From chemistry-request@server.ccl.net Wed Dec 18 16:53:03 2002 Received: from concord.org ([4.19.234.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBILr2i11487 for ; Wed, 18 Dec 2002 16:53:02 -0500 Received: from fc.concord.org (fc.concord.org [4.19.234.60]) by concord.org (8.11.6/8.11.6) with ESMTP id gBILr2I32655 for ; Wed, 18 Dec 2002 16:53:02 -0500 Received: from dhcp165.concord.org (4.19.234.165) by fc.concord.org (FirstClass Mail Server v7.0) with ESMTP (Sender: qxie@concord.org) transient id 987; Wed, 18 Dec 2002 16:52:57 -0500 Message-Id: <5.1.1.6.2.20021218164510.00a88220@secure.concord.org> X-Sender: qxie@secure.concord.org (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 18 Dec 2002 16:52:50 -0500 To: chemistry@ccl.net From: Qian Xie Subject: Concord Modeling Workbench Version 1.1 available (formerly Concord Modeler) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi folks, We would like to announce the release of our educational molecular simulation freeware, the Concord Modeling Workbench Version 1.1. The software can be downloaded at: http://workbench.concord.org/modeler/index.html The Concord Modeling Workbench is a set of educational tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using molecular mechanics forces. Meso-scale objects and their interactions based on the Gay-Berne model are supported. The resulting ensembles can illustrate energy conservation, gas laws, pressure, phase transitions, chemical bonding, chemical reactions, Maxwell velocity distribution, osmosis, electrolysis, electrophoresis, liquid crystals, polymers, and more. The Concord Modeling Workbench also provides an integrated software environment that can be used to easily create, visualize, annotate, contextualize, cross-link and distribute molecular dynamics models. High school and college students can use it to explore a vast range of preexisting models, or to develop models of their own. The International Center The Concord Consortium 978-369-2715 From chemistry-request@server.ccl.net Thu Dec 19 02:45:19 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJ7jIi26242 for ; Thu, 19 Dec 2002 02:45:18 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 1192E706624; Thu, 19 Dec 2002 08:45:08 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 8A2B3706621; Thu, 19 Dec 2002 08:45:06 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 19 Dec 02 08:45:06 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 19 Dec 02 08:45:03 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Connie Chang Date: Thu, 19 Dec 2002 08:44:34 +0100 Subject: Re: CCL:Gaussian98W and hessian again.... Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <8395C82626F@virgil.ruc.dk> Connie Chang: > I obtained the hessian from the archive portion of the output file > starting from NImag=0|| and ending at ||. I read this is as lower > triangular matrix and filled in the blanks. THen I converted it to > units of erg/cm^2 and divided by the mass (my molecule contains all > of the same atoms). Then I diagonalize this matrix to get the > eigenvalues and eigenvectors. My question is -- Why don't the > eigenvectors I get this way match the eigenvectors given by the > output part of the file: > 6 7 8 9 > AG BU AG BG > Frequencies --- 133.7777 217.8831 219.3526 220.1136 > > etc.etc.? I need the entire eigenvector matrix and not just 3*N-6 > translation/rotational modes. The eigenvalues seem to match up > fine, but the eigenvectors are different. Am I somehow scrambling > the atom order or something? If I understand your procedure correctly, you obtain the normal modes in terms of mass-weighted displacement coordinates. But the 'normal modes' printed by Gaussian are expressed in cartesian displacement coordinates and normalized to unit length. - You may see the Gaussian web-place for further information. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Dec 19 08:37:35 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJDbZi17388 for ; Thu, 19 Dec 2002 08:37:35 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 61A3070AAD1; Thu, 19 Dec 2002 14:37:34 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 8BD7470AAC9 for ; Thu, 19 Dec 2002 14:37:30 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 19 Dec 02 14:37:31 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 19 Dec 02 14:37:29 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Thu, 19 Dec 2002 14:37:03 +0100 Subject: CCL:Gaussian98W and hessian again.... Reply-To: spanget@ruc.dk X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <83F3C6528CE@virgil.ruc.dk> Dear Connie, I elaborate a little bit: If I understand your procedure correctly, you obtain the normal modes Q in terms of mass-weighted displacement coordinates. Your normal mode vectors