From chemistry-request@server.ccl.net Mon May 29 23:54:18 2000 Received: from valiant.cnchost.com (valiant.concentric.net [207.155.252.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA03497 for ; Mon, 29 May 2000 23:54:17 -0400 Received: from CC911078A (cc911078-a.abdn1.md.home.com [24.9.150.137]) by valiant.cnchost.com id XAA15071; Mon, 29 May 2000 23:54:08 -0400 (EDT) [ConcentricHost SMTP Relay 1.8] Errors-To: Reply-To: From: "Dr. Guillermo A. Morales" To: "Elena Fioravanzo" , "ccl" Subject: RE: molecular diversity Date: Mon, 29 May 2000 23:54:10 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <023201bfc71d$22376d20$070000c0@CADD> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Importance: Normal These are other articles you might find useful: 1) "Measuring Molecular Diversity: Evaluation of Alternative Subsets Selected from Reagent Building Block Libraries for Combinatorial Chemistry." Blankley, C. J., Pharm. Pharmacol. Commun. 1998, 4, pages 139-146 2) "The Diversity Challenge in Combinatorial Chemistry." Kauvar, L. M. and Laborde, E., Drug Discovery and Development 1998, 1, pages 66-70 3) "Validated Descriptors for Diversity Measurements and Optimization." Martin, Y. C., Bures, M. G. and Brown, R. D., Pharm. Pharmacol. Commun. 1998, 4, pages 147-152 4) "Assesing Similarity and Diversity of Combinatorial Libraries by Spatial Autocorrelation Functions and Neural Networks." Sadowski, J., Wagener, M. and Gasteiger, J., Angew. Chem. Int. Ed. Engl. 1995, 34, pages 2674-2677 5) "Novel Software Tools for Addressing Chemical Diversity" R. S. Pearlman, Laboratory for Molecular Graphics and Theoretical Modeling, College of Pharmacy, University of Texas (From June/July, 1996). You can read this article on line at http://www.netsci.org/Science/Combichem/feature08.html 6) "Computational methods in molecular diversity and combinatorial chemistry." Bures, M.G., and Martin, Y.C., Curr. Opin. Chem. Biol. 1998, 2, pages 376-380 7) "Targeted molecular diversity in drug discovery: Integration of structure-based design and combinatorial chemistry." Li, J., Murray, C.W., Waszkowycz, B., and Young, S.C., Drug Discovery Today 1998, 3, pages 105-112 I hope this helps. Guillermo Morales ----- Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Elena Fioravanzo Sent: Friday, May 26, 2000 9:00 AM To: ccl Subject: CCL:molecular diversity Dear collegues, please excuse me if I send this message again, but I was asked to re-send it in text format (I did not notice the former one was in HTML format) to allow everybody to read it. Thanks again. Elena Hi, there are many methods and indices to estimate molecular similarity, but it is quite difficult to estimate-calculate molecular diversity. Could someone give me, please, references (articles, web-site, softwares) about this point? Thanks in advance, I will sumarize if someone is interested. Elena --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue May 30 01:08:41 2000 Received: from [209.193.72.3] (topaz.vcn.com [209.193.72.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA03843 for ; Tue, 30 May 2000 01:08:41 -0400 Received: from coffey.com (unverified [209.193.68.189]) by (Vircom SMTPRS 4.2.181) with ESMTP id for ; Mon, 29 May 2000 23:08:34 -0600 Message-ID: <39334DAC.A44C0EDF@coffey.com> Date: Mon, 29 May 2000 23:13:07 -0600 From: phil stortz Reply-To: pstortz@coffey.com Organization: THUB R/D To: chemistry@ccl.net Subject: software recomendations References: <000701bfc961$c5171c20$3b8506c1@chem.klte.hu> can anyone recommend a good package for modeling inorganic compounds/crystals and their band gaps? i'm interested in the visible and uv spectra, i.e. electronic spectra of inorganics, in their pure state and doped both as single crystals and pressed solids. i'm self learning inorganic chemistry after having some college. i'm very computer literate so i could probably use some of the open source programs if appropriate and would have no trouble compiling them etc. as i'm partially disabled on a fixed income cost is definitely an issue, although i could afford some of the lower cost commercial packages (<$1000). platform is not to much of an issue as i have access to pc's and mac, although i do prefer the mac. i'd also be very interested in the "legendary" atomic energy levels compilation by charlotter moore and the Nist tables mentioned by John Kerkines, if they applied to condensed states. i won't be making a purchase for several months. i've been lurking on this list for over a year and hope to eventually contribute. my previous