From chemistry-request@server.ccl.net Fri Dec 17 01:50:10 1999 Received: from eeyore.chem-eng.nwu.edu (eeyore.chem-eng.nwu.edu [129.105.205.150]) by server.ccl.net (8.8.7/8.8.7) with SMTP id BAA02051 for ; Fri, 17 Dec 1999 01:50:10 -0500 Received: (qmail 16241 invoked by uid 1119); 17 Dec 1999 05:46:07 -0000 Message-ID: <19991217054607.16234.qmail@eeyore.chem-eng.nwu.edu> Date: 16 Dec 1999 23:46:07 -0600 To: chemistry@ccl.net Subject: How to increase max number of geometry optimization steps in G98? X-Mailer: nmh 1.0 / exmh 2.0.2 X-URL: http://winnie.chem-eng.nwu.edu/~scott/ From: Scott McMillan Reply-To: Scott McMillan Date: Thu, 16 Dec 1999 23:46:07 -0600 Sender: scott@eeyore.chem-eng.nwu.edu Hello, I'm performing pm3 geometry optimizations in Gaussian 98 on systems with some atoms fixed at their cartesian position. I'm using the keyword opt=z-matrix to fix these atoms. Some of my calculations do not have enough geometry iterations to complete. From the G98 manual, it appears that setting iop(1/6=N) should set the maximum number of geometry optimizations to N. However, G98 seems to have some other maximum setting as well. The manual also suggests that opt(maxcycle=M) would have a similar effect as iop(1/6), but it appears to do nothing. For example, from my output: Number of steps in this run= N maximum allowed number of steps= 204. I can set N to any value less than or equal to 204 with iop(1/6), but not larger. How do I increase the second value above 204? The 204 value depends on the system (# degrees of freedom); there's nothing special about that particular number. I know I can save the checkpoint file and then keep restarting the calculation, but I'm looking for a solution that won't require this level of manual intervention. Thanks, Scott -- Scott McMillan - smcmilla@nwu.edu - http://winnie.chem-eng.nwu.edu/~scott/ Institute for Environmental Catalysis Department of Chemical Engineering Northwestern University From chemistry-request@server.ccl.net Thu Dec 16 17:14:44 1999 Received: from watson.bcm.tmc.edu (bcm.tmc.edu [128.249.2.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA31182 for ; Thu, 16 Dec 1999 17:14:44 -0500 Received: from bcm.tmc.edu (njing.phys.bcm.tmc.edu [128.249.82.231]) by watson.bcm.tmc.edu (8.8.8/8.8.8) with ESMTP id PAA15890 for ; Thu, 16 Dec 1999 15:03:34 -0600 (CST) Sender: jliu@bcm.tmc.edu Message-ID: <3858F127.D4DB782E@bcm.tmc.edu> Date: Thu, 16 Dec 1999 15:03:19 +0100 From: Jie Liu To: chemistry@ccl.net Subject: a question about AutoDoc/Insight II Dear CCLers: I want to do some work by using AutoDock program. It need to creare the PDBQS file in SYBYL. But in our lab, we only have insighII/98.0. Thus how can I use AutoDock combined with insightII? Must only "KOLLUA"partical charges be assigned to the protein? May I chose other kind of partical charges? Thanks for answer my question. Merry Christmas to everyone. Jie Liu -- Jie Liu, Ph.D. Department of Molecular Physiology and Biophysics Baylor College of Medicine Houston, TX 77030 From chemistry-request@server.ccl.net Fri Dec 17 03:19:29 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 DAA02392; Fri, 17 Dec 1999 03:19:29 -0500 Received: from bedrock.ccl.net (bedrock.ccl.net [192.148.249.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id CAA16812; Fri, 17 Dec 1999 02:15:23 -0500 (EST) Date: Fri, 17 Dec 1999 02:15:24 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: All the best to CCL members from the CCL maintainers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Have a lot of fun during this Holiday season. Get some rest... Do not drink and drive... Enjoy your family... And all the best in the coming year. Jan Labanowski, and the CCL Team. ------------------------------------------------------------------------------- + ! XXX ! XXXXX ! XXXXXXX ! XXXXXXXXX ! "BOAS FESTAS" ! "JOYEUX NOEL" \ / * ! "VESELE VANOCE" --O-- XXX ! "MELE KALIKIMAKE" / \ "HOME" ! "NODLAG SONA DHUIT" "PEACE." ! "BLWYDDYN NEWYDD DDA" "BON NADAL." ! "GOD JUL" "BOLDOG UJ EVET" ! "BUON ANNO" \ / "CHANUKAH SAMEACH" ! \ / "FELIZ NATAL" --O-- "DOSIEGO!" ! --O-- "FELIZ NAVIDAD" / \ "HAPPY HANUKKAH" ! / \ "KALA CHRISTOUGENA" "PARI ARTSAGOURT" ! "VROLIJK KERSTFEEST" "KELLEMES UNNEPEKET" ! "FROEHLICHE WEIHNACHTEN" "NAYA VARSH SHUBH HO" ! "BUON NATALE-GODT NYTAR" "ATHBHLIAIN FAOI MHAISE ! "HUAN YING SHENG TAN CHIEH" "IYI YILLAR-HYVAEAE LOMAA ! "WESOLYCH SWIAT-SRETAN BOZIC" \ / "NA ZDOROVE" ! "MOADIM LESIMHA-LINKSMU KALEDU" --O-- "MERRY CHRISTMAS" ! "HAUSKAA JOULUA-AID SAID MOUBARK" / \ "FELICHAN JARFINON" ! "'N PRETTIG KERSTMIS" "#-SHUB NAYA BARAS-@" ! "ONNELLISTA UUTTA VUOTTA" ! "INPAKARAMAANA VIDUMURAI! "Z ROZHDESTYOM KHRYSTOVYM" >+< "STASTNY NOVY ROK-CHEERS!! "NADOLIG LLAWEN-GOTT NYTTSAR" ! "CHING CHI SHEN TAN-@@@@@!! "CRACIUN FERICIT-GOJAN KRISTNASKON" *** **!! ! "S NOVYM GODOM-FELIZ ANO NUEVO" .