From chemistry-request@server.ccl.net Thu Jan 16 07:04:40 2003 Received: from smtp.uibk.ac.at ([138.232.1.142]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GC4dV28337 for ; Thu, 16 Jan 2003 07:04:40 -0500 Received: from localhost (web-mail.uibk.ac.at [138.232.1.245]) by smtp.uibk.ac.at (8.12.5/8.12.5/F1) with ESMTP id h0GC4c6l005546 for ; Thu, 16 Jan 2003 13:04:39 +0100 Received: from 62.47.210.54 ( [62.47.210.54]) as user c72409@mail1.uibk.ac.at by web-mail1.uibk.ac.at with HTTP; Thu, 16 Jan 2003 13:04:38 +0100 Message-ID: <1042718678.3e269fd6cccff@web-mail1.uibk.ac.at> Date: Thu, 16 Jan 2003 13:04:38 +0100 From: Hannes Loeffler To: chemistry@ccl.net Subject: CHARMM doc files MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 62.47.210.54 X-Spam-Score: -1.3 () SPAM_PHRASE_00_01,USER_AGENT,USER_AGENT_IMP X-Scanned-By: MIMEDefang 2.26 at uibk.ac.at (www . roaringpenguin . com / mimedefang) Hello, the CHARMM doc files are obviously in GNU info format. I wonder if they have been prepared from *.texi files and if so if they would be available so that I could process them with TeX. Hannes. From chemistry-request@server.ccl.net Wed Jan 15 16:10:40 2003 Received: from mail.bancorp.ru ([217.107.81.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0FLAdV15126 for ; Wed, 15 Jan 2003 16:10:40 -0500 Received: from 81.25.172.97 (97-kazan.telebit.ru [81.25.172.97] (may be forged)) by mail.bancorp.ru (8.11.3/8.11.3) with ESMTP id h0FLARt12749 for ; Thu, 16 Jan 2003 00:10:27 +0300 Date: Thu, 16 Jan 2003 00:11:05 +0300 From: Gregory Shamov X-Mailer: The Bat! (v1.61) Personal Reply-To: Gregory Shamov Organization: KSU X-Priority: 3 (Normal) Message-ID: <9783070974.20030116001105@bancorp.ru> To: chemistry@ccl.net Subject: polyphosphate Kurrol's salt MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello All, There are polyphosphate salts like Kurrol's salt M(PO3)n, M= Na, K, Ag. Some of them in the solid state are glasses, some -- regular cristals formed from {-(O=PO2)-}n spirals. I'm looking for experimental (say, X-ray) geometries of these species. Could someone help me with it? Many thanks in advance. -- Best regards, Gregory Shamov, Dept. Chemistry Kazan State University Kazan, Russian Federation mailto:gas5x@bancorp.ru From chemistry-request@server.ccl.net Wed Jan 15 09:34:41 2003 Received: from mail.unina.it ([192.132.34.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0FEYfV22071 for ; Wed, 15 Jan 2003 09:34:41 -0500 Received: (from root@localhost) by mail.unina.it (8.12.6/8.12.6) id h0FETgOK012374 for chemistry@ccl.net; Wed, 15 Jan 2003 15:29:42 +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 h0FETZ1Z012348 for ; Wed, 15 Jan 2003 15:29:37 +0100 Message-Id: <5.0.0.25.0.20030115151153.00a71280@cds.unina.it> X-Sender: lavecchi@cds.unina.it X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 15 Jan 2003 15:26:52 +0100 To: chemistry@ccl.net From: Antonio Lavecchia Subject: Non integral total charge in Autodock Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_94886702==_.ALT" X-scanner: scanned by Inflex 1.0.12.5 on mail.unina.it --=====================_94886702==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, when starting an autodock job, I receive the following warning message: "non integral total charge (-0,014e) on molecule". Does anyone know what does it mean and how to avoid it? Thanks for the attention. 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 --=====================_94886702==_.ALT Content-Type: text/html; charset="us-ascii" Dear All,
when starting an autodock job, I receive the following warning message: "non integral total charge (-0,014e) on molecule".
Does anyone know what does it mean and how to avoid it?
Thanks for the attention.