experience is mostly with electronics and vacuum systems, i'd be more than happy to offer advice or design help to anyone who could help. thanks! -- Duckman and Cornfed in 2000! we already know ones a womanizer and the other's a pig, but at least they're both honest and one's smart. From chemistry-request@server.ccl.net Tue May 30 02:06:30 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA04198 for ; Tue, 30 May 2000 02:06:29 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id KAA04133 for ; Tue, 30 May 2000 10:06:25 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <39335A61.7367DE04@cacr.ioc.ac.ru> Date: Tue, 30 May 2000 10:06:25 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: Queueing System and Linux cluster Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCl members, We are going to create a cluster from Linux PC's for quantum chemistry calculations. The question arose what kind of Queueing System should be used. As I know, NQS and DQS are very popular queueing system, but may be some others as well. Of course, an ideal version should be easy to install, menage and use. Which system would be preferred for Linux based PC's ? Is the answer the same from users' and administrators' points of view? will be summarized, Valentin. ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Tue May 30 10:01:53 2000 Received: from mail2.organik.uni-erlangen.de (lesath.chemie.uni-erlangen.de [131.188.127.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07046 for ; Tue, 30 May 2000 10:01:42 -0400 Received: from wtewael.chemie.uni-erlangen.de (wtewael [131.188.127.223]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id QAA14344; Tue, 30 May 2000 16:01:18 +0200 (MET DST) Received: from localhost (wdi@localhost) by wtewael.chemie.uni-erlangen.de (8.8.7/8.1.59-FAU) with ESMTP id OAA18872; Tue, 30 May 2000 14:01:17 GMT X-Authentication-Warning: wtewael.chemie.uni-erlangen.de: wdi owned process doing -bs Date: Tue, 30 May 2000 16:01:17 +0200 From: Wolf-Dietrich Ihlenfeldt X-Sender: wdi@wtewael.chemie.uni-erlangen.de To: Keisuke Ishida cc: CCL Subject: Re: CCL:How to convert MDL's SD-file automatically. In-Reply-To: <000701bfc982$d364e700$7bce9ed2@taiho.co.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Ishida, I think I have the tools to perform this task. Can you tell me in more detail how in general a transformation should be controlled? How should the partial structure and their canges be identified? If you could please send me a sample SD file, a substructure (for example, as MDL query-molfile) and some description of the bond changes, I could easily set up a script for you. Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ On Tue, 30 May 2000, Keisuke Ishida wrote: > Hi, > I want to convert a partial structure in a SD-file that contains many > compounds > to other structure automatically. > For example, > 1. Search a partial structure in a SD-file. > 2. Convert a partial structure to other structure automatically. > (ex. cyclehexane ring ---> benzene ring) > Please tell me some idea or information. > Thanks. > > ************************************************** > Keisuke Ishida > Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd. > Hanno, Saitama, 357-8527 Japan > TEL. +81-429-72-8900 > FAX. +81-429-72-8913 > E-mail. ishida@taiho.co.jp > ************************************************** > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue May 30 10:44:02 2000 Received: from lithium.theochem.uni-duesseldorf.de (root@lithium.theochem.uni-duesseldorf.de [134.99.82.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07196 for ; Tue, 30 May 2000 10:37:11 -0400 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.8.7/8.8.8) with ESMTP id QAA27281; Tue, 30 May 2000 16:35:46 +0200 Received: from [[UNIX: localhost]] ([[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.8.7/8.8.8) id QAA05290; Tue, 30 May 2000 16:35:48 +0200 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: CHEMISTRY@ccl.net Subject: Hoover NPT relaxation times Date: Tue, 30 May 2000 16:07:46 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: wibke@theochem.uni-duesseldorf.de MIME-Version: 1.0 Message-Id: <00053016354700.05026@borussia> Content-Transfer-Encoding: 8bit Dear CCLers, could anybody give me advice how to choose the relaxation time constants for a Hoover thermostat/barostat in a NPT molecular dynamics simulation (rule of thumb, order of magnitude, ...)