From chemistry-request@server.ccl.net Mon Jul 17 08:28:57 2000 Received: from psimd-nt.baltimore.oxmol.com (psimd-nt.baltimore.oxmol.com [134.172.64.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA16601 for ; Mon, 17 Jul 2000 08:28:52 -0400 Message-ID: <1C9A542974ECD21199820020AF267C0035E96D@psimd-nt.baltimore.oxmol.com> From: "Douglas A. Smith" To: chemistry@ccl.net Subject: Dan Dolata Date: Mon, 17 Jul 2000 08:33:04 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Can anyone provide me with the current contact information for Dan Dolata? I would like very much to speak with him. Doug Douglas A. Smith, Ph.D. voice: 410-527-4571 Product Manager fax: 410-527-4599 Oxford Molecular Group email: dsmith@oxmol.com Executive Plaza III, Suite 1100 http://www.oxmol.com 11350 McCormick Road Hunt Valley, MD 21031 From chemistry-request@server.ccl.net Mon Jul 17 02:17:15 2000 Received: from fep6.online.sh.cn ([202.96.209.79]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA14168 for ; Mon, 17 Jul 2000 02:17:14 -0400 Received: from cadd ([61.129.170.105]) by fep6.online.sh.cn (InterMail vM.4.01.02.39 201-229-119-122) with SMTP id <20000717061652.KUMP493.fep6.online.sh.cn@cadd> for ; Mon, 17 Jul 2000 14:16:52 +0800 Date: Tue, 18 Jul 2000 14:18:28 +0800 From: yunlong song To: "CHEMISTRY@ccl.net" Subject: Conforamation composition Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20000717061652.KUMP493.fep6.online.sh.cn@cadd> Dear computational chemists, I am performing conformational analysis on a drug molecule.I want to know the exact population of each conformer. I want to know how to calculation the conformation population analysis based on Boltzmann law? Can you help me ? Also, I want to know how to calculate torsion energy profile according a torsion bond.The interal coordinates may be useful,however the molecule is quite large.I use its cartesian coordinate.So can I use cartesian coordinate to comput the pofile. In literature, people often referred to reaction coordinate drive method.Can someone give me an exact explanation? Thanks in advance! From chemistry-request@server.ccl.net Mon Jul 17 04:28:41 2000 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA14790 for ; Mon, 17 Jul 2000 04:28:39 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id KAA22254 for ; Mon, 17 Jul 2000 10:28:25 +0200 (MET DST) Message-ID: <00cd01bfefc8$8bc367c0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "CCL" Subject: ORAC Date: Mon, 17 Jul 2000 10:25:14 +0200 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCLers, I'm looking for a version of ORAC package, specifically compiled for Pentium II/III (if exists). Thank you in advance Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Mon Jul 17 07:13:07 2000 Received: from citrin.chemie.uni-dortmund.de (citrin.Chemie.Uni-Dortmund.DE [129.217.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA16283 for ; Mon, 17 Jul 2000 07:13:06 -0400 Received: from citrin.chemie.uni-dortmund.de (unknown [129.217.221.9]) by citrin.chemie.uni-dortmund.de (Postfix) with ESMTP id 702C61DA003 for ; Mon, 17 Jul 2000 13:12:55 +0200 (CEST) Message-ID: <3972EA62.8495947A@citrin.chemie.uni-dortmund.de> Date: Mon, 17 Jul 2000 13:13:39 +0200 From: dck X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: de,en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:SUMMARY:geometry with an applied e-field Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers! Some days ago I had the following question: > Does anyone know what quantumchemical program is able to optimize a > geometry with an applied electrical field? All programs that I have > used until now allow only single point calculations with an E-field. here is a selection of the answers. by the way, gaussian allows single point energy, Force, and Scan calculations only with the field keyword. So all answers in this regard are skiped in this summary. Thanks for the answers dirk _________________________________ Christoph van Wuellen (Christoph.van.Wuellen@ruhr-uni-bochum.de) wrote: As far as I recall, Turbomole does the job. You have to specify the "Geo-Field" option ($geofld). Christoph van Wuellen. _________________________________ Tao Li (lit@engr.sc.edu) wrote: GAMESS allows you to optimize a geometry with an applied electric field. But, as far as I know, this kind of optimization can be done just for neutral molecules. To optimize charged molecules, you have to modify the original GAMESS code yourself. Tao _________________________________ Scheila Braga (scheila@ifi.unicamp.br) wrote: Try the new version of hyperchem 6, you can dowload a demo version in the hypercube site (http://www.hyper.com). Just one thing, the units of electrical field in this program is atomics units, I don't know this relation with V/m or N/C. Please , if you know this relation tell me. Scheila Braga _________________________________ Irena Efremenko (chrirena@techunix.technion.ac.il) wrote: I tried to solve a similar problem and found that for surfaces it may be reasonably modeled only by ASED MO method (by Alfred B. Anderson). Other programs suggest to include (point) charges instead of changing potentials. Sincerely, -- Dr. Irena Efremenko _________________________________ Theresa L. Windus (Theresa.Windus@pnl.gov) wrote: I believe that GAMESS US can do this calculation. Check out http://www.msg.ameslab.gov/GAMESS/GAMESS.html Theresa __________________________________ At last there were some answers in german language: Anselm Horn (Anselm.Horn@Organik.Uni-Erlangen.DE) advises the semiempirical package VAMP. _ _ _ _ _ _ _ _ _ Uwe Huniar (uwe@tchibm2.chemie.uni-karlsruhe.de)recommends Turbomole. He is pointing to pages 165/166 in the turbomole-docu available under http://www.chemie.uni-karlsruhe.de/PC/TheoChem/turbomole/index.html _______________________________________________________________________________ From chemistry-request@server.ccl.net Mon Jul 17 09:33:17 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17093 for ; Mon, 17 Jul 2000 09:33:16 -0400 Received: from granby.ccc.nottingham.ac.uk ([128.243.40.43] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13EB0y-0007ec-00 for chemistry@ccl.net; Mon, 17 Jul 2000 14:32:56 +0100 Received: from ppcwtly.nottingham.ac.uk ([128.243.125.200] ident=jjxu) by unix.ccc.nottingham.ac.uk with smtp (Exim 3.11 #2) id 13EB0y-0005cC-00 for chemistry@ccl.net; Mon, 17 Jul 2000 14:32:56 +0100 From: JJ Reply-To: jjxu@yifan.net To: chemistry@ccl.net Subject: molpro Date: Wed, 12 Jul 2000 15:38:06 +0100 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00071215431700.01550@ppcwtly.nottingham.ac.uk> Content-Transfer-Encoding: 8bit Dear Netters, Can somebody tell me how I can get the basis sets, overlap integrals etc. from the output of Molpro. Thanks. From chemistry-request@server.ccl.net Mon Jul 17 09:33:17 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17094 for ; Mon, 17 Jul 2000 09:33:16 -0400 Received: from granby.ccc.nottingham.ac.uk ([128.243.40.43] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13EB0y-0007ee-00 for chemistry@ccl.net; Mon, 17 Jul 2000 14:32:56 +0100 Received: from ppcwtly.nottingham.ac.uk ([128.243.125.200] ident=jjxu) by unix.ccc.nottingham.ac.uk with smtp (Exim 3.11 #2) id 13EB0y-0005cC-01 for chemistry@ccl.net; Mon, 17 Jul 2000 14:32:56 +0100 From: JJ Reply-To: jjxu@yifan.net To: chemistry@ccl.net Subject: help for molpro Date: Wed, 12 Jul 2000 15:44:20 +0100 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00071215461601.01550@ppcwtly.nottingham.ac.uk> Content-Transfer-Encoding: 8bit Dear Netters, can somebody tell me how I can get the basis sets, overlap integrals from the output of Molpor? Thanks. From chemistry-request@server.ccl.net Mon Jul 17 11:50:14 2000 Received: from vax2.concordia.ca (SYSTEM@Vax2.Concordia.CA [132.205.1.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17780 for ; Mon, 17 Jul 2000 11:50:14 -0400 Received: from vax2.concordia.ca by vax2.concordia.ca (PMDF V5.2-33 #36969) id <01JRVFH5K7V400438V@vax2.concordia.ca> for chemistry@ccl.net; Mon, 17 Jul 2000 11:52:46 EDT Date: Mon, 17 Jul 2000 11:52:46 -0400 (EDT) From: srhughes@vax2.concordia.ca Subject: Lanthanides To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hello, I am currently performing single-point calculations of the euorpium ion in both Gamess and Gaussian98. An HF/SDD calculation yields energies of -629.54 and -706.97 Hawtrees respectively. I am quite confident that no errors are present in the input files as it relates to the basis sets. Has anyone else experienced similar problems or can provide me with any insight to resolve this discrepancy? Thank you for your time. Sean Hughes, COTC Dept. Chemistry and Biochemistry Concordia University 1455 de Maisonneuve Blvd. West Montreal, Quebec Canada H3G 1M8 Tel: (514)-848-4260 Fax: (514)-848-2868 From chemistry-request@server.ccl.net Mon Jul 17 11:21:16 2000 Received: from sjc3-1.relay.mail.uu.net (sjc3-1.relay.mail.uu.net [199.171.54.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17644 for ; Mon, 17 Jul 2000 11:21:15 -0400 Received: from wodc7-1.uucp-gw.mail.uu.net by sjc3sosrv11.alter.net with ESMTP (peer crosschecked as: wodc7-1.uucp-gw.mail.uu.net [199.171.54.178]) id QQiygb08838; Mon, 17 Jul 2000 15:20:44 GMT Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-3.uucp.uu.net [199.171.54.181]) id QQiygb00592; Mon, 17 Jul 2000 15:20:43 GMT Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Mon, 17 Jul 2000 15:20:43 +0000 Received: from gershwin by m10.gaussian.com; Mon, 17 Jul 2000 11:06:54 -0400 Received: (from ochtersk@localhost) by gershwin (980427.SGI.8.8.8/980728.SGI.AUTOCF) id LAA39224; Mon, 17 Jul 2000 11:09:52 -0400 (EDT) Date: Mon, 17 Jul 2000 11:09:52 -0400 From: Joseph Ochterski To: dck , chemistry@ccl.net Subject: Re: CCL:SUMMARY:geometry with an applied e-field Message-ID: <20000717110952.A139201@gershwin> References: <3972EA62.8495947A@citrin.chemie.uni-dortmund.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.4i In-Reply-To: <3972EA62.8495947A@citrin.chemie.uni-dortmund.de>; from dck on Mon, Jul 17, 2000 at 01:13:39PM +0200 On Mon, Jul 17, at 01:13:39PM +0200, dck wrote: > > Some days ago I had the following question: > > > Does anyone know what quantumchemical program is able to optimize a > > geometry with an applied electrical field? All programs that I have > > used until now allow only single point calculations with an E-field. > > here is a selection of the answers. > by the way, gaussian allows single point energy, Force, and Scan > calculations only with the field keyword. So all answers in this regard > are skiped in this summary. > Gaussian can, in fact, do optimizations with an applied external field. In some cases, Opt=Z-matrix and/or NOSYMM may be needed, depending on what the perturbation does to the molecule. -- Joseph Ochterski, Ph.D Senior Customer Service Scientist help@gaussian.com From chemistry-request@server.ccl.net Mon Jul 17 10:22:43 2000 Received: from octane.nybc.org ([192.94.249.91]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA17369 for ; Mon, 17 Jul 2000 10:22:43 -0400 Received: from nybc.org (localhost [127.0.0.1]) by octane.nybc.org (SGI-8.9.3/8.9.3) with ESMTP id KAA40118 for ; Mon, 17 Jul 2000 10:23:10 -0400 (EDT) Sender: debnath@octane.nybc.org Message-ID: <397316CE.F2943901@nybc.org> Date: Mon, 17 Jul 2000 10:23:10 -0400 From: "Dr. Asim K. Debnath" Organization: New York Blood Center X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock3.0 problem Content-Type: multipart/alternative; boundary="------------95A112693FEDE5B98BC29EEC" --------------95A112693FEDE5B98BC29EEC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Everybody: I am getting an error message while using mkdpf3 in Autodock3.0. The message is as follows: -- ...Using "dpf3gen". /usr/local/bin/autodock3/dpf3gen[18]: /usr/bin/nawk: arg list too long Sorry, I could not create XXXX.dpf ------------------------------------------------------------------------ The FAQ in the AUTODOCK Home page has mentioned about a similar error message and suggested to download gpf3gen.awk program to solve the problem with gpf3gen. The User guide also mentioned that to run mkdpf3 one need dpf3gen and dpf3gen.awk. I could not find dpf3gen.awk any where. I would appreciate very much if someone can help me to find the dpf3gen.awk program or to solve this problem. Thank you in advance for your help. Asim ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@nybc.org ************** --------------95A112693FEDE5B98BC29EEC Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Everybody:
    I am getting an error message while using mkdpf3 in Autodock3.0. The message is as follows:
  
--
...Using "dpf3gen".

/usr/local/bin/autodock3/dpf3gen[18]: /usr/bin/nawk: arg list too long

Sorry, I could not create  XXXX.dpf
------------------------------------------------------------------------
    The FAQ in the AUTODOCK Home page has mentioned about a similar error message and suggested to download  gpf3gen.awk program to solve the problem with gpf3gen. The User guide also mentioned that to run mkdpf3 one need dpf3gen and dpf3gen.awk. I could not find dpf3gen.awk any where.

    I would appreciate very much if someone can help me to find the dpf3gen.awk program or to solve this problem.
    Thank you in advance for your help.

Asim
=======================================================================

             ***
             ***                
            ****                Asim K. Debnath, Ph.D.
           ****                 Lindsley F. Kimball Research Institute 
          ****  ***             The New York Blood Center
         ****    ****           310 E 67 Th Street
        ****  **  ****          New York, NY 10021
       ****  ****  ****         Tel. (212) 570-3373
      ****    **    ****        Fax. (212) 570-3299
       ****************         E-mail: adebnath@nybc.org
        **************
  --------------95A112693FEDE5B98BC29EEC-- From chemistry-request@server.ccl.net Mon Jul 17 12:03:06 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA17973 for ; Mon, 17 Jul 2000 12:03:00 -0400 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id NAA26436 for ; Mon, 17 Jul 2000 13:00:37 -0300 (BSC) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id NAA22980 for ; Mon, 17 Jul 2000 13:00:35 -0300 (BSC) Received: from giselle.ifi.unicamp.br(143.106.72.217) via SMTP by lua.ifi.unicamp.br, id smtpdAAAa005aG; Mon Jul 17 13:00:24 2000 Message-Id: <4.3.2.7.0.20000717123407.00c3ee70@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Mon, 17 Jul 2000 12:49:40 -0300 To: chemistry@ccl.net From: Demetrio Antonio da Silva Filho Subject: G94 CI-Singles method Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id MAA17974 Dear Netters, I'm in doubt about the CI-Singles method and the number of single substitutions that this method uses on its calculation. In Pople's paper (J. B. Foresman, M. Head-Gordon, J. A. Pople and M. J. Frisch, Toward a Systematic Molecular Orbital Theory for Excited States, J. Phys. Chem. 96, 135 (1992).) the CI-Singles method is defined as configuration interaction among "all" singly substituted determinants. In Gaussian manual, there is a keyword for this method (NStates) which sets the number of states that will be solved. This keyword (Mstates) sets the number of states used in the CI expansion of the wavefunction or independent of the number used in this keyword all singly substituted determinants will be used? Thanks in advance, Demetrio FIlho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Mon Jul 17 14:03:48 2000 Received: from efriedman.biomath.nyu.edu (EFRIEDMAN.BIOMATH.NYU.EDU [128.122.250.118]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA19302 for ; Mon, 17 Jul 2000 14:03:44 -0400 Received: from localhost (strahs@localhost) by efriedman.biomath.nyu.edu (8.9.3/8.9.3) with ESMTP id OAA1115082 for ; Mon, 17 Jul 2000 14:04:23 -0400 (EDT) Date: Mon, 17 Jul 2000 14:04:23 -0400 From: Dan Strahs To: chemistry@ccl.net Subject: Announcing Workshop on Methods for Macromolecular Modeling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ============================================================== International Workshop on Methods for Macromolecular Modeling (M3) October 12-14, New York University, New York City ============================================================== Dear Colleague, We are sending you this notice to announce the International Workshop on Methods for Macromolecular Modeling (M3) which will be held October 12-14, 2000 at New York University in New York City. Please forward this announcement to anyone who might be interested in attending. The purpose of our multidisciplinary workshop on Methods for Macromolecular Modeling (M3) --- the third in a series of meetings (1994: Lawrence, Kansas; and 1997: Berlin, Germany) --- is to bring together both developers of computational tools for biomolecular simulations and those biological and chemical scientists who utilize (or are interested in applying) computer modeling to macromolecular problems. TOPICS The topics to be highlighted in M3 2000 are: (1) long-term molecular dynamics simulations; (2) conformational sampling: equilibrium and nonequilibrium processes; (3) multiscale modeling; (4) quantum/classical mechanics; (5) fast electrostatics; and (6) applications to DNA modeling, enzyme catalysis, and DNA/protein systems. SPEAKERS Confirmed speakers include: Peter Kollman (UCSF), Andy McCammon (UCSD), Harold Scheraga (Cornell), Tom Darden (NIEHS), Dave Beveridge (Wesleyan), Steve Burley (Rockefeller), Ron Elber (Cornell), James Glimm (Stony Brook), Leslie Greengard (Courant), Sharon Hammes-Schiffer (Penn. State), Barry Honig (Columbia), Robert Krasny (U. Michigan), Ron Levy (Rutgers), Wilma Olson (Rutgers), Dinshaw Patel (Sloan-Kettering), Nina Pastor (UAEM, Mexico), Ursula Roethlisberger (ETH, Zurich), Benoit Roux (Cornell Med. Sch.), Andrej Sali (Rockefeller), Chris Schuette (Freie U, Berlin), Jeff Skolnick (Danforth Center), Arieh Warshel (USC), and Eric Westhof (CNRS, France). We expect the participation of biomolecular modelers, applied mathematicians, computer scientists, and anyone interested in the broad themes. TRAVEL AWARD The National Science Foundation, Department of Energy, and Burroughs Wellcome Fund are providing funds for partial travel support and living expenses for a number of participants in M3 2000. The funds are targeted for graduate students, postdocs, women, and minorities interested in macromolecular modeling research who will present posters (exceptions may be granted to beginning graduate students or those who are considering switching his/her field to biomolecular research). To apply for support, send an email to workshop organizers at workshop@biomath.nyu.edu outlining the (1) reasons for your interest in attending the workshop; (2) provide an estimate of the cost needed to attend; (3) submit an abstract before September 1, 2000 for a poster presentation; (4) students and postdocs should have a letter of recommendation from a faculty member sent to us directly (preferably by email). We are likely to offer a set amount to each eligible applicant. Inquiries may also be directed to Drs. Tamar Schlick and Hin Hark Gan at our addresses below. REGISTRATION We encourage those who would like to attend to apply early since the attendance at the workshop is limited. To register, send an email to workshop@biomath.nyu.edu. More information about the workshop can be found on our website http://monod.biomath.nyu.edu/~hgan/conf_00.html We look forward to hearing from you. Sincerely yours, Hin Hark Gan Email: hgan@biomath.nyu.edu Tel: (212) 998-3594 Tamar Schlick, Chair of Organizing Committee Email: schlick@nyu.edu Tel: (212) 998-3116 Fax: (212) 995-4152 Mailing address: Courant Institute of Mathematical Sciences New York University 251 Mercer Street New York, New York, 10012 USA International Advisory Committee Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. Mark, Sebastian Reich, Tamar Schlick, Robert Skeel Local Organizing Committee Richard Friesner, Hin Hark Gan, Barry Honig, Andrej Sali, Mark Tuckerman, Harel Weinstein Co-sponsoring organization Society for Industrial and Applied Mathematics (SIAM) Activity Group on Life Sciences (SIAG/LS) We appreciate the support from **************************************************** * Burroughs Wellcome Fund * * Department of Energy * * National Science Foundation * * * * Courant Institute of Mathematical Sciences, NYU * * Computational Biomedicine Initiative, * * Mount Sinai School of Medicine * * Department of Chemistry, NYU * * Science Council, NYU * **************************************************** From chemistry-request@server.ccl.net Mon Jul 17 15:07:12 2000 Received: from dalton.quimica.unlp.edu.ar (dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA19648 for ; Mon, 17 Jul 2000 15:07:10 -0400 Received: from bilbo (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.10.2/8.10.2) with SMTP id e6HKAdv19651 for ; Mon, 17 Jul 2000 16:10:39 -0400 Message-Id: <3.0.6.32.20000718040656.007ab620@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 18 Jul 2000 04:06:56 -0300 To: chemistry@ccl.net From: Dr Reinaldo Pis Diez Subject: G98: Oniom energies Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear ccl'ers, I'm doing some calculations using the oniom method as implemented in g98. My system is a 30-atoms organic molecule surrounded by almost hundred solvent molecules. I'm using dft/mm (svwn:uff) for higher and lower layers, respectively. The first calculation seems to be a mm one giving an energy which I call E_3. Then, the program jumps into the dft job achieving self consistency with an energy E_scf. As a third step, it enters into another job having less electrons than the higher layer, organic molecule, giving an energy E_1. Finally, the program enters link 102 and prints the following ONIOM: calculating energy. E123= E_1 E_scf E_3 (three real numbers) ONIOM: extrapolated energy = (a fourth real number calculated as, I guess, E_scf - E_1 + E_3) Now my questions: i) Is the "oniom extrapolated energy" the valid energy in an oniom job? ii) What does E_1 mean? Thanks in advance. I summarize to the list. Regards, Reinaldo From chemistry-request@server.ccl.net Mon Jul 17 15:11:50 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA19694 for ; Mon, 17 Jul 2000 15:11:50 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA10377; Mon, 17 Jul 2000 12:14:16 -0700 (EDT) Date: Mon, 17 Jul 2000 12:14:15 -0700 From: Rick Venable To: yunlong song cc: "CHEMISTRY@ccl.net" Subject: Re: CCL:Conforamation composition In-Reply-To: <20000717061652.KUMP493.fep6.online.sh.cn@cadd> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 18 Jul 2000, yunlong song wrote: > I am performing conformational analysis on a drug molecule.I want to > know the exact population of each conformer. I want to know how to > calculation the conformation population analysis based on Boltzmann > law? Can you help me ? Monte Carlo simulations use Boltzmann based sampling to build up a family of conformations with a Boltmann energy distribution. Typically, these calcs use rotation around single bonds as the free variables, especially for smaller molecules like drugs. Because the calcs are usually run in a vacuum environment, the distribution represents the gas phase of the molecule. > Also, I want to know how to calculate torsion energy profile > according a torsion bond.The interal coordinates may be > useful,however the molecule is quite large.I use its cartesian > coordinate.So can I use cartesian coordinate to comput the pofile. > In literature, people often referred to reaction coordinate drive > method.Can someone give me an exact explanation? Both sampling of a single torsion and Monte Carlo sampling are best done using internal coordinates for generating configurations. Many progs require Cartesian coords to evaluate energy, and so must use perturbed internal coords to compute the Cartesian coords, and then the energy. Reaction coordinate usually refers to some movement (rotation, translation) used to study an energy profile, and typically represents a simplification to a single movement with the assumption that other parts of the system remain in some fixed geometry. For a drug molecule with multiple freely rotating single bonds, this can be a problem; the energy profile for one single bond torsion may depend on the conformational state of other single bonds in the molecule. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Mon Jul 17 20:39:22 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA20830 for ; Mon, 17 Jul 2000 20:39:22 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.2.0r) with ESMTP id RAA05932 for ; Mon, 17 Jul 2000 17:37:18 -0700 (PDT) Received: from localhost (jesusmc@localhost) by redox.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id RAA10485; Mon, 17 Jul 2000 17:37:48 -0700 (PDT) Date: Mon, 17 Jul 2000 17:37:48 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: chemistry@ccl.net cc: Mike Pique Subject: BOF session on Molecular Graphics at SIGGRAPH In-Reply-To: <3.0.6.32.20000716105029.0079ab10@compchem.dfh.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Posting this message for friends at SIGGRAPH ---- Molecular Graphics Gathering at ACM SIGGRAPH 2000 New Orleans Tuesday Afternoon, 25 July, 1:30 PM, Convention Center Room 285 Yes, we are gathering at ACM SIGGRAPH 2000 in New Orleans for our annual Molecular Graphics "Birds-of-a-feather" session. One change this year: a different day. We are meeting 1:30-2:30 PM on Tuesday afternoon, 25 July 2000, (instead of our traditional Wednesday). This afternoon slot should leave people free to attend the morning opening session, Professor Brooks' Turing Award presentation (The Design of Design) at 12:15, and the afternoon technical sessions after our gathering. Again this year you are encouraged to bring a few slides or prints of new molecular graphics techniques, applications, software, or results, for an informal showing. We have requested a VHS video player and data projector; a laptop PC (running MS Windows) with floppy and CD-ROM will likely also be available. Do let your interested friends know about the meeting: it's for everyone interested in molecular graphics, whether static or interactive, commercial or experimental. Come with news and rumors, tell us what's interesting you've spotted in the SIGGRAPH program or on the exhibit floor, impressions, highlights. With your help and participation we can have a good time again. A reminder that anyone reading this would benefit from joining the international Molecular Graphics and Modelling Society; visit "http://www.mgms.org" and click on ``apply''. You are also welcome at our "Component-based visualization environments" gathering Sunday 23 July, 5:30 PM, same room. Michael Pique and Arthur Olson 16 July 2000 The Scripps Research Institute: Molecular Biology MB-5 10550 N. Torrey Pines Road La Jolla, CA 92037 (858) 784-9775 mp@scripps.edu, fax (858) 784-2860 (858) 784-9702 olson@scripps.edu, fax (858) 784-2860 ----- -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ PalmPilot Stuff: http://www.geocities.com/jm_castagnetto/