-'-. mmmmmm !!!! ! "GLEDILEG JOL-NOELINIZ KUTLU OLSUM" .-' .-. '-.! ! xxxx ! "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC" .-' .-' '-. '-.! . ! "KRIHSTLINDJA GEZUAR-KALA CHRISTOUGENA" .-' '-. '-. ! "SELAMAT HARI NATAL - LAHNINGU NAJU METU"' '-. '-. ! "SARBATORI FERICITE-BUON ANNO" ! ___________ !-..!- ! "ZORIONEKO GABON-HRISTOS SE RODI" ! !__o_!__!__! ! ! "BOLDOG KARACSONNY- VESELE VANOCE" ! !_ooo!__@__! ! ! "MERRY CHRISTMAS**JOY**HAPPY NEW YEAR" !ooooo__#__! ! (\_/)-=)) ! "ROOMSAID JOULU PUHI -KUNG HO SHENG TEN" . ! =('.')=// ! "FELICES PASUAS-EIN GLUCKICHES NEUEJAHR*.-.-' -.._________! ( ~~~ )/ ! "PRIECIGUS ZIEMAN SVETKUS SARBATORI VESLLE" '-.-''-.. `w---w` ! "BONNE ANNEE-BLWYDDYN NEWYDD DDA*FELIZ NATAL" '-.... ! SHENORAVOR SOORP TSENOONT,SHENORAVOR NOR DARI" ! XXXXXX ! XXXXXX ! XXXXXX ! ------------------------------------------------------------------------------- So here we come again... Another year has passed... This one is supposed to be special since odometers change from 1999 to 2000 and it can produce a lot of problems. I hope, you already bought few submachine guns, a ton of canned food, filled up a big container with water, and checked if the walls of your anti-nuclear shelter are thick enough and your filtering system works. While some say that drinking urine is very healthy, I am not in health foods yet, so I will not tell you... I do not want to get into the argument on the "End of millennium" thing, since it depends on which programming language you use. I use both... If you are a FORTRAN programmer, you count from 1, and the millennium ends on midnight of Dec. 31, 00. If you are a C (or Java) geek, your millennium is about to end. So... Which are you? And do not dare to step out of your line and do not bring religion into it {:-)}. I am in a special environment, which is much different that the environment of the typical academic department. We are more like industrial setting since we do service and contracts. I probably see things >from a different perspective. But looking at the "University in Transition" I will offer the following JOKE for those with enough endurance to read through. I hope, you will have some fun, and you understand that it is not my official position, but something to cheer you up. Please do not discuss it on the list, and just junk it when finished. It is not worth commenting. PLEASE... In any case, from my perspective, the signs of millennium ending are everywhere. No... I do not mean the "End of the world" stuff, since it would be too easy... The believers, and nonbelievers agree that we do not know the day and time... What I actually mean is the "End of the world as we know it" thing, and the decadence of "fin du siecle" around. The consumerism is everywhere and the notion of GOOD and BAD does not exist anymore. (O tempora! O mores!...). It was replaced by: "Can they sue me or not?". The science and arts for the mortals are not about the quest for truth anymore. They are the quest for money. Some think that when they get the money, they can catch some air and do some science. Wrong... It is time to write another proposal, so you can make sure that you will have money to support your group when you are writing your next grant proposal. Occasionally my local newspaper does a "Local-Rising-Science-Star" piece (They have this Distinguished Scholar thing in Ohio and "Public-Scrutiny" requires that the "Public-is-informed" where the money goes). The actual topic of research is usually a one-liner. The success is measured (and the position endowment justified) solely on the basis of "How much money he/she brought". Occasionally the size of his/her group is brought up (the bigger the better, of course...). I wonder, why not simplify the landscape and introduce the "Buy the Professorship" program (Or "Rent-To-Own-The-Professorship", for the middle class)? [I admit, I am inspired by the spam which I get regularly about Prestigious University Dyplomas -- No courses or exams needed.]