? Is the timestep somehow affected? I have read somewhere that the thermostat/barostat relaxation times should correspond to the smallest frequency in the choosen system. The system I am interested in is a partly flexible (torsion) organic molecule dissolved in small constraint solvent molecules. Thank you very much in advance for your help! Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany From chemistry-request@server.ccl.net Tue May 30 10:59:29 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07337 for ; Tue, 30 May 2000 10:59:28 -0400 Received: from iaf.uquebec.ca ([198.168.44.40]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 351 for ; Tue, 30 May 2000 10:55:54 -0400 Message-ID: <3933D96B.F375BC73@iaf.uquebec.ca> Date: Tue, 30 May 2000 11:08:27 -0400 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: Large loop+Binding site Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Last week, I asked a question about constructing a large loop (55 residues). It seems that it is a mission impossible if there is no suitable template. I would like to thank Professor Goldblum for his help. Please find my original question and the respond as follow. Sincerely, Jian Hui Wu *******Original question*************************** To model a large flexible loop in the protein modelling is risky. However, if the loop is found to involve with ligand binding (it happens!), then the key step is to get a good model of the loop. Moreover, the loop conformation usually will change on the binding of ligand. In my case, the loop contains about 55 residues. What is the state of the art in modelling this kind of loop? Do you know any successful case? I got several models of this large loop, most of them point away from the protein surface! Any suggestion will be greatly appreciated. *********Response********************************* Dear Jian Hui Wu, I am afraid that there can not be a very useful response at this moment to your question about loop construction, unless there is a way to use homology modelling and compare your loop sequence to a known structure to which it is homologous. Your loop size brings it really to the size of a small protein. Modelling de novo such a long loop coincides with protein folding, and no one has yet succeeded in such protein folding experiments over about 30-35 residues. We are at this moment developing a loop prediction algorithm, which may be useful for loops of 20-30 residues. This is a huge combinatorial problem if one wishes to determine all the main chain + side chain rotamers. There are some examples of such long loops in proteins, I can remember now the caspase inhibitor protein which has such a loop (three different solutions appear on the pdb file) which is, as you imply, close to the protein's surface. Sorry for not being more useful... Yours Sincerely, Amiram Goldblum Prof. of Medicinal Chemistry School of Pharmacy Hebrew University of Jerusalem, Israel 91120 Tel: 972-2-6758701 FAX: 972-2-6410740 email: amiram@vms.huji.ac.il ********************************************* E.O.F. From chemistry-request@server.ccl.net Tue May 30 03:49:04 2000 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA04696 for ; Tue, 30 May 2000 03:49:01 -0400 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id KAA09059; Tue, 30 May 2000 10:50:15 +0300 (EET DST) Date: Tue, 30 May 2000 10:50:58 +0300 (EET DST) From: Ulrike Salzner X-Sender: salzner@pinar To: Jim Kress cc: CCL , Gaussian Subject: Re: CCL:G98W and dual processors on NT In-Reply-To: <003701bfc9ba$f7aad010$0300a8c0@mindspring> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have similar problems with the memory on a PentiumIII single board PC with 512 Mb. This are 64 MW if I am not mistaken. I checked the largest -M- specification in the defoult route that works: 28 MW or 244 MB. Everything larger than that bombs. One job paused with the error message that "global memory recources have become low". Execution required 2,147,483,648 bytes, presently free were 1,858,035,712 bytes. According to this 1.77 GB memory were free but my computer has only 512 MB. Is it possible that there is a plain arithmetic mistake in the program that reads the default route and that we are asking for much more memory than we think we do? =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== On Mon, 29 May 2000, Jim Kress wrote: > On May 23 I asked the list about the "low memory" warning and significant > thrashing I get with Gaussian 98W on a dual processor NT machine. > > The responses I received are given below (I even got one from Gaussian!). > > I also did some testing on my computer. It appears that G98W exhibits > interesting