should form an orthonormal set. But the "normal modes" printed by Gaussian are expressed in cartesian displacement coordinates and normalized to unit length (1 Angstrom). They are not necessarily orthogonal. You may try the following: First multiply the coefficients printed by Gaussian by the inverse square root of the reduced mass; the reduced mass is printed by Gaussian in units of u (or AMU, atomic mass unit). This produces the cartesian displacement vectors X associated with unit displacement along the corresponding normal coordinates Q. Then multiply the elements of X by the square roots of the pertinent atomic masses m(i). If my reasoning is correct, this should produce the proper normal modes Q in terms of mass-weighted displacement coordinates in units of sqr(u)*Angstrom. Hopefully, the resulting normal modes agree with the ones you have computed. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Dec 19 06:08:13 2002 Received: from mail.unina.it ([192.132.34.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJB8Di13173 for ; Thu, 19 Dec 2002 06:08:13 -0500 Received: (from root@localhost) by mail.unina.it (8.12.6/8.12.6) id gBJB4RcO029300 for chemistry@ccl.net; Thu, 19 Dec 2002 12:04:27 +0100 Received: from lavecchia.cds.unina.it (alpha.farmacia.unina.it [143.225.223.185]) by mail.unina.it (8.12.6/8.12.6) with ESMTP id gBJB4OnA029221 for ; Thu, 19 Dec 2002 12:04:26 +0100 Message-Id: <5.0.0.25.0.20021219115119.00a69760@cds.unina.it> X-Sender: lavecchi@cds.unina.it X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Thu, 19 Dec 2002 12:01:03 +0100 To: chemistry@ccl.net From: Antonio Lavecchia Subject: Autodock Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_3482535==_.ALT" X-scanner: scanned by Inflex 1.0.12.5 on mail.unina.it --=====================_3482535==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hello all, Is it possible to perform docking experiments with Autodock program making the side chains of the receptor flexible? If so, which procedure do I need to use to do that? Thank you in advance for all the help. Antonio ANTONIO LAVECCHIA, PhD Computational Chemistry Dept of Pharmaceutical Chemistry University of Naples Via D. Montesano, 49 80131 NAPOLI E-Mail: lavecchi@unina.it Phone: ++39 081 678613/619 Fax: ++39 081 678644 --=====================_3482535==_.ALT Content-Type: text/html; charset="us-ascii" Hello all,
Is it possible to perform docking experiments with Autodock program making the side chains of the receptor flexible? If so, which procedure do I need to use to do that?
Thank you in advance for all the help.
Antonio

ANTONIO LAVECCHIA, PhD
Computational Chemistry
Dept of Pharmaceutical Chemistry
University of Naples
Via D. Montesano, 49
80131 NAPOLI
E-Mail: lavecchi@unina.it
Phone: ++39 081 678613/619
Fax:      ++39 081 678644 --=====================_3482535==_.ALT-- From chemistry-request@server.ccl.net Thu Dec 19 17:37:56 2002 Received: from mailrelay1.lanl.gov ([128.165.4.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJMbti32388 for ; Thu, 19 Dec 2002 17:37:55 -0500 Received: from swan.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay1.lanl.gov (8.12.3/8.12.3/(ccn-5)) with ESMTP id gBJM1r9i025143; Thu, 19 Dec 2002 15:01:53 -0700 Received: from heron.lanl.gov (heron.lanl.gov [128.165.96.39]) by swan.lanl.gov (8.12.1/8.12.1) with ESMTP id gBJM1boR006045; Thu, 19 Dec 2002 15:01:37 -0700 Received: from localhost (tamulis@localhost) by heron.lanl.gov (8.12.1/8.12.1) with ESMTP id gBJEtdwf005690; Thu, 19 Dec 2002 07:55:39 -0700 Date: Thu, 19 Dec 2002 07:55:39 -0700 (MST) From: "Temporary Guest Account;CNLS;7-1444;9999999" To: cc: , Subject: HFS in the presence of isotopes and magnetic field B Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I have two questions: 1) How to calculate with Gaussian 98 Fermi Contact Coupling of radical molecules with N(15 isotope) adding Spin of N(15) nuclei equal to 1/2 and Magnetogyric ratio (rad/T s) equal to -2.712 x 10^7 (and maybe changing the constant 8*pi/3 by 4*pi/3 due to different N(15) nucleus spin=1/2 comprarison with N(14) nucleus spin=1). Does it exist some special keyword or something like that allowing in G98 to calculate Fermi Contact Coupling with less popular atoms isotopes? If no, maybe somebody can give me some software for calculations of Fermi Contact Couplings with different atom isotopes? 2) I am asking also for software that might to calculate HFS interactions of radicals possessing different isotopes in the presence of magnetic field. I agree to include owners of these software in the list of authors for sharing the programes and for help in the begining of calculations. Thanking your in advance. With bst regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Temporal address until 28 February 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: (505) 667-7278 Fax: (505) 665-2659 e-mail: tamulis@cnls.lanl.gov ******************************************************************* From chemistry-request@server.ccl.net Thu Dec 19 11:31:34 2002 Received: from gold.csi.cam.ac.uk ([131.111.8.