. Some wealthy people could be interested (we see examples all over the world that some want/ed to be presidents, some may want to be professors), and the revenues would pay for those misfits who do not bring enough overhead, but try to publish some stupid papers which people will understand 20 years from now. [Do not worry, peer-review works, reviewers will not let this garbage through. It is a pity that they did not have reviewers in the Renaiasance -- ww would fill better believing that we are the center of the Universe]. The program could even pay for these "economically impaired" access to a phone, copy machine, Internet, and the stock room. We all want to preserve the security of the tenure, since we can only be productive for so long, and since teaching is not important and considered degrading, we need a solution. During the transition phase, the program could even require a few research papers to be published as a condition. With the overall quality of research publications, postdocs or brighter grad students could crank them in spare time for a small fee (or, alternatively, Universities could expand existing "Hire-The-Scientist" programs to cover these particular needs. For example: "We-Read-What-We-Write" or "Pay-securely-for-your-paper-with-a-credit- card-over-the-Internet2.-Satisfaction-guaranteed.-Our-Professors-are-Editors- You-Know...", ). There is a problem with grad students and postdocs writing papers in the US, at least. They do not speak English. The bright kids who are born in US know that science is not a career, and they try professional degrees (lawyers, dentists, MBA's, etc.) or they start Macro$ofts. Unfortunately, in some less forward thinking cultures, the kids are misguided and dream about being a scientist. They read a lot of propaganda books on discovering new things, about constant struggle to find the secrets of the nature, etc., and they think it is similar to playing "Command and Conquer" or "Pokeman". Their professors tell them: "If you like your job, you do not have to go to work anymore... To be a scientist you need a call from within... It is like entering the convent... Yes, you can... Do or do not -- There is no try". Those cynical swine do that since they need grad students to do their work, and this is unfair. We as a community should fight these myths. Younger generation needs to be told the truth that the humanity is overloaded with all this new stuff and "we do not need no scientists no more". If you really have this call from within, you better sell it under the right label. There is no basic science anymore. And it should not be... One could by mistake discover another bomb. Or something really usefull and forget to patent it (which would result in extermination by the Intelectual Property Squad at your Alma Mater). Sell what they buy. What sells is: "save life", "save money", and "be happy". So, if you want the politicians to give money for your research try to put at least right titles on your papers. For example: "Organic ferromagnets will not scratch your refrigerator", "Muonic atoms will give you more matter for the money", "Computational Chemistry is cheaper and more reliable than psychics in predicting properties", or "Electronic structure of N20 reveals the secret of happiness". Remember, your work is paid by the taxpayer, and the taxpayer elects the politicians who (which?) give you money. And the politicians, to be elected, have to make taxpayer confident that they will bring good things to light. So help them, and they will help you. Give them "success stories", "tremendous savings", "competitive edge", and "future now". Do not worry if they say that they discovered this. You did not expect that politicians tell the truth in the first place, did you? The notion that science costs is passe. Use the term "good investment". Science saves money and creates wealth. It