behavior with NT (maybe all 32 bit) systems where the swap file > exceeds (approximately) 2200MB. > > I found the following: > > SFS = swap file size (MB) > -M- = -M- parameter in default.rou (MB) > LMW = Low memory warning > TH = thrashing > > SFS -M- Result > 2500 960 LMW and TH > 2500 250 no LMW > 2200 960 no LMW > > For SFS between 2200MB and 2500MB, G98W exhibits some very strange behavior. > For some SFS values (e.g 2250MB) when G98W is invoked it will respond with > an "Insufficient > free memory. Need 4 MB minimum" error message and then terminate. > > Also, as the SFS approaches 2200MB (from 2500MB) the difference between the > "memory needed" and "memory available" in the "Low Memory Warning" message > decreases. > > This behavior is reminiscent of some of the disk i/o observations in G98W > that result from the 32 bit integer word size. > > In addition, I have found that there is a significant interaction between > the -M- parameter in the default.rou file, the SFS, and cpu time necessary > to run the test case (qs.gjf). Here are some results (cpu time is in > seconds): > > SFS -M- cpu time > 2000 960 106 > 2000 96 10 > 1400 960 98 > 1400 240 17 > 1400 128 11 > 1400 ns 8 > > -M- of ns implies not specified in default.rou so used G98W default > established upon installation of the software (install program stated that > default.rou set up for machine with > 48 MB memory). Larger values of -M- > result in thrashing (SFS is fixed and larger than -M-). It appears the > memory management in G98W is unkind to jobs that are small relative to the > value of -M-. > > In any event, it appears that I've identified the source of the error > message. Take the information as you will. > > Thanks for the help from the people who responded! > > Jim > > Check out my web site http://www.kressworks.com/ > > > ----- Original Message ----- > From: Jim Kress > To: CCL > Sent: Tuesday, May 23, 2000 11:02 PM > Subject: CCL:G98W and dual processors on NT > > > > I am using G98W on a dual processor WinNT4.0SP5 machine with 1GB of RAM. > I > > do NOT specify MKL_NPROCS to be 2. > > > > However, when I run G98W, it pauses with a 'low memory' warning. It > states > > that I need 480MB of RAM to continue (which is the amount specified in the > > default.rou file) but that I have only (approx.) 231MB. If I allow it to > > proceed, it thrashes badly. If I specify a memory value of LE 256MB in > the > > default.rou file, the program runs normally with no warnings or thrashing. > > > > The problem is not resolved by specification of MKL_NPROCS to be 1 > > > > In all cases I am using the qs.gjf example from the C:\G98W\quick > > subdirectory. > > > > Anybody know what I need to do to get this to run properly with the larger > > default.rou memory specification? I've asked Gaussian but they have not > > replied ... > > > > Thanks and I will summarize. > > > > Jim > > > > Check out my web site http://www.kressworks.com/ > > > > > Response 1: > > I am not sure about G98W, but GAMESS would do that if the amount of the swap > space was low. It should be 2xRAM or more. With GAMESS I could run a job > with 720 MB RAM on a 768 MB machine with 2GB of swap space. > > Slawomir Janicki > janicki1@earthlink.net > > Response 2: > > Dr. Kress, > > We have attempted to model this on a Win2000 machine with 512MB and dual > processors using various sizes of virtual memory. With small virtual memory > settings, 128MB, we do see a loss of efficiency but never a 'low memory' > warning. Running with 750MB of virtual memory this seems to run fine with > a memory request of 400MB. > > What setting do you have in place for your virtual memory? > > -- > > Douglas J. Fox > Technical Support > Gaussian, Inc. > help@gaussian.com > > Response 3: > > Well, I don't know what is happening. Loosing cache coherency perhaps? You > would think that GAUSSIAN could make their software SMP friendly... > > Slawomir Janicki > janicki1@earthlink.net > > ----- Original Message ----- > From: "Jim Kress" > To: "Slawomir Z. Janicki" > Sent: Tuesday, May 23, 2000 11:12 PM > Subject: Re: G98W and dual processors on NT > > > > Thanks for the info. > > > > Actually, pcGAMESS is my preferred software. Unfortunately, pcGAMESS > > doesn't have DFT capabilities and that is why I'm using G98W. > > > > Also, it's not a matter of swap space. I have 2.5GB of swap to go with > the > > 1GB of RAM. I never had these problems with G98W until I put in the 2nd > > processor. > > > > Jim > > > > Check out my web site http://www.kressworks.com/ > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue May 30 08:56:44 2000 Received: from mail1.mclink.it (net128-007.mclink.it [195.110.128.