From chemistry-request@server.ccl.net Tue Apr 11 04:31:03 2000 Received: from sg2.csrsrc.mi.cnr.it (sg2.csrsrc.mi.cnr.it [155.253.3.253]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA09147 for ; Tue, 11 Apr 2000 04:30:56 -0400 Received: from csrsrc.mi.cnr.it by sg2.csrsrc.mi.cnr.it via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id HAA10463; Tue, 11 Apr 2000 07:39:32 -0700 Sender: alex@csrsrc.mi.cnr.it Message-ID: <38F2E4BE.BE949C9A@csrsrc.mi.cnr.it> Date: Tue, 11 Apr 2000 10:39:26 +0200 From: Alessandro Pandini X-Mailer: Mozilla 4.03 [en] (X11; I; AIX 4.1) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:Rotamer library backbone dependent References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > I'm doing the work of side chain construction at the protein-protein > interface. The computational result was suffered from the incompleteness > of the rotamer library, which is backbone independent and contains more > than 300 elements. Can anyone tell me where can I get a more detailed > library? Thanks in adance! > > Liang > I used SCWRL to refine a protein obtained via homology modelling. (http://www.cmpharm.ucsf.edu/~bower/scwrl/scwrl.html) This works with a backbone-dependent library. You can find the update version at: http://www.fccc.edu/research/labs/dunbrack/index.html Maybe it could be helpful. By Alex From chemistry-request@server.ccl.net Tue Apr 11 08:40:15 2000 Received: from tca7.dl.ac.uk (tca7.dl.ac.uk [193.62.112.105]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA11129 for ; Tue, 11 Apr 2000 08:40:11 -0400 Received: from localhost by tca7.dl.ac.uk; (5.65v4.0/1.1.8.2/06Oct95-0132PM) id AA19902; Tue, 11 Apr 2000 13:26:51 +0100 Sender: hgs@dl.ac.uk Message-Id: <38F31A0B.91C4C977@dl.ac.uk> Date: Tue, 11 Apr 2000 13:26:51 +0100 From: Georg Schreckenbach Reply-To: h.g.schreckenbach@dl.ac.uk Organization: CLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: CCL Subject: Summary: all-electron basis sets for actinides Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, this is my summary for a question that I posted some time ago. I got a few useful answers -- thank you! Regards, Georg Original question: ========================================== Subject: CCL:all-electron Gaussian basis for actinides Dear everybody, does anyone know of ALL-ELECTRON Gaussian basis sets for actinide elements, published or unpublished? I'd be particularly interested in the early actinides, Th thru' Am, say. I have already searched the CCL archives and the EMSL basis set repository but with no success. I know, of course, that one would normally use ECPs or related methods for these heavy elements. (... and there are a couple of ECP basis sets in the EMSL library ...) I also know that the ADF program provides all-electron SLATER basis sets for these elements. Would it, perhaps, be possible to use the basis sets that were developed for four-component relativistic methods? If so, would they have to be modified? (I suppose so ... e.g. take the large component only?) Where are they to be found? ========================================== Replies: ========================================== From: noj malcolm you will find some references in a recent paper by Tilson, Shepard, Naleway, Wagner and Ermler (JCP 112#5 (2000) p2292) the basis sets employed seem to be private communications unfortunately, but you may get soemwhere by getting in touch with the authors. noj Dr. N.O.J. Malcolm e-mail:noj@yeager5.chem.tamu.edu Department of Chemistry Texas A&M University College Station TX 77845 U.S.A ============================================ From: "Han Young-Kyu" Hello. To my knowledge, Dr. K. G. Dyall optimized all-electron basis sets for U, Th, and Pa. [Mol. Phys. 96, 511 (1999)]. A uranium basis set is also found at W. A. De Jong et al. [Int. J. Quantum Chem. 58, 203 (1996)]. You have to optimize the contraction coefficients for your purpose. Best regards, Young-Kyu Han Young-Kyu Han (Ph.D. Korean) Department of applied chemistry, Graduate school of engineering, The university of Tokyo, Hongo 7-3-1 Bunkyo-ku, Tokyo 113-8656, Japan Phone(or Fax) : +81-3-5841-7242(Lab) Email : ykhan@qcl.t.u-tokyo.ac.jp or ykhan@orbit.kaist.ac.kr ================================================ From: Helene BOLVIN Dear Georg, I will advise you the all-electron basis sets made by Knut Faegri, professor i Oslo.They are not published, but you can ask him: knut.faegri@kjemi.uio.no But do not forget to include relativistic effect by the mean, for example of the Douglas-Kroll integrals. Sincerly Helene Helene BOLVIN Institutt for kjemi tlf: (+47) 77 64 40 61 Universitetet i Tromsoe fax: (+47) 77 