brings the "returns on investment" and "buys ticket to the future for our children". When they ask you why you have only foreign grad students and postdocs, do not answer that there ain't any Americans (for example) available -- you would undercat your support base. Tell them that you use foreign talent to foster national goals. They do not understand that it means that our grandchildren will have to go abroad to attend a decent university. But we will be dead by that time, so who cares... To circumvent the fact that the "grant/peer-review" system forces us to do contracts rather than try new things, we usually propose stuff which is already done, and when/if we get money, we use these funds to develop stuff which will be proposed in the future. [BTW, did you send the Greeting Card to your friend on the Study Section? -- Note: e-mail does not work, the spammers took over and you need to be more oldfashioned -- a phone call will do too, or try to attend his/her talk]. Of course, we cannot talk about stuff which is not yet published, since someone can propose this. At the same time, we cannot publish the stuff before we apply for the money to do it. But we also want to make everybody aware that we were the first. I see a way out of this with the publishers. They should provide the deposit service. We would simply send the paper with the annotation: "Review after YYYY.MM.DD", and then, when paper is finally published, instead of traditional "received" and "accepted" dates, we would have: "deposited", "received", "accepted". Of course, the publishers should allow for extension of "Review after" date, so, when we fail to receive funds to develop the the stuff which is reported in the paper, we can always reapply, and push the review date. While I could go forever like this, I better save the bandwidth. I hope you smiled at least once... From chemistry-request@server.ccl.net Fri Dec 17 06:47:50 1999 Received: from mserv3.dl.ac.uk (root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03810 for ; Fri, 17 Dec 1999 06:47:49 -0500 Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id KAA08369 for ; Fri, 17 Dec 1999 10:44:12 GMT Sender: H.J.J.VanDam@dl.ac.uk Message-ID: <385A115E.91AD803A@dl.ac.uk> Date: Fri, 17 Dec 1999 10:33:02 +0000 From: Huub van Dam Organization: CCLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Workshop on advanced Data Storage / Management Techniques for HPC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Workshop on advanced Data Storage / Management Techniques for HPC Invitation and Call for Papers 23rd - 25th February 2000 Workshop on Advanced Data Storage / Management Techniques for HPC Daresbury Laboratory, Warrington, UK There is a growing awareness that it is not enough to provide leading edge computational facilities on their own. Many of today's modelling codes produce large amounts of data, which have to be handled appropriately. Keeping records, archiving, preserving and exploring results, granting access to and disseminating new findings, as well as providing back-up capacities are major tasks and without adequate data archival and exploration, research data may well be lost. The rapidly increasing amount of stored data provides new challenges for the existing computing and data centres, as new techniques have to be developed to capture, store, manage and explore this data efficiently. The Computational Science and Engineering Department (CSE) at CLRC - Daresbury Laboratory and the data storage and data management group and the data inter-operability group of the European DIRECT project are jointly organizing a workshop on advanced data storage and data management techniques for high performance computing users. The aim of the workshop is to provide a forum for vendors, data and computing centres, developers and users to discuss available solutions, new technological developments and user requirements, during this 3 day workshop. Topics to be discussed are: High Performance Storage Systems Data Management Tools High Performance I/O on Supercomputers Data Mining Data Processing and Visualisation Data formats and Data interoperability The workshop will also provide an forum to discuss future data storage/management requirements of various scientific disciplines. We would like to invite contributions from the areas of: Environmental Science, Quantum Chromodynamics, Materials Chemistry, Computational Chemistry, Biology, Engineering, Astrophysics, Particle Physics, Medical and Social Sciences. Please pass this message on to other interested groups. For more information see URL: http://www.dl.ac.uk/TCSC/datamanagement/conf2.html Kerstin Kleese (CLRC,UK) Michael Lautenschlager (DKRZ,D) Micheal King (Univ. of Essex, UK) From chemistry-request@server.ccl.net Fri Dec 17 12:10:18 1999 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05618 for ; Fri, 17 Dec 1999 12:10:18 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with SMTP id LAA17951; Fri, 17 Dec 1999 11:06:06 -0500 (EST) Date: Fri, 17 Dec 1999 11:06:06 -0500 (EST) From: "C.F. Matta" Reply-To: "C.F. Matta" To: Scott McMillan cc: chemistry@ccl.net Subject: Re: CCL:How to increase max number of geometry optimization steps in G98? In-Reply-To: <19991217054607.16234.qmail@eeyore.chem-eng.nwu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Scott, Sometime ago I ran into the same problem. The number of geometry optimization steps can be set to any value in Gaussian94 by a command like: opt=(z-matrix, maxcycle=300) This does work in G94, I do not know if it it the same with G98, but you can try it. Take care. Cherif ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ....................................................................... On 16 Dec 1999, Scott McMillan wrote: > > Hello, > > I'm performing pm3 geometry optimizations in Gaussian 98 on systems > with some atoms fixed at their cartesian position. I'm using the > keyword opt=z-matrix to fix these atoms. Some of my calculations do not > have enough geometry iterations to complete. From the G98 manual, it > appears that setting iop(1/6=N) should set the maximum number of > geometry optimizations to N. However, G98 seems to have some other > maximum setting as well. The manual also suggests that opt(maxcycle=M) > would have a similar effect as iop(1/6), but it appears to do nothing. > > For example, from my output: > Number of steps in this run= N maximum allowed number of steps= 204. > > I can set N to any value less than or equal to 204 with iop(1/6), but > not larger. How do I increase the second value above 204? The 204 > value depends on the system (# degrees of freedom); there's nothing > special about that particular number. > > I know I can save the checkpoint file and then keep restarting the > calculation, but I'm looking for a solution that won't require this > level of manual intervention. > > Thanks, > Scott > -- > Scott McMillan - smcmilla@nwu.edu - http://winnie.chem-eng.nwu.edu/~scott/ > Institute for Environmental Catalysis > Department of Chemical Engineering > Northwestern University > > -= 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 Fri Dec 17 12:42:56 1999 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05816 for ; Fri, 17 Dec 1999 12:42:48 -0500 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.9.1b+Sun/8.9.2) with ESMTP id NAA25229 for ; Fri, 17 Dec 1999 13:38:30 -0300 (CDT) Date: Fri, 17 Dec 1999 13:38:30 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: force field assignement: TINKER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! I am looking for a program or function for assigning the atom type within the .xyz(tinker) file from mm3.prm or another force field of TINKER ( organic molecules) the PDBXYZ program leaves the atom type as zero. Thanks a lot! Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Fri Dec 17 13:13:57 1999 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06216 for ; Fri, 17 Dec 1999 13:13:57 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with SMTP id MAA14006 for ; Fri, 17 Dec 1999 12:09:46 -0500 (EST) Date: Fri, 17 Dec 1999 12:09:45 -0500 (EST) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: SUMMARY: Superposing 2 MoleculesB Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody A couple of weeks ago I posted the following question: "Is there a free (or inexpensive) software to superimpose a floppy structure (F) on a rigid template structure (R). The objective is to obtain a geometry of (F) in