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA06812 for ; Tue, 30 May 2000 08:56:42 -0400 Received: from Attila (net144-175.mclink.it [195.110.144.175]) by mail1.mclink.it (8.9.1/8.9.0) with SMTP id OAA03882; Tue, 30 May 2000 14:56:13 +0200 (CEST) Message-ID: <007601bfca36$dca50430$070000c0@CADD> From: "Elena Fioravanzo" To: "ccl" Cc: , , , , Subject: Summary: Molecular Diversity Date: Tue, 30 May 2000 14:46:19 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear CCL members, Please find my original question and replies. Thanks a lot to collegues who contributed. ================= there are many methods and indices to estimate molecular similarity, but it is quite difficult to estimate-calculate molecular diversity. Could someone give me, please, references (articles, web-site, softwares) about this point? ================= 1 >>>>>>>>>>>>>>>>> While by no means complete, here is a list that could get you started. 1. Van Drie, J. H., Lajiness, M. S. 1998. Approaches to virtual library design. DDT 3:274-83 2. Pearlman, R. S., Smith, K. M. 1998. Software for chemical diversity in the context of accelerated drug discovery. Drugs of the Future 23:885-95 3. Hassan, M., Bielawski, J. P., Hempel, J. C., Waldman, M. 1996. Optimization and visualization of molecular diversity of combinatorial libraries. Molecular Diversity 2:64-74 4. Jamois, E. A., Hassan, M., Waldman, M. 1999. Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets. J. Chem. Inf. Comput. Sci. 40:63-70 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 2 >>>>>>>>>>>>>>>>> Go to http://cisrg.shef.ac.uk and look under Recent Work for the program SELECT and accompanying references. Nick (lip97nej@sheffield.ac.uk) 3 >>>>>>>>>>>>>>>>> Molecular Diversity: http://www.phar.cam.ac.uk/DDG/ Try our site and my supervisor's new book "Molecular Diversity in Drug Design (1999)" Contact him P.M.Dean@ddg.phar.cam.ac.uk if and he might be able to help. Quantitaive approaches depend on small molecule or binding site diversity. Texts on QSAR might help. James Smith _________________________________________________________________________ James Smith Drug Design Group 01223 338 600 (College) St John's College Department of Pharmacology 01223 331 985 (Office) Cambridge University of Cambridge 01223 331 740 (Fax) CB2 1TP CB2 1QJ 07625 395 084 (Pager) United Kingdom United Kingdom js252@cam.ac.uk http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ 4 >>>>>>>>>>>>>>>>> I suggest you to contact Dr. Antonio Jerez, at UNED Madrid: ajerez@ccia.uned.es ***************** Julio César Llópiz Yurell IMRE, UH Zapata y G, Habana 10400, CUBA Tel (537) 781182 Fax (537) 334247 --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ From chemistry-request@server.ccl.net Tue May 30 12:28:41 2000 Received: from mail1.mclink.it (net128-007.mclink.it [195.110.128.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA08315 for ; Tue, 30 May 2000 12:28:40 -0400 Received: from Attila (net144-153.mclink.it [195.110.144.153]) by mail1.mclink.it (8.9.1/8.9.0) with SMTP id SAA05342; Tue, 30 May 2000 18:28:17 +0200 (CEST) Message-ID: <02fa01bfca54$7701e620$070000c0@CADD> From: "Elena Fioravanzo" To: "ccl" Subject: CCL:DNA protein complex minimization Date: Tue, 30 May 2000 17:08:52 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Dr. Song, we studied DNA and DNA adducts both with simple energy minimization and with molecular dynamics runs obtaining structures with an acceptable overlap with the experimental (x-ray structures) ones. Best results were achieved with MD. We employed AMBER force field (not the original one but the implementation of the software we used). Since the calculations were performed for the vacuum state, the following procedure were adopted to simulate the solvent effects: 1. a distance dependent dielectric of the form epsilon = 4R 2. a reduction of the charges on phosphate groups MM 500 cycles of Polak Ribiere Conjugate Gradient MD T = 300 K, time-step of 1 fs, SHAKE algorithm, equilibration run: 50 ps, MD run: 500 ps. Hope this may be heplful Elena On Mon, 22 May 2000, Haitao Ji wrote: > Hello everybody! > I have a problem with DNA protein complex minimization.I think it a challenge,because it is quite difficult to maintain the inter-strand H-Bonds > when relax all the complex.Can you give me some suggestions on the details ,such as forcefields,strategy and minimization procedure? > If I have to add some kind