64 47 37 N-9037 TROMSOE From chemistry-request@server.ccl.net Tue Apr 11 08:51:34 2000 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA11262 for ; Tue, 11 Apr 2000 08:51:28 -0400 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id PAA19695 for ; Tue, 11 Apr 2000 15:47:17 +0300 (EET DST) Date: Tue, 11 Apr 2000 15:47:16 +0300 (EET DST) From: John Kerkines To: chemistry@ccl.net Subject: Re: CCL:triplet and singlet gap of C2 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 10 Apr 2000, Ohyun Kwon wrote: > Dear CCLer's; > Could anybody give some information about C2? > C2 can have triplet or singlet state and I would like to know which is > more stable and what is the energy gap between two states? > Thank you in advance. > > yours > Hi Ohyun, Huber and Herzberg's "Constants of Diatomic Molecules" (1979) gives a 'singlet sigma g plus' ground state with a first excited 'triplet pi u' state and an experimental gap of 716.2 cm**-1 (i.e. a gap of only ~2 kcal/mol). I guess that the ground state should correlate to the M=+/-1 and -/+1 ground state carbons (triplet P), and the first excited to the M=0 and M=+/-1 ground state carbons. Regards, John Kerkines University of Athens, Greece From chemistry-request@server.ccl.net Mon Apr 10 15:06:13 2000 Received: from sdnt1.Acadia-SD (mail.acadia-pharm.com [209.77.18.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA05189 for ; Mon, 10 Apr 2000 15:06:12 -0400 Received: by sdnt1 with Internet Mail Service (5.5.2650.21) id <2N2GQWN1>; Mon, 10 Apr 2000 12:06:09 -0700 Message-ID: <15189A4705A8D31189B700805F85410B1D821D@sdnt1> From: Daniel Severance To: "CCL (E-mail)" Cc: Daniel Severance Subject: CAS Numbers Date: Mon, 10 Apr 2000 12:06:08 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hi, I have a list of about 2000 CAS numbers - is there a reasonably inexpensive way to use those numbers to retrieve the corresponding structures? Also one that wouldn't take weeks of a human's time would be nice :-). Thanks! Dan ____________________________________________________ Daniel L. Severance Ph.D. Computational Chemistry ACADIA Pharmaceuticals 3911 Sorrento Valley Boulevard San Diego CA 92121-1402 USA phone (858) 558 2871 fax (858) 558 2872 dseverance@acadia-pharm.com www.acadia-pharm.com From chemistry-request@server.ccl.net Tue Apr 11 09:33:04 2000 Received: from alfa.chem.uw.edu.pl (alfa.chem.uw.edu.pl [212.87.3.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA11444 for ; Tue, 11 Apr 2000 09:12:17 -0400 Received: from alfa (panso236.chem.uw.edu.pl [212.87.3.83]) by alfa.chem.uw.edu.pl (8.10.0.Beta10/8.10.0.Beta10) with SMTP id e3BDHJM22884 for ; Tue, 11 Apr 2000 15:17:19 +0200 (MET DST) Message-Id: <3.0.6.32.20000411151216.00796100@alfa.chem.uw.edu.pl> X-Sender: alenie@alfa.chem.uw.edu.pl X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 11 Apr 2000 15:12:16 +0200 To: chemistry@ccl.net From: Andrzej Leniewski Subject: Re: CCL:isomer software Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I encountered one at the site http://www.mathe2.uni-bayreuth.de/molgen4/start.html, although it is not freeware. Andrzej Leniewski At 3:36 PM 4/4/00 +0800, you wrote: >Dear Netters, >could someone please tell me what software >(preferably freeware) is available for >drawing structures of isomers upon entering >a given bruto molecular formula!? >Many thanks!! >Yours sincerely >I.Novak >Dept.of Chemistry >National University of Singapore >Singapore 117543 >chmigorn@nus.edu.sg > From chemistry-request@server.ccl.net Tue Apr 11 09:38:36 2000 Received: from mjco-s2.ice.mpg.de (mjco-s2.ice.mpg.de [195.37.47.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA00441 for ; Tue, 11 Apr 2000 09:38:31 -0400 Received: from ice.mpg.de (unverified [195.37.47.130]) by mjco-s2.ice.mpg.de (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 11 Apr 2000 15:22:05 +0200 Message-ID: <38F326BE.47659A06@ice.mpg.de> Date: Tue, 11 Apr 2000 15:21:02 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: ccl CC: David van der Spoel Subject: Re: Is CML dead? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Last year in May there was a vivid discussion on the CCL about using > XML/CML for storing chemical information. I recently checked up the > website http://www.xml-cml.org and it seems quite dead... > The only software available is a bunch of java classes and the CML DTD > (DocumentTypeDescription). > > If I would like to read or write CML/XML files from my programs written in > C or Fortran do I have to write a complete library to do it? If I would do > that, would others be interested to use it in their software? To extend > the library? I don't think it's dead. I'm just sitting here at this years meeting of the Chemistry-Information-Computers section of the German Chemical Society at the Analytica in Munich. Tomorrow we will have at least two talks dealing with CML. Having already talked to some people here about the subject of CML, it seems that there is a considerable amount of uncertainty about the future of CML and whether it will be possible to implement it as "the standard of coding chemical documents". The most important concern is too many people doing to many different things (not with, but) to CML, which is also my biggest concern. If I don't forget it I will comment on what will have been discussed tomorrow. Greetings, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Tue Apr 11 11:07:41 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA00720 for ; Tue, 11 Apr 2000 11:07:40 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12f2CS-0004jN-00 for CHEMISTRY@ccl.net; Tue, 11 Apr 2000 16:03:32 +0100 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12f2CE-0004F6-00 for CHEMISTRY@ccl.net; Tue, 11 Apr 2000 16:03:18 +0100 Received: from rzepa.ch.ic.ac.uk ([155.198.234.86]) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 12f2CM-001yxS-00; Tue, 11 Apr 2000 16:03:26 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: <200004102044.WAA29861@studs3.sci.kun.nl> References: <200004102044.WAA29861@studs3.sci.kun.nl> Date: Tue, 11 Apr 2000 16:03:12 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:Is CML dead? Content-Type: text/plain; charset="us-ascii" We have mounted a number of XML tests using CML on http://www.xml-cml.org/test/ (a mirror site if the above is slow is http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet Explorer 5.0 or 5.5 for Windows. This has to be Java enabled in the Security settings. Internet Explorer 5.0 for MacOS SHOULD work, but fails. We are currently in contact with Microsoft to help resolve this problem (if you are using MacOS, then http://www.ch.ic.ac.uk/chimeral/test/mactest1.xml DOES work!. Tests 2-5 do not!) What the browser should then do is the following 1. A request for an XML Schema defining CML is made. 2. An XML document is retrieved and validated against the CML schema 3. If valid, an XSL stylesheet is retrieved and applied 4. This produces display HTML which in turn invokes the tools needed to display the content. 5. We have developed a range of XSL stylesheets to make use of various Java software available, some OpenSource (JMol, JSpec, etc) some not (JME, Marvin, etc). We also have a server-side implementation which needs some debugging (ie the XSL transforms are done server side rather than browser side). Shortly, we will offer a server-side CML validation service against the schema noted above We in particular seek a) Information about freely available Java programs to incorporate into our demos (these can be seen at http://www.ch.ic.ac.uk/chimeral/ ) b) Contributions to the OpenSource Stylesheet library c) Any other similar demos others might have come up with. A Markup Languages workshop, including XML and CML, will be held at Chemint2000 (www.chemint.org) this September, and if you wish to participate, do please come along! There was an interesting debate about Graphical user interfaces for Chemistry on this list a few months back. I note with interest the development by Netscape (Netscape 6 does not yet support XSL, and so does not run the above demos) of XUL (eXtensible User-interface Language). One presumes that libraries of XUL might develop in a manner we anticipate XSL libraries developing. Finally, I note XML-Signature Syntax and Processing", http://www.w3.org/TR/xmldsig-core/ which will allow digital signatures to be added to XML/XSL documents (see J. Chem. Inf. Comp. Sci., 1999, 39, 483-490. ) -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Tue Apr 11 17:13:24 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02551 for ; Tue, 11 Apr 2000 17:13:23 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Tue, 11 Apr 2000 23:14:45 +0200 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA20280; Tue, 11 Apr 2000 23:13:27 +0200 Date: Sat, 8 Jul 2000 23:02:25 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: "Rzepa, Henry" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Is CML dead? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 11 Apr 2000, Rzepa, Henry wrote: >We have mounted a number of XML tests using CML on >http://www.xml-cml.org/test/ (a mirror site if the above is slow is >http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet >Explorer 5.0 or 5.5 for Windows. I think this is close to the heart of the problem. The current efforts are directed to *new* tools for visualisation (I work in a Windows-Free (tm) environment) while we have plenty of old tools which do the job, but are just not CML/XML enabled. In the tests there are examples of combined structure/spectra files. Instead of dumping the CML in a slow browser I would like to give the CML file to rasmol to view the structure and the same file to e.g. xmgrace to see a spectrum. What is needed for that is a simple comprehensive C-library which can be called by the respective programs. I realize that there is a need for (web) publishing tools, and that the current java tools are a means to this end, however without programs that generate CML there is nothing to publish. I am willing to contribute to the library, as long as someone else (Henry?) keeps the overview and coordinates things, which as Christoph Steinbeck pointed out is crucial. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue Apr 11 20:08:11 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA03557 for ; Tue, 11 Apr 2000 20:08:10 -0400 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id RAA32297 for ; Tue, 11 Apr 2000 17:08:10 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id UAA02500 for ; Tue, 11 Apr 2000 20:08:03 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Tue, 11 Apr 2000 20:08:03 -0400 (EDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:Is CML dead? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hear, hear. It was a lack of such tools several years ago that caused us to shy away from XML/CML when designing our new Maestro interface. It is disappointing if, indeed, there are no such tools linkable to C, Fortran and C++ even today. Henry, what sayest thou? -P. On Sat, 8 Jul 2000, David van der Spoel wrote: > On Tue, 11 Apr 2000, Rzepa, Henry wrote: > > >We have mounted a number of XML tests using CML on > >http://www.xml-cml.org/test/ (a mirror site if the above is slow is > >http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet > >Explorer 5.0 or 5.5 for Windows. > > I think this is close to the heart of the problem. The current efforts > are directed to *new* tools for visualisation (I work in a > Windows-Free (tm) environment) while we have plenty of old tools which > do the job, but are just not CML/XML enabled. > > In the tests there are examples of combined structure/spectra > files. Instead of dumping the CML in a slow browser I would like to > give the CML file to rasmol to view the structure and the same file to > e.g. xmgrace to see a spectrum. What is needed for that is a simple > comprehensive C-library which can be called by the respective > programs. I realize that there is a need for (web) publishing tools, > and that the current java tools are a means to this end, however > without programs that generate CML there is nothing to publish. > I am willing to contribute to the library, as long as someone else (Henry?) > keeps the overview and coordinates things, which as Christoph Steinbeck > pointed out is crucial. > > Groeten, David. > ________________________________________________________________________ > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > phone: 46 18 471 4205 fax: 46 18 511 755 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > -= 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 > > > > > -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Tue Apr 11 20:55:40 2000 Received: from leonis.nus.edu.sg (leonis.nus.edu.sg [137.132.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA03852 for ; Tue, 11 Apr 2000 20:55:39 -0400 Received: from bic.nus.edu.sg (arrakis.bic.nus.edu.sg [137.132.45.220]) by leonis.nus.edu.sg (8.9.3/8.9.3) with ESMTP id IAA11792 for ; Wed, 12 Apr 2000 08:55:34 +0800 (SST) Sender: linkui@leonis.nus.edu.sg Message-ID: <38F3CB79.CA16FE02@bic.nus.edu.sg> Date: Wed, 12 Apr 2000 09:03:53 +0800 From: Lin Kui Organization: BIC, NUS X-Mailer: Mozilla 4.51 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: "CCL (E-mail)" Subject: How flexible a peptide ligand can be? References: <15189A4705A8D31189B700805F85410B1D821D@sdnt1> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I am trying to dock a pepdide onto a protein using AutoDock, After having tried it as a rigid ligand, I'll go to the next step to allow the peptide flexible, would anyone like to tell me how to relax a peptide being flexible? I mean whether there are any essentail principles described in reviews or papers? Thanks a lot. Kui Lin Structural Biology and Bioinformatics Institute of Molecular and Cell Biology 30 Medical Drive, Singapore 117609 e-mail: linkui@bic.nus.edu.sg phone: (+65) 874-3367