From chemistry-request@server.ccl.net Tue Mar 20 05:23:04 2001 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KAN4D24707 for ; Tue, 20 Mar 2001 05:23:04 -0500 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id MAA08176 for ; Tue, 20 Mar 2001 12:36:17 +0100 (CET) Date: Tue, 20 Mar 2001 12:36:17 +0100 From: Christian Pilger To: chemistry@ccl.net Subject: AutoDock/LINUX In-Reply-To: <3AB68987.6250A476@umbi.umd.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I have a question about the script "mol2topdbq" that comes with AutoDock 3.0.5. I changed the "nawk" in the very beginning to the awk-version I'm using on my PC (Suse Linux 7.1) "gawk", but this scripts does not work properly - upon exeution, I get the following message: gawk: cmd. line:33: fatal: expression for `<' redirection has null string value When I use the very same input mol2-file on our SGI, the same script (apart from nawk/gawk) works without any problems. Did anybody experience something similar and can give me a hint on how to fix it ? Ciao, Christian ----------------------------------------------------------------- Dr. Christian Pilger Istituto di Strutturistica Chimica "Giordano Giacomello" C.N.R. - Sezione di Trieste Area Science Park - Basovizza Strada Statale 14 - Km. 163.5 I-34012 Trieste/Italy Tel.: +39+040+226881 Fax : +39+040+9221126 e-mail: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 20 01:14:37 2001 Received: from server3.safepages.com ([216.127.146.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2K6EbD23575 for ; Tue, 20 Mar 2001 01:14:37 -0500 Received: from quantumnt (5131-013-230.008.popsite.net [209.69.13.230]) by server3.safepages.com (Postfix) with SMTP id 3CEA6230F8 for ; Tue, 20 Mar 2001 06:13:52 +0000 (GMT) Message-ID: <000d01c0b104$efa13940$0300a8c0@quantumnt> From: "Jim Kress" To: References: <062801c0af8d$f9300fe0$b9ac323f@josiah> <200103191755.SAA04714@chinon.cnrs-orleans.fr> <3AB6D022.319959E9@sunesis-pharma.com> Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) Date: Tue, 20 Mar 2001 01:13:51 -0500 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 >After all, if you are not going to commercialize your code, then why not make it >available to other scientists unconditionally? Commercialization means different things to different people. When someone develops code that gives them a 'competitive advantage' in getting grant money, they aren't inclined to distribute the code to others. Isn't that another form of 'commercialization'? Jim ----- Original Message ----- From: "Warren DeLano" To: Sent: Monday, March 19, 2001 10:36 PM Subject: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) > Konrad Hinsen wrote: > > > > I don't know what can be done to limit this (in my mind) > > > needless duplication of effort. > > > > Open Source code would be an important first step. In fact, I do not > > understand why this concept isn't standard for academic applications. > > Much academic code is already free, so why not take the next step and > > make it freely redistributable, also in modified form? And for those > > academic packages that are not free, I seriously doubt that they are > > in any sense profitable. > > > > Some academic code is very profitable. MSI and others make a living (or should I > say a killing?) off of academic packages that have been commercialized. I think > the critical question is whether we as computational Scientists are happy with this > arrangement or whether we and our Science would benefit from more free source code > written by other scientists. My guess is that the impact of significant amounts of > *reusable* source-code building blocks would be profound and world changing. At > the very least, competition from open-source would force commercial software > developers to greatly improve the quality of their packages. > > I applaud the work Konrad has done in this direction with the MMTK package. My > efforts to create a free professional-strength, interoperable, and open-source > molecular graphics/editing system (PyMOL) reflect this shared vision. If only more > scientists/developers would do likewise with their projects! > > After all, if you are not going to commercialize your code, then why not make it > available to other scientists unconditionally? Instead of allowing your great work > to languish on some back-up tape, please release it to the world and allow it to be > *modified* and *redistributed*. By doing so, you will change the field irrevocably > and enable the next generation of computational research tools to be built on > *your* foundation. As it stands, each of us is so busy pouring foundations that we > never get around to building cathedrals. Let's change that. > > Thanks to the internet's exceedingly low distribution costs, and the advent of > modular, extensible scripting languages such as Perl and Python, you now have no > excuse other than vanity for allowing your good code to remain restricted and > unutilized. > > I propose initiating an effort to accumulate unrestricted computational chemistry > source-code into a single curated distribution, probably on a SourceForge > instance. This "Free Molecule Project" would require a significant number of > volunteers -- so I am going to float this trail balloon: If you have interest in > such a project and would consider contributing, please email me directly. Assuming > there are enough interested parties, I'll set up a mailing list, and we will start > a discussion about how such a project might come together. > > - Warren > > > -- > mailto:warren@sunesis-pharma.com > Warren L. DeLano, Ph.D. > Informatics Scientist > Sunesis Pharmaceuticals, Inc. > 3696 Haven Ave., Suite C > Redwood City, CA 94063 > (650)-562-3106 fax: (650)-556-8824 > > > > > > -= 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 Mar 20 04:55:36 2001 Received: from gensig.nibsc.ac.uk ([193.62.43.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2K9taD24505 for ; Tue, 20 Mar 2001 04:55:36 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA61239; Tue, 20 Mar 2001 09:55:41 GMT Message-ID: <3AB72958.1C34EF9D@nibsc.ac.uk> Date: Tue, 20 Mar 2001 09:56:41 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Pornthep Sompornpisut , chemistry@ccl.net Subject: Re: CCL:textbook or reference of distance geometry References: <3.0.6.32.20010319172759.0097a6c0@unix.mail.virginia.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Pornthep I can the following text which provides a full and detailed exposition of the theory, along pseudo-code listings for the important algorithms. Crippen, G.M., Havel, T.F., 1988. Distance geometry and Molecular Conformation (Chemometrics Series, Vol 15) Research Studies Press Ltd, Taunton, England John Wiley and Sons Inc, New York. ISBN 0 86380 073 4 ISBN 0 471 92061 4 (Wiley) Mark Forster Pornthep Sompornpisut wrote: > Dear Sir, > > Are there any good references to learn and to help in writing a program > using distance geometry approach in structure calculation? Any comments are > appreciated. Thank you. > > Thep > ======================================================================= > Pornthep Sompornpisut, Ph.D > Postdoctoral Fellow > Department of Physiology > University of Virginia > Tel: 804-924-5473 > Fax: 804-982-1616 > Email:ps2t@virginia.edu > ======================================================================= > -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Tue Mar 20 06:37:49 2001 Received: from mailhost1.rdg.ac.uk ([134.225.16.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KBbnD25078 for ; Tue, 20 Mar 2001 06:37:49 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=indyp.chemistry.rdg.ac.uk) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {14fKST-00018q-00} for CHEMISTRY@server.ccl.net; Tue, 20 Mar 2001 11:37:49 +0000 Received: from reading.ac.uk (localhost [127.0.0.1]) by indyp.chemistry.rdg.ac.uk (SGI-8.9.3/8.9.3) with ESMTP id LAA21029 for ; Tue, 20 Mar 2001 11:37:43 GMT Sender: dave@reading.ac.uk Message-ID: <3AB74106.4EB981C3@reading.ac.uk> Date: Tue, 20 Mar 2001 11:37:42 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Re: CCL:g94 under RedHat Linux 7.0 with g77/f2c - SOLUTION Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Fellow CCLers Just after I posted the question regarding g94 under linux (see subject) I sorted out the problem by applying the fix for g98 (editing makefile to remove bd0402.o from the linking of l402.exe. Thanks to all that suggested answers. Sorry to waste people's time. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Mar 20 08:25:00 2001 Received: from localhost.smateo1.sfba.home.com ([65.0.162.234]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KDOxD26442 for ; Tue, 20 Mar 2001 08:24:59 -0500 Received: from localhost (ee@localhost) by localhost.smateo1.sfba.home.com (8.11.0/8.11.0) with ESMTP id f2KDOxn02493; Tue, 20 Mar 2001 05:24:59 -0800 X-Authentication-Warning: localhost.localdomain: ee owned process doing -bs Date: Tue, 20 Mar 2001 05:24:59 -0800 (PST) From: Erik Evensen X-Sender: Reply-To: To: cc: Subject: Re: CCL:Orthographic projections in VMD: SUMMARY In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 19 Mar 2001, Devapriya Choudhury wrote: > > > Hi All, > Thanks to Barry Israelevich for the quick reply. Although in Raster3D > there are no explicit camera position or zoom variables. But I think I > managed to do that by tweaking the global X-form matrix. > Come to think of it, it would be nice if once the > orthographic/perspective projections are set, the same be taken into > account while generating the ray-tracer input file. > > Thanks once again. > Devapriya > > Original question: > > > > Hi All, > > When I generate a picture in VMD using the Orthographic projection mode > > and subsequently render the image (Raster3D), the view seems to > > automatically shift to perspective projection mode. > > Does anyone know a fix ? > > ----Replies--------------------------------------------- > (1) From: Barry Isralewitz > A near-perfect way to simulate orthographic coordinates with > any raytracing program (such as Raster3D) is: move the camera far > back, increase the zoom appropriately. Most raytracing programs have > these two paramaters early in their input files (written by VMD), so > just alter the settings, then re-run the ouput file (i.e. plot.r3d) > through the renderer. > > (2) From: Adrian E. Roitberg > would love to know the answer to that one ! > THe same thing happens with povray... > povray supports orthographic projections, you can get an orthographic projection by changing the camera portion of the povray input file to look something like this: camera { orthographic location <0.000000, 0.000000, -2.000000> look_at <-0.000000, -0.000000, 2.000000> up <0.0000, 2.0000, 0.0000> right <2.666666, 0.0000, 0.0000> direction <0, 0, 0.8> sky <0.000000, 1.000000, -0.000000> } Note that you have to tweak out the 'up' and 'right' vectors to get the image sizing correct, but be sure to maintain the aspect ratio. You can also do a lot with lighting by changing the header and material types in pov file. You can a lot more information at povray.org, specifically, documentation for povray is in http://povray.org/ftp/pub/povray/Official/Docs/ Hope this helps... Erik Evensen, Ph.D. DuPont Pharmaceuticals Research Labs San Francisco, CA From chemistry-request@server.ccl.net Tue Mar 20 08:32:18 2001 Received: from zambeze.ujf-grenoble.fr ([152.77.2.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KDWHD26468 for ; Tue, 20 Mar 2001 08:32:17 -0500 Received: from volga.ujf-grenoble.fr (volga.ujf-grenoble.fr [152.77.6.1]) by zambeze.ujf-grenoble.fr (Pro-8.9.3/8.9.3/Configured by AD & JE 25/10/1999) with ESMTP id OAA28232 for ; Tue, 20 Mar 2001 14:29:16 +0100 (MET) Received: from ujf-grenoble.fr (IDENT:antoine@cahn.ujf-grenoble.fr [152.77.209.147]) by volga.ujf-grenoble.fr (8.9.3/8.8.5) with ESMTP id OAA27319 for ; Tue, 20 Mar 2001 14:28:15 +0100 (MET) Sender: Pierre.Antoine@ujf-grenoble.fr Message-ID: <3AB75B92.B4B73AB9@ujf-grenoble.fr> Date: Tue, 20 Mar 2001 14:30:58 +0100 From: Antoine X-Mailer: Mozilla 4.76 [fr] (X11; U; Linux 2.2.17-21mdk i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 To: CCL Subject: CCL:AutoDock/LINUX Christian Pilger a écrit : > Dear CCLers, > > I have a question about the script "mol2topdbq" that comes with > AutoDock 3.0.5. I changed the "nawk" in the very beginning to the > awk-version I'm using on my PC (Suse Linux 7.1) "gawk", but this scripts > does not work properly - upon exeution, I get the following message: > > gawk: cmd. line:33: fatal: expression for `<' redirection has null string > value > > When I use the very same input mol2-file on our SGI, the same script > (apart