of constraints,can you tell me the exact parameters? > > Any information from you will be appreciated ! > > sincerely yours, > > yunlong song,PhD > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dept. of Medicinal Chemistry > College of pharmacy > Second military medical university > 325 Guohe Road, Shanghai 200433 > P. R. China > e-mail: songyunlong@263.net > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ From chemistry-request@server.ccl.net Tue May 30 11:46:54 2000 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA08045 for ; Tue, 30 May 2000 11:46:54 -0400 Received: (from mn1@localhost) by helix.nih.gov (8.9.3/8.9.3) id LAA9222558; Tue, 30 May 2000 11:46:40 -0400 (EDT) Date: Tue, 30 May 2000 11:46:40 -0400 From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: "M. Nicklaus" Subject: SUMMARY: UCITA In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear list members, Here's the summary of my question from 17 May 2000 regarding UCITA. It appears that no one (who responded) seems to be in favor of it. Marc ############################# Original Question ################################ > This is slightly off-topic since it doesn't concern computational chemistry > software exclusively. On the other hand, since it *does* potentially affect > buyers and users (at least in the U.S.) of *all* software, including > computational chemistry, I'd like to pose the question to this list. (I > apologize to those CCL members who are outside the U.S.; however, I believe > software users are facing similar issues in other countries as well.) > > > There has been an intense discussion in trade publications for months, and > recently also in the general press, about a new law proposal governing software > sales and licensing, the Uniform Computer Information Transaction Act (UCITA). > This draft model law is intended to be passed by the individual state > legislatures. I'll not go into the history, background and details of UCITA, > all of which can be read about on web sites such as http://www.4cite.org/. > > The general criticism I've seen voiced against UCITA is that it dramatically > shifts the balance of existing contract law in favor of software vendor. > Specific provisions that have been deemed particulary worrisome include the > right for software vendors to shut down mission critical software remotely > without court approval and without incurring liability; to permit software > vendors to avoid liability for damage caused by bugs known to the vendor, and > undisclosed to the licensee, when the software was bought; to allow software > vendors to prohibit public criticism of their product; to bind the purchaser to > licensing terms disclosed only after the purchaser pays for the software, and > allows the software vendor to change the terms unilaterally by e-mail; and > others. > > Such licensing terms were often part of license agreements in the past, but they > turned out to be rarely enforceable in court. Now, the critics say, UCITA would > sanction all this by law. > > I am not a legal expert, and I don't know how much the computational chemistry > software field would be affected by it. Since UCITA is about to become law in > Maryland, I'd like to ask the CCL members how they see UCITA affecting their > future software purchases, and how they plan to handle the situation: just > accept it; or try to renegotiate licensing contracts with software vendors; > contact their legislators; ignore the licensing terms; simply not buy > UCITA-governed software; only use open source and GPL'd programs; or...? ############################# Answers ################################ From: Anita Ilze Zvaigzne I am also against the UCITA for the very reasons that you had mentioned in the CCL posting. However, it seems to me that this law should not be able to survive judicial review, because of the vendors ability to unilaterally change the terms of the agreement after the purchase has been made. I am no legal expert, but it seems to me that this would violate the basic tenets of a contract. Please let me know if there is anything that I can do to assist in protesting and stopping the implementation of UCITA. Thanks. --- In my previous message, I forgot to say that I would probably boycott UCITA in the purchase of new software products -- where possible. If that failed, I would try to renegogiate a contract that would limit the vendor's ability to apply the more distressing portions of UCITA to shut down my research. ---------------------------------------------------------------------- From: Christoph Weber (Note: I am not speaking officially for my institute. However, I will definitely voice my opinion if and when such issues come up around here.) Remote shutdown: While this sounds scary and is clearly offensive, I think it will be largely a non issue for most companies in our field and many universities also. The reason is that most places have firewalls in place. In order to shut down software remotely, there needs to be a communication link from the software to the 'mothership'. I don't think we would knowingly allow such communication through our firewall, especially not if we don't know what the payload of such communication would be. Additionally, I expect that for large software purchases our purchasers and lawyers would try to introduce language to exclude such practices. Limited/nonexistent liability for known bugs: Again, I am pretty certain that for large software purchases, our purchasing staff would negotiate better terms. We have successfully dealt with vendors who knowingly mislead us. I don't think we would let up on this practice. Changing terms unilaterally: See above. Also, if such stuff becomes a trend, I expect uniform language being developed by our lawyers that protects us, and that we'd mostly or exclusively deal with vendors who agree to our terms. On the whole, I expect that UCITA won't harm us much. This doesn't mean, though, that UCITA is not a problem. In fact, it stinks. I think that the most problems will be with individual small purchases over the web or at PC retailers and such, where individual scientists expose themselves (unknowingly?) to bad contract terms and will most likely be bound by them. Likewise, we as private individuals will be hurt because we don't wield a lot of purchasing power individually. That basically means that computational chemistry software won't change much as a result of UCITA becoming law in some states. What will be most affected will be productivity software, utilities and perhaps desktop OSes. It will quickly become apparent who the black sheep are in the software industry, and I would expect that this would significantly hurt such vendor's sales figures. I also expect a further boost for PD and GPL'd code, if UCITA plays out as bad as some make it out to be. I have seen our scientists jump ship very quickly when prices were hiked up by a vendor. They are a very fickle bunch, and that's a good thing. Vendors will need to think about what a PR and bottomline disaster it could become if they decide to play tough with us. ---------------------------------------------------------------------- From: Jesus M. Castagnetto My take on UCITA is that is being pushed by big software vendors to cover their legal liabilities, not with the intention of helping them "innovate" or "make the next software of the future", as some of the proponents have said in other forums. Personally, I'll stick w/ Open Source software (GPL is but one of the several licenses available, see www.opensource.org), which in the long run tends to be more flexible and robust than closed source proprietary software. I like the philosophy of fixing bugs when you find them, and as Raymond said "given enough eyeballs, all busg are shallow" I see that all these legaleze arises from the mentality of looking who to blame for problems. A user (and in particular a company), should educate itself enough to make a rational decision on the software that he/she/it purchases. Most users look for the remedy of suing a software vendor instead of trying to work with it, or picking a more robust solution from the beginning. Of course, this a vicious circle, because makes the vendors defensive, so they are not too receptive to critics and are burdened by legal rules, so it takes them longer to fix a problem. Thus UCITA is the worse defensive response from them trying to get a legal fix, instead of doing the "right thing" (TM), and make robust software, and be open about bugs and their fixes. Software and information cannot be treated like real state, or other tangible posesions. Wrong perspective from the part of the vendors when they bent the legal system to try and do just that, and then avoid any responsability whatsoever. You can tell that I do not particularly like UCITA. ---------------------------------------------------------------------- Marc (As always, these are my personal views and not necessarily those of NIH) ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 402-2275 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------