a conformation that mimic (R) as closely as possible (in a least square sense)." I got the replies, form: G. Matthias Ullman, Per-Ola Norrby, Christian Rummey, Nick Jewell, Alexander Klinsky Gregory Durst, Thomas E. Wiese, Soaring Bear, and Dayong He which are very much appreciated. G. Matthias Ullman has a C code that he generously sent, and for which I am very greatful. Here are the replies: ---------------------REPLY 1------------------------------------------- I have some code in C that does the job using the Kabsch-Algorithm. you may however have to modify it. If you don't find anything better, let me know. Matthias G. Matthias Ullmann Department of Molecular Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., TPC-15 La Jolla, CA 92037 USA Phone: 858-784-8889 Fax: 858-784-8896 e-mail: ullmann@scripps.edu www: http://www.scripps.edu/~ullmann ----------------------------------------------------------------------- ---------------------REPLY 2------------------------------------------- You can do that with MacroModel. It's not free, but if you're academic it's relatively inexpensive. Check out: http://www.schrodinger.com/macromodel2.html You can specify which atoms in both molecules to overlap, and what torsions to rotate. We use it for testing pharmacophore hypotheses. Two drawbacks with this procedure: there is no "global best fit" finding, so you have to check through several possible overlap conformations, and there is no possibility to bias the fit against high energy structures. On the other hand, MacroModel includes a good set of conformational searching and constrained minimization tools, which can frequently be applied to the same kind of problems. Best regards, Per-Ola Norrby * Per-Ola Norrby, Dept. of Med. Chem., Danish School of Pharm. * peo@dfh.dk, http://compchem.dfh.dk/PeO/ * tel. +45-35306506, fax +45-35306040 ----------------------------------------------------------------------- ---------------------REPLY 3------------------------------------------- I attach a tar file with the code. There is a very short README file how to use it and two examples. I hope you figure out what to do and how to modify the program for your need. Please let me know if you need more help. But I am very busy right now, writing papers and proposals. (That's the reason why I am still here :-). Large parts of the code I send you are "dead". You should be only interested in my-kabsch.c and in superimp.c. Have fun, Matthias G. Matthias Ullmann Department of Molecular Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., TPC-15 La Jolla, CA 92037 USA Phone: 858-784-8889 Fax: 858-784-8896 e-mail: ullmann@scripps.edu www: http://www.scripps.edu/~ullmann ----------------------------------------------------------------------- ---------------------REPLY 4------------------------------------------- there is a (in the meantime comercial, sold by Tripos) programm doing exactly this. If it is no option for you to buy it (it is part of the programm package SYBYL), you should at least look at C. Lemmen, T. Lengauer, J. Comput.-aided Molecular Design, 11 (1997) 357-368. I can send you a postscript-file of it if you wish. I obtained the programm itself ("FLEXS") from The GMD (cartan.gmd.de) when it was in test phase. Maybe it can still be obtained from there. I am very interested in the alternatives ! --cr Christian Rummey, Dipl. Chem. Institut fuer Organische Chemie, Universitaet Wuerzburg mailto:rummey@chemie.uni-wuerzburg.de registered linux user #92917 ----------------------------------------------------------------------- ---------------------REPLY 5------------------------------------------- There are a number of alignment methods you could try, for example: the SEAL code is often available through this group (as Fortran 77 code) and there's FlexS (http://cartan.gmd.de/flex-bin/FlexS) which allows you to either procure a license from the authors or have quite a few 'free tries' through allocation at their web site. In our group at Sheffield we have the Field Based Similarity Searcher (FBSS) which uses a GA to align molecular fields, although the flexibility issue is still a problem within the code, and is more useful for rigid fitting. If you have SYBYL, there are superposition procedures in this program, including SUPERIMPOSE and FIELD_FIT, but I understand that this program is relatively expensive(!) Hope this helps, Nick Jewell Research Student Department of Information Studies University of Sheffield Sheffield, UK ----------------------------------------------------------------------- ---------------------REPLY 6------------------------------------------- There is a program named SEAL which does what you want. It was distributed with the original paper and is obtainable via QCPE. On a PC you can download a 30-day trial of powerfit from www.microsimulations.com. This uses also the SEAL algorithm but comes with a graphical user interface. In April 99 there was a paper from the same authors of SEAL about a new approach called SQ (J. Med. Chem) but i ewas not able to test this program up to this time. Kind regards, Alexander Klinsky Inst. of theoretical chemistry Univ. of Vienna Austria ----------------------------------------------------------------------- ---------------------REPLY 7------------------------------------------- An inexpensive piece of software to do superimposing is SEAL from QCPE in Bloomington, IN, USA. It requires the ability to read Sybyl mol2 files to visualize. (Babel could probably convert these to other formats). SEAL is no. QCPE-634. Check out the QCPE web page at: http://www.ccl.net/ccl/qcpe/QCPE2/index.html regards, Greg +-----------------------------------------------------------+ | Gregory L. Durst computational chemist | | Lilly Research Laboratories tele: 317/433-3386 | | Lilly Corporate Center email: gdurst@lilly.com | | Indianapolis, IN 46285 USA | +-----------------------------------------------------------+ ----------------------------------------------------------------------- ---------------------REPLY 8------------------------------------------- I have just done an evaluation of FlexS and it seems to be very useful. I also found that it can be run from within sybyl (with special interface). Since we have sybyl, I will purchase it from Tripos Assoc (~$1500). For FlexS info : http://cartan.gmd.de/flex-bin/FlexS For sybyl info (no info on FlexS yet, but you can call them): http://www.tripos.com/ Good luck, Tom Wiese Thomas E. Wiese, Ph.D. Assistant Professor of Biochemistry Division of Basic Pharmaceutical Sciences College of Pharmacy Xavier University of Louisiana 7325 Palmetto St New Orleans, LA 70125-1098 Email: twiese@xula.edu Phone: (504) 483-7433 FAX: (504) 485-7930 Assistant Professor Department of Environmental Health Sciences (SL-29) School of Public Health and Tropical Medicine Tulane University Medical Center 1430 Tulane Avenue New Orleans, LA 70112-2699 Email: twiese@tcs.tulane.edu Phone: (504) 988-6376 FAX: (504) 585-6428 ----------------------------------------------------------------------- ---------------------REPLY 9------------------------------------------- REPLY TO A SIMILAR QUESTION IN THE PAST ======================================= Subject: CCL:Summary :Superimposition Program I am not sure if this helps; but did you take a look at swisspdb viewer http://www.expasy.ch Dr. Y. U. Sasidhar, Associate Professor, Department of Chemistry Indian Institute of Technology, Powai, Mumbai 400 076, INDIA ---------- You can use the CCP4 program PolyPose for the purpose. If you don't have CCP4 (which, I believe you don't). You can use Gerard's program LSQMAN which is the most versatile superimposition program I've seen, but requires some inspired script writing. Lastly I've got a fast superimposer, which is a debugged and improved version of the one I wrote in Pune. For more info. see the following: LSQMAN http://alpha2.bmc.uu.se/~gerard/manuals/lsqman_man.html CCP4 (PolyPose and many other useful programs) http://www/dl.ac.uk/CCP/CCP4/main.html super_duper.c (That's mine) Can superimpose using the whole molecule or any sub-set which you define. The algo. is the same as the one I wrote in Pune, but now re-written and de-bugged. I can send you OSF1 Version 4.0 (DEC-ALPHA) executable, or the C-sources. Finally if you want any special things to be done, it may be possible to incorporate them. Devapriya Choudhury Office: Home: Deptt. of Molecular Biology Oskar Arpis Vag 2,2 Box 590, BMC, S75650, Uppsala