from nawk/gawk) works without any problems. Did anybody experience > something similar and can give me a hint on how to fix it ? > > Ciao, > > Christian > Check the Autodock Home page and Autodock HOWTO for Linux ... http://foo.medstv.unimelb.edu.au/~pierre/autodock/AutoDock-HOWTO.html "Abstract ": Some of the supplied scripts in the share directory call the nawk program, which is synonymous to awk. To fix the bug type the commands: cd ${SRC} perl -pi -e "s,nawk,awk," ${SRC}/dist_3.0/share/* Best regards Antoine -- ---------------------------------------------- Antoine FORTUNE Ingénieur Modélisation Moléculaire Département de Pharmacologie Moléculaire - DPM UMR 5063 - Universite Joseph Fourier Domainde de la Merci 38706 LA TRONCHE - FRANCE Tel : +33 4 76 63 71 40 Fax : +33 4 76 51 86 67 e-mail : Antoine.Fortune@ujf-grenoble.fr ICQ : 106018150 ---------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 20 09:09:36 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KE9ZD26579 for ; Tue, 20 Mar 2001 09:09:35 -0500 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id PAA07725 ; Tue, 20 Mar 2001 15:09:31 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id PAA05874; Tue, 20 Mar 2001 15:06:42 +0100 Date: Tue, 20 Mar 2001 15:06:42 +0100 Message-Id: <200103201406.PAA05874@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@ccl.net CC: warren@sunesis-pharma.com In-reply-to: <3AB6D022.319959E9@sunesis-pharma.com> (warren@sunesis-pharma.com) Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) References: <062801c0af8d$f9300fe0$b9ac323f@josiah> <200103191755.SAA04714@chinon.cnrs-orleans.fr> <3AB6D022.319959E9@sunesis-pharma.com> > My guess is that the impact of significant amounts of > *reusable* source-code building blocks would be profound and world > changing. At the very least, competition from open-source would > force commercial software developers to greatly improve the quality > of their packages. I agree completely, but I wonder how many others do. After all, many computational scientists do not do any development at all, but use ready-to-run packages. I am convinced that more people *could* do development (which can be as minor as combining two existing methods) *if* the reusable building blocks were available, but they'd also have to be aware of these building blocks and of their advantages. > I propose initiating an effort to accumulate unrestricted > computational chemistry source-code into a single curated > distribution, probably on a SourceForge instance. This "Free Some sort of coordination sounds like a very good idea. But I am not sure if a single distribution would be that useful, given that most of the existing Open Source packages are not interoperable and often address very different user communities. But it would be nice to have a catalogue of projects, and a discussion forum to discuss improved interoperability etc. And SourceForge looks like a good place, given its high visibility in the Open Source world. So I support your proposition (and am ready to contribute), even if I see the single distribution only as a far away goal for the moment. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 20 11:17:57 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KGHuD27964 for ; Tue, 20 Mar 2001 11:17:56 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA81404; Tue, 20 Mar 2001 11:11:11 -0500 (EST) Date: Tue, 20 Mar 2001 11:11:11 -0500 From: Rick Venable To: water Miller cc: Richard Wood , chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution In-Reply-To: <20010319222807.54184.qmail@web12708.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here's a topical reference: Dynamics of Water Molecules in Aqueous Solvation Shells Kropman, MF and Bakker, HJ Science v. 291, no. 5511; pp. 2118-2120 (16 Mar 2001) It's an experimental paper examining solvation of halide ions using an IR technique with measurement times on the femtosecond scale. On Mon, 19 Mar 2001, water Miller wrote: > I can imagine someone may have been sick of such > discussions away from the topic, however, it's still > related, and the only problem could be that the title > wasn't changed... > > The real problem could be almost no experimental > evidence available, at lease