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJGVYi22840 for ; Thu, 19 Dec 2002 11:31:34 -0500 Received: from ursus.ch.cam.ac.uk ([131.111.121.19] helo=ursus.cam.ac.uk) by gold.csi.cam.ac.uk with esmtp (Exim 4.10) id 18P3a4-00051T-00; Thu, 19 Dec 2002 16:31:28 +0000 Message-Id: <5.1.1.6.0.20021217192949.0295a158@hermes.cam.ac.uk> X-Sender: pm286@hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 19 Dec 2002 16:32:28 +0000 To: Konrad Hinsen , gamercier@yahoo.com From: Peter Murray-Rust Subject: Re: CCL:[MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd) Cc: pyquante-users@lists.sourceforge.net, pymol-users@lists.sourceforge.net, mmtk@python.net, chemistry@ccl.net In-Reply-To: References: <20021212183033.56193.qmail@web80301.mail.yahoo.com> <20021212183033.56193.qmail@web80301.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 10:41 13/12/2002 +0100, Konrad Hinsen wrote: >Gustavo Mercier writes: >As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it >would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface >with other technologies. I recognize that there are problems with CML, but this should not stop the community > from considering >this "standard". >Gustavo > > As a suggestion, let's consider the chemistry implementation of XML > > -- CML. Whatever the details of the object "molecule", it would be > > beneficial to input and output to/from CML. A specification of > >I don't agree. I looked at CML a while ago, thought about implementing >it in MMTK, but quickly found out that almost none of the information >I needed to store about molecules could be represented in CML, except >by adding "conventions" of my own - but then I could just as well >define my own XML format. CML is based on the right intentions, but is >too weak as an implementation. CML is designed to be extensible by a variety of mechanisms such as external ontologies and we would be delighted to hear from those who find it "too weak". We are currently developing a computational chemistry implementation (CCML) as previously mentioned on this list. The feature of XML languages is that XML requires semantics to be well designed and interoperable, *and* to have communally available software tools for reading, validating and writing and linking to ontologies. CML is designed for collaborative working and we shall shortly announce the mailing list. P. Unilever Centre for Molecular Informatics Cambridge University, UK From chemistry-request@server.ccl.net Thu Dec 19 09:39:03 2002 Received: from hermes.csd.unb.ca ([131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJEd3i19568 for ; Thu, 19 Dec 2002 09:39:03 -0500 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id gBJEcvAV020426 for ; Thu, 19 Dec 2002 10:38:57 -0400 (AST) Received: FROM pop.unb.ca BY mailserv2 ; Thu Dec 19 10:38:49 2002 -0400 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.6+Sun/8.11.6) with ESMTP id gBJEcnK28717; Thu, 19 Dec 2002 10:38:49 -0400 (AST) X-WebMail-UserID: l72k6 Date: Thu, 19 Dec 2002 10:38:49 -0400 Sender: Robert Flight From: Robert Flight To: Antonio Lavecchia , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:Autodock Message-ID: <3E02B22F@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hi Antonio, Unfortunately that feature is not yet implemented in Autodock, although there have been some papers published investigating side chain flexibility (see Osterberg et al., (2002) Automated Docking to Multiple Target Structures: Incorporation of Protein Mobility and Structural Water Heterogeneity in Autodock. Proteins 46:34-40) and the Autodock webpage announces that it will be available in the next release. The other possibility would be to do a molecular dynamics simulation of the receptor to produce multiple side chain conformers and then dock the ligand to each conformer (I cant find the reference, but I have seen it done). Cheers, Robert >===== Original Message From Antonio Lavecchia ===== >Hello all, >Is it possible to perform docking experiments with Autodock program making >the side chains of the receptor flexible? If so, which procedure do I need >to use to do that? >Thank you in advance for all the help. >Antonio > >ANTONIO LAVECCHIA, PhD >Computational Chemistry >Dept of Pharmaceutical Chemistry >University of Naples >Via D. Montesano, 49 >80131 NAPOLI >E-Mail: lavecchi@unina.it >Phone: ++39 081 678613/619 >Fax: ++39 081 678644 ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy