.com (ds-img-rel-1.compuserve.com [149.174.206.140]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id XAA15300 for ; Wed, 15 Sep 1999 23:27:23 -0400 (EDT) Received: (from mailgate@localhost) by spdmraaa.compuserve.com (8.9.3/8.9.3/SUN-REL-1.0) id XAA07790 for chemistry@www.ccl.net; Wed, 15 Sep 1999 23:26:56 -0400 (EDT) Sender: tony@acdlabs.com Received: from noteb-tony.acdlabs.com (ppp02.acdlabs.com [207.176.233.42]) by spdmraaa.compuserve.com (8.9.3/8.9.3/SUN-REL-1.0) with SMTP id XAA07761; Wed, 15 Sep 1999 23:26:48 -0400 (EDT) Message-Id: <3.0.6.32.19990915185912.007d6100@mail.acdlabs.com> X-Sender: tony@mail.acdlabs.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 15 Sep 1999 18:59:12 -0700 To: tony@acdlabs.com From: Tony Williams Subject: Advanced Chemistry Development Scientific Scholar of the Year Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Advanced Chemistry Development Scientific Scholar of the Year Award Advanced Chemistry Development proudly announces our Scientific Scholar of the Year Award. In our venture to further support academia we now offer the opportunity to all scientific students to participate in our award system. In order to enter the competition we request that any student from the fields of Chemistry or BioChemistry send us a short report (maximum 5 pages) of a particular research study or lab work that they have been involved with in 1999. This can include synthesis, spectroscopy, analytical measurements, theoretical or method development. The report should be submitted to us in Word RTF format and should include all structure drawings and lab sketches in the document. The one caveat of the competition is that all structures should have been drawn with ACD/ChemSketch, either the Free version available from http://www.acdlabs.com/download/chemsk.html or the commercial version. The first prize winner will win $500 for themselves, a copy of ACD/ChemFolder, an ACD T-shirt and a site licence of Chemsketch for their academic facility. They will also be identified as the Advanced Chemistry DEvelopment scholar of the Year, a valuable addition to any resume. The second prize winner will win $250 for themselves, a copy of ChemFolder and an ACD T-shirt The third prize winner will win $100 for themselves, a copy of Chemsketch and an ACD T-shirt. All notable entries and winners will be posted to the ACD website Encourage fellow students and colleagues to participate. Entries should be sent to info@acdlabs.com by February for announcement at the Spring 2000 ACS. Good luck! From chemistry-request@server.ccl.net Thu Sep 16 10:30:35 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03303 for ; Thu, 16 Sep 1999 10:30:35 -0400 Received: from ccshst01 (wtian@ccshst01.cs.uoguelph.ca [131.104.96.81] (may be forged)) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id KAA15840 for ; Thu, 16 Sep 1999 10:24:21 -0400 (EDT) Date: Thu, 16 Sep 1999 10:24:21 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: chemistry@ccl.net Subject: DFT on NLO Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all: I have a question on DFT with NLO (Non-linear optical coefficient or frequency-dependent polarizablity and hyperpolarizability): I learn that there are several programs dealing nol-linear optical coefficient by conventional ab initio methods (HF, MP2, CC), for example, Gaussian (Static NLO, i.e. polarizablity), ACES and so on. Also I know ADF (Amsterdam Density Functional) can calculate such properties. Could anyone tell me there is any other program handling NLO or anyone is trying to inplement such subprogram on any DFT program? Thanks for any information! I will make summary if anyone interested. Wei Quan From chemistry-request@server.ccl.net Thu Sep 16 15:08:10 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04817 for ; Thu, 16 Sep 1999 15:08:10 -0400 Received: from tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id PAA25864 for ; Thu, 16 Sep 1999 15:01:52 -0400 Sender: richard@tc.cornell.edu Message-ID: <37E13EA1.4B6B9DD9@tc.cornell.edu> Date: Thu, 16 Sep 1999 15:01:53 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Urey-Bradley terms for Discover? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit One of our users is using Discover to simulate liquid benzene. The normal modes calculated from the default cvff assignment are evidently not good enough for their purposes and they would like to add Urey-Bradley 1-3 terms. Although these terms don't seem to be available in cvff, it seems like it should be possible to add harmonic restraints to get the same result. Has anyone tried this trick? Is it a reasonable thing to do? Thanks Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Thu Sep 16 23:16:48 1999 Received: from chu.Chem.nthu.edu.tw (Chu.Chem.nthu.edu.tw [140.114.45.233]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA07176 for ; Thu, 16 Sep 1999 23:16:46 -0400 Received: by chu.Chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA15098; Fri, 17 Sep 1999 10:32:49 +0800 From: hyl@chu.Chem.nthu.edu.tw (Hsin-Yi Liow) Message-Id: <9909170232.AA15098@chu.Chem.nthu.edu.tw> Subject: ccsd(t) To: chemistry@server.ccl.net Date: Fri, 17 Sep 1999 10:32:49 +0800 (TAIST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear CCL Netters, I was encounter a problem when doing geometry optimization using ccsd(t) method in Gaussian 98. The output said "UNABLE TO DETERMINE LAMDA IN FmD114" How can I do to solve this problem? Any reply will be appreciated. Thank you very much in advance! Han-Yen Lee hyl@chu1.chem.nthu.edu.tw