for those listers who > know how to use email and are kind rnough to share > their knowledge with others :-)... > > > Water Miller > > > >From: Richard Wood > >To: chemistry@ccl.net > >Subject: CCL:experiment of H-bond strength in > solution > > >Jordi Villa wrote: > > >> because at the end of the original message the > >>author asked about how > >> to simulate them. Please, read the messages before > >implying anything. > > >I wasn't the one doing the implying. > > >The following is from the ORIGINAL post. > > >========================================= > >Dear all, > > >Since it's well-known that the H-bond strength will > be > >highly weaken in solution, compared with that in gap > >phase, I am curious if there is any experimental > >evidence or hint available. > >========================================= > > >Notice the words "theoretical" or "calculated" are > not >anywhere > >to be seen. > > > >Richard > > -- > >Richard L. Wood, Ph. D. > >Physical/Computational Chemist > >Post-doctoral Associate > >Cornell University, Ithaca, NY 14853 > > --- Richard Wood wrote: > > Hi all > > > > I thought that the subject of this posting was the > > "experimental H-bond > > strength in solution"? > > If so, why does everyone cite theoretical > > papers/methods/results? > > > > Richard-- > > Richard L. Wood, Ph. D. > > Physical/Computational Chemist > > Post-doctoral Associate > > Cornell University, Ithaca, NY 14853 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Mar 20 11:42:47 2001 Received: from server3.safepages.com ([216.127.146.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KGglD28168 for ; Tue, 20 Mar 2001 11:42:47 -0500 Received: from Hppav (5131-013-230.008.popsite.net [209.69.13.230]) by server3.safepages.com (Postfix) with SMTP id E2E0325553 for ; Tue, 20 Mar 2001 16:41:02 +0000 (GMT) Message-ID: <007e01c0b15c$8cdee7a0$e60d45d1@webrise.net> From: "Jim Kress" To: "CCL" Subject: Summary of responses to: Universal Force Field Software question Date: Tue, 20 Mar 2001 11:41:01 -0500 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Thanks to all who responded. Looks like AMMP is the best choice (so far ...) Jim ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Original question: Anybody know where I can get software (preferably free) that implements the Universal Force Field (for example, A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff, J. Am. Chem. Soc. 114, 10024-10035 (1992)) ? Thanks. Jim ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Responses: From: Per-Ola Norrby Hi Jim, Several program include it as a preoptimizer, but they usually won't let you see results (like energies). One such is Jaguar from Schrodinger. The force field is also implemented in Gaussian98, primarily for use as the MM part of QM/MM. A release which gives you access to UFF in conjunktion with standard modeling tools can be found in the Cerius2 software. If you can find a more recent version (especially a free one), I'd be very interested to hear about it. Best, Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark tel +45-45252123, fax +45-45933968 Email: pon@kemi.dtu.dk (alt. peo@compchem.dfh.dk) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From: Peter Bagossi, Ph.D. If you interesting in simulations of proteins, try AMMP which implements a modified version of UFF: http://www.cs.gsu.edu/~cscrwh/ Hope this helps, Peter **************************************************************************** **** * Peter Bagossi, Ph.D. tel/fax: (+36-52) 416-432 * * Department of Biochemistry and Molecular Biology * * Medical and Health Science Center, Faculty of Medicine * * UNIVERSITY OF DEBRECEN * * Debrecen, Nagyerdei krt. 98., P.O.Box 6., H-4012, HUNGARY * **************************************************************************** **** ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From: Prashant Desai I don't know of any free package but Cerius2 from MSI has this force field. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From: Didier Mathieu I remember a paper reporting some results obtained through "a modified version of UFF" using AMMP: http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html However, I don't know whether the force field parameters are built into the program or have to be introduced by the user. Sorry for the lack of details. Didier, -- Didier Mathieu CEA - Le Ripault BP 16 37260 Monts +33 02 47 34 41 85 From chemistry-request@server.ccl.net Tue Mar 20 16:11:30 2001 Received: from mserve1.acs.ucalgary.ca ([136.159.34.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KLBUD29329 for ; Tue, 20 Mar 2001 16:11:30 -0500 Received: from ucalgary.ca (mserve2.acs.ucalgary.ca [136.159.34.55]) by mserve1.acs.ucalgary.ca (Postfix) with ESMTP id 0F7E7156C; Tue, 20 Mar 2001 14:09:30 -0700 (MST) Received: from zinc14.chem.ucalgary.ca(136.159.82.218) by mserve2.acs.ucalgary.ca via smap (V2.0) id ZZ561210; Tue, 20 Mar 2001 14:08:12 -0700 Mime-Version: 1.0 X-Sender: senn@s.imap.ucalgary.ca (Unverified) Message-Id: In-Reply-To: <007e01c0b15c$8cdee7a0$e60d45d1@webrise.net> References: <007e01c0b15c$8cdee7a0$e60d45d1@webrise.net> Date: Tue, 20 Mar 2001 14:08:09 -0700 To: "Jim Kress" From: Hans Martin Senn Subject: Re: CCL:Summary of responses to: Universal Force Field Software question Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Thanks to all who responded. Looks like AMMP is the best choice (so far >>...) > >Jim > >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > >Original question: > >Anybody know where I can get software (preferably free) that implements the >Universal Force Field (for example, A. K. Rappe, C. J. Casewit, K. S. >Colwell, W. A. Goddard III, and W. M. Skiff, J. Am. Chem. Soc. 114, >10024-10035 (1992)) ? There is also ArgusLab by Mark Thompson (http://www.planaria-software.com/) which includes the UFF and is (still) free. Cheers, Hans -- ........................................................ Dr. Hans Martin Senn Phone +1 403 220 3232 University of Calgary Fax +1 403 289 9488 Department of Chemistry E-Mail senn@ucalgary.ca 2500 University Drive N.W. Calgary, Alberta Canada, T2N 1N4 From chemistry-request@server.ccl.net Tue Mar 20 12:41:11 2001 Received: from nenuphar.saclay.cea.fr ([132.166.192.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KHfBD28612 for ; Tue, 20 Mar 2001 12:41:11 -0500 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20+Y2K) with ESMTP id SAA25354 for ; Tue, 20 Mar 2001 18:41:10 +0100 (MET) Received: from petunia.bruyeres.cea.fr (petunia.bruyeres.cea.fr [132.165.64.1]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id SAA14900 for ; Tue, 20 Mar 2001 18:41:10 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by petunia.bruyeres.cea.fr (8.9.3/jtpda-5.3.2) with ESMTP id SAA11345 for ; Tue, 20 Mar 2001 18:41:07 +0100 (MET) Received: by styx.bruyeres.cea.fr; id SAA05417; Tue, 20 Mar 2001 18:41:26 +0100 (MET) Message-Id: <200103201741.SAA05417@styx.bruyeres.cea.fr> Sender: Didier.MATHIEU@cea.fr Date: Tue, 20 Mar 2001 18:28:34 +0100 From: Didier MATHIEU X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: SUMMARY : how to calculate I.P. of large compounds Thanks for the advice and pointers concerning methods for efficient evaluation of chemical potentials. I am especially grateful to Stefan Grimme for pointing out that the Delta SCF method using B3LYP should yield I.P.s within 0.5 eV or better with extended basis sets. I had tried this approach before but obtained poor results owing to my lack of experience with the Jaguar program. Indeed, even taking care of the symmetry of the wf, the SCF iterations for the cation doublet often lead to spurious excited states. I have tested only few of the many options for the initial guess, however, to converge systematically to the cation ground state, I had to use the following procedure: 1. calculations on the molecule using only Abelian point group symmetry. 