S75124, Uppsala Sweden Sweden e-mail deva@xray.bmc.uu.se ----------- it's called profit and does exactly what ou want! cheers, gerald Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna, Molecular Biology Department Email: Gerald.Loeffler@vienna.at ---------- You may try the molecular modelling package MOLMOL from ETH Zuerich. It is a graphical program which can also be run in batch-mode (without graphics-display. It can be controlled from shellscripts or directly at the commandline. It is able to superimpose as many molecules as you wish in several modes (to first, to mean, circular), and you can choose, which atoms or residues to consider for superposition. It is freeware! Take a look at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ There are versions for UNIX (IRIX, DEC OSF, SOLARIS, LINUX), VMS, and Windows95/NT. You can also get the source and adapt it to whatever you want. Marc Saric Lehrstuhl fuer Biophysik Projektgruppe Theoretische Biophysik http://www.bph.ruhr-uni-bochum.de/ Ruhr-Universitaet Bochum Germany ---------- Try MOLMOL: There is a nice way to run it in batch as well. http://www.mol.biol.ethz.ch/wuthrich/software/molmol Jurgen Drs Jurgen F. Doreleijers NMR spectroscopy, Utrecht University, The Netherlands mailto:jurgen@nmr.chem.uu.nl http://www-nmr.chem.uu.nl/~jurgen ---------- make a search in the web for a programm Profit, it is a powerfull unix programm that allow you to make a protein superimposition also in batch mode. Maybe you can find it at http://www.biochem.ucl.ac.uk/~martin/swreg.html || Dr. Rino Ragno E-mail: ragno@uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design or: ragno@axcasp.caspur.it || || Box8036, Washington University Phone : 314-362-2272 || || 700 South Euclid Avenue FAX : 314-362-0234 || || St. Louis, Missouri 63110 || ---------- Have a look at the Molecular Modelling toolkit at: http://starship.skyport.net/crew/hinsen/mmtk.html It contains the necessary superposition code, and making a batch mode program that uses it is a simple matter (maybe 10 lines of code). I could even write you that small piece of code, if I knew what exactly you want the program to do with the superposed structure! Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------- You might look into a program called MOE, by the Chemical Computing Group. It has very nice 3D homology modeling capabilities and will run in batch mode. Abby Parrill, Ph.D. Currently: Chemistry Department Michigan State University East Lansing, MI 48824-1322 parrill@argus.cem.msu.edu Soon: Chemistry Department University of Memphis Memphis, TN 38152 Computational Research on Materials Institute at University of Memphis (CROMIUM) ---------- I'd highly recommend VMD. It's available for many platforms (SGI, Linux, AIX, HPUX), it's free and very flexible due to a (TCL-like?) scripting language. Check http://www.ks.uiuc.edu/Research/vmd/ for more. Dr. Christoph Steinbeck (mailto:steinbeck@ice.mpg.de - http://seneca.ice.mpg.de/~stein) Max-Planck-Institute of Chemical Ecology (http://www.ice.mpg.de) Tatzendpromenade 1a, 07745 Jena, Germany Soaring Bear Ph.D. Research Pharmacologist, Informatics, Chemistry & Biochemistry, Herbalist & Healthy Lifestyles Herbal Science: http://www.amfoundation.org/herbmed.htm My web tools: http://www.dakotacom.net/~bear email: bear@dakotacom.net, sbear@uswestmail.net fax: 559-663-5833, 520-795-9350 ----------------------------------------------------------------------- ---------------------REPLY 10------------------------------------------ Hi again, think you misunderstood me, I already have the postscript-code (we do not have this journal here), so I got i sent from somewhere else. lookin forward to your summary... bye, cr Christian Rummey, Dipl. Chem. Institut fuer Organische Chemie, Universitaet Wuerzburg mailto:rummey@chemie.uni-wuerzburg.de registered linux user #92917 I suggest you try TINKER from Dr. Ponder's group. Dave ----------------------------------------------------------------------- --------------------END OF REPLIES------------------------------------- THANK YOU ALL, MERRY CHRISTMASS AND HAPPY Y2K! Cherif ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. .......................................................................