2. calculation on the doublet cation using the resulting orbitals from the molecule as a initial guess, and again allowing only Abelian point group symmetry assignment. The restriction to Abelian symmetry in step 1 is useful in view of reusing the orbitals as initial guess in step 2, otherwise an excited state was found in few cases. Out of test calculations on a set of 12 aromatic molecules, I got average and maximum errors of resp. 0.12 and 0.30 eV at the B3LYP/6-311G**//B3LYP/6-31G** level. With regard to Green fct techniques, I was first led to consider OVGF methods in combination with semi-empirical hamiltonian that have been implemented, apparently in a commercial version of MOPAC. However, the use of MNDO-type hamiltonians appear to have a significant impact on the accuracy: I recently received P. Diet et al. J. Chem. Soc. Perkin Trans 2 (8) 1653 (1999) where such calculations are reported. The errors of this approach to I.P.s, although 40% < that obtained through Koopmans theorem, are c.a. 3x > that obtained through Delta SCF / B3LYP. Regards, -- Didier Mathieu CEA - Le Ripault BP 16 37260 Monts +33 02 47 34 41 85 From chemistry-request@server.ccl.net Tue Mar 20 14:10:14 2001 Received: from sundown.cs.cornell.edu ([128.84.96.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KJAED28914 for ; Tue, 20 Mar 2001 14:10:14 -0500 Received: from fafe.cs.cornell.edu (IDENT:avijit@fafe.cs.cornell.edu [128.84.97.167]) by sundown.cs.cornell.edu (8.9.3/8.9.3/R-3.2) with ESMTP id OAA15112 for ; Tue, 20 Mar 2001 14:10:14 -0500 (EST) Date: Tue, 20 Mar 2001 14:10:14 -0500 (EST) From: Avijit Ghosh X-Sender: To: Subject: CCL:GPL'd (and friends) MM/QM packages :: Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Wow the GPL discussion has popped up again. I asked something a bit similiar to this tread a few months ago and compiled a list of packages that seemed related. The series of packages eventually evolved into a bit beyond GPL'd into the more general "Source available" packages. There are two corrections from the original post : (1) I mistakenly called David Case's NAB GPLish rather than GPL and (2) B (Java based MD) whose license is actually "less restrictive" than GPL rather than unknown. I've deleted all the original responses for brevity this time but I am sure they are in the archives somewhere.. Regards, -avi ------ I've extracted out the links into a compiled list as well as included the responses as a whole below that for some of the details w/ regards to particular programs. I've also added a few descriptors etc etc.. Here is the original question : --------------------original message---------------------------------- I was wondering whether anyone has any GPL'd code for MD? Particularly, whether there are any GPL'd force field implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a package (MOIL) here that is more or less public domain which includes an Amber88/(soon to be 95 implementation). There are a series of very nice programs that are available with source (NAMD/VMD from UIUC), Tinker from wustl (which is a really nice package btw) but is definitely copyrighted. However the licensing on these doesn't really encourage code reuse rather just personal code modification, and it would seem to me that code reuse might be beneficial in some circumstances rather than everyone reimplementing everyone elses algorithms/methods/force fields. In any case i'm curious as to what is out there already if anything. end-message---------------------------------------------------------------- Summary :: The programs below all have source, i've put the GPL'd code and GPLLike code at the top . I did some culling from the meta pages and put in some brief descriptions. As is hopefully obvious, don't trust me or my descriptions but take a look at the pages (links provided) for the real details. Hopefully this list will be useful to anyone who'd like to join incorporated their code into a GPL'd program and/or use algorithms from a gpl'd project. Apologies for all ytpos and any/all misrepresentations etc.. -Avi. Set (1) GPL'd Code. AMMP GPL MD Code (Apparantly has DFT incorporated!) http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html MOLDY GPL'd rigid body md http://www.earth.ox.ac.uk/~keith/moldy.html MOSCITO :: MD Code. ||ized. OPLS/AMBER/Gromacs. GPL'd http://ganter.chemie.uni-dortmund.de/~pas/moscito_info.html MMTK Open Sourced python based molecular modelling tool kit http://starship.python.net/crew/hinsen/MMTK/ Ghemical GPL Molecular modelling package http://www.uku.fi/~thassine/ghemical/ EGO_VIII || MD Code (GPL). http://www.lrz-muenchen.de/~heller/ego/egointro.html NAB :: Nucleic Acid Builder (implements amber95 :: has Generalized Born) (GPL) http://www.scripps.edu/case MPQC :: Massively Parallel Quantum Chemistry program. GPL'd. http://aros.ca.sandia.gov/~cljanss/mpqc/ ORAC MD for solvated biomolecules. GPL'd. http://www.chim.unifi.it:8080/orac/ Set two :: (soon to be) GPLish?? Allows redistribution?? CHIMP :: "generic tool for modelling of chemical phenomena." GPL'd. but "unavailable" ?? http://chimp.sourceforge.net/ GROMACS : || MD code . Being considered for GPL http://md.chem.rug.nl/~gmx NAMD :: || MD Code. "Licensee may redistribute without restriction works with up to 1/2 of their non-comment source code derived from at most 1/10 of the non-comment source code developed by Illinois and contained in the Software, provided that the above directions for notice and acknowledgement are observed." (see below) http://www.ks.uiuc.edu/Research/namd/ Cornell's Computational Biology TOOLS (Lots of free MD etc packages from R. Elber and H. Scheraga) :: Free for all use, as long as you don't sell it to people for $$. http://www.tc.cornell.edu/CBIO/ NWCHEM Massively || QM/MM code (free as long as you aren't a U.S. "baddy" ) http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html B :: Java based MD Code (Less restrictive than GPL) http://www.scripps.edu/~nwhite/Biomer/index.html Set (3) Other. Many here are "Free for Academic use" which generally means no redistribution (Free use; no abuse :)), but as always look at the pages. Incidentally, free for academic use is nice but *imho* GPL (and friends or at least allowing redistribution) is nicer as it means i (and my friends) can try out your algorithm/force field/minimizer/integrator/solvation model etc etc w/ my (insert previous list in reverse order) and let others try it w/out having to reimplement each spoke on this wheel, which as far as I can gather pretty much everyone is doing. Tinker :: (Copyright WUSTL/Tinker but see below w/ regards using/redistributing source) http://dasher.wustl.edu/tinker/ DYNAMO :: F90 modules for QM/MM (OPLS-AA) free of charge. No redistribution. http://www.ibs.fr/ext/labos/LDM/projet6/welcome_fr.htm LAMMPS :: || MD code. Free for academic use. No redistribution. http://www.cs.sandia.gov/~sjplimp/lammps.html GULP :: simulation of periodic solids/clusters.. :: free for academics. no redist. http://www.ch.ic.ac.uk/gale/Research/gulp.html DL_POLY || MD code :: Free for Academic Scientists pursing non-commercial science. http://www.dl.ac.uk/TCSC/Software/DL_POLY/main.html ARTWork :: MD/MC code based on "Effective Medium Theory" , avail. for acad. purposes "as is" http://www.fysik.dtu.dk/~stoltze/artwork/artwork.html Autodock :: Docking code, free for academic use. http://www.scripps.edu/pub/olson-web/doc/autodock/ MDYNAMIX :: source code available (couldn't find license on web page) http://www.fos.su.se/physical/sasha/md_prog.html From chemistry-request@server.ccl.net Tue Mar 20 11:07:38 2001 Received: from femail1.sdc1.sfba.home.com ([24.0.95.81]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2KG7cD27924 for ; Tue, 20 Mar 2001 11:07:38 -0500 Received: from structbio.vanderbilt.edu ([65.14.17.27]) by femail1.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with ESMTP id <20010320160704.HBSW21765.femail1.sdc1.sfba.home.com@structbio.vanderbilt.edu>; Tue, 20 Mar 2001 08:07:04 -0800 Sender: jsmith@ccl.net Message-ID: <3AB7817C.9B828902@structbio.vanderbilt.edu> Date: Tue, 20 Mar 2001 10:12:44 -0600 From: Jarrod Smith Organization: Vanderbilt University X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-XFS i686) X-Accept-Language: en MIME-Version: 1.0 To: Christian Pilger CC: chemistry@ccl.net Subject: Re: CCL:AutoDock/LINUX References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Christian Pilger wrote: > > Dear CCLers, > > I have a question about the script "mol2topdbq" that comes with > AutoDock 3.0.5. I changed the "nawk" in the very beginning to the > awk-version I'm using on my PC (Suse Linux 7.1) "gawk", but this scripts > does not work properly - upon exeution, I get the following message: > > gawk: cmd. line:33: fatal: expression for `<' redirection has null string > value Try changing "nawk" to "gawk --traditional" and see if that helps. -- Jarrod A. Smith Research Asst. Professor, Biochemistry Asst. Director, Center for Structural Biology Computation and Molecular Graphics Vanderbilt University