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 --=====================_94886702==_.ALT-- From chemistry-request@server.ccl.net Wed Jan 15 13:09:11 2003 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0FI9BV01644 for ; Wed, 15 Jan 2003 13:09:11 -0500 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id h0FI9Gp24984 for ; Wed, 15 Jan 2003 12:09:16 -0600 (CST) Received: from abtapn561.northamerica.intra.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id h0FI9Bk01357 for ; Wed, 15 Jan 2003 12:09:11 -0600 (CST) To: chemistry@ccl.net Cc: james.metz@abbott.com Subject: CCL: Docking accuracy versus computational time, demonstrated examples ? X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Wed, 15 Jan 2003 12:08:23 -0600 X-MIMETrack: Serialize by Router on ABTAPN561/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 01/15/2003 12:04:55 PM, Serialize complete at 01/15/2003 12:04:55 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 0063B71086256CAF_=" This is a multipart message in MIME format. --=_alternative 0063B71086256CAF_= Content-Type: text/plain; charset="us-ascii" CCL, Does anyone have first-hand experience or know of published papers which discuss docking accuracy versus computational time (for adjustable parameters within the various docking programs)? For example, many docking programs have adjustable parameters that affect docking results including accuracy (ligand coordinate RMS error relative to the crystal structure) and average computational time to compute each pose. Sometimes, the goal is to quickly dock a large set of compounds and obtain a (reasonable) set of poses for each compound. Sometimes, the goal is to dock a much smaller set of compounds with the greatest accuracy possible, even if it takes 30 min - 1 hr (or more) of CPU time per compound. One must make goal-oriented choices of parameters such as grid size, conformational analysis, treatment of short-range and long-range forces and interaction energies, etc. Regards, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com --=_alternative 0063B71086256CAF_= Content-Type: text/html; charset="us-ascii"
CCL,

        Does anyone have first-hand experience or know of published papers which discuss docking accuracy versus computational
time (for adjustable parameters within the various docking programs)?

        For example, many docking programs have adjustable parameters that affect docking results including accuracy (ligand
coordinate RMS error relative to the crystal structure) and average computational time to compute each pose.  Sometimes, the goal is to
quickly dock a large set of compounds and obtain a (reasonable) set of poses for each compound.  Sometimes, the goal is to dock a
much smaller set of compounds with the greatest accuracy possible, even if it takes 30 min - 1 hr (or more) of CPU time per compound.
One must make goal-oriented choices of parameters such as grid size, conformational analysis, treatment of short-range and long-range
forces and interaction energies, etc.

        Regards,
        Jim Metz


James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz@abbott.com
 --=_alternative 0063B71086256CAF_=-- From chemistry-request@server.ccl.net Tue Jan 14 14:30:59 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EJUx417687 for ; Tue, 14 Jan 2003 14:30:59 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0EJUxj28867; Tue, 14 Jan 2003 14:30:59 -0500 (EST) Date: Tue, 14 Jan 2003 14:30:58 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: 03.02.25-28 Daylight MUG '03 Registration (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 14 Jan 2003 11:47:10 -0700 (MST) From: Daylight Announcements To: jkl@ccl.net Subject: Daylight MUG '03 Registration Daylight Users: The Eldorado Hotel, site of MUG '03, has graciously extended the DEADLINE for room reservations at the MUG rate of $141 through this FRIDAY, JANUARY 17. After that, the price goes up. We have a great MUG brewing and we hope you will be able to join us. Please register soon! See you there, The Daylight Krewe ANNOUNCEMENT ANNOUNCEMENT ANNOUNCEMENT ANNOUNCEMENT ANNOUNCEMENT Daylight Chemical Information Systems Inc. >>>>>>>>> MUG 2003 <<<<<<<<< Daylight User Group Meeting February 25 - 28, 2003 Eldorado Hotel Santa Fe, New Mexico Daylight Chemical Information Systems, Inc. is pleased to invite you and your colleagues to join us for our seventeenth annual user-group meeting, which will take place February 25-28, 2003 in Santa Fe, New Mexico. Our three and a half-day format includes both presentations from Daylight staff and Daylight users. Users will present talks on the work they are doing utilizing Daylight software. These presentations offer the opportunity to share and learn on a peer-to-peer level with other Daylight users. Daylight staff will present on new developments and directions for Daylight. All individuals interested in Daylight, regardless of their level of experience or familiarity with our software, are invited to attend. All users are invited to present original work with Daylight software in a scheduled talk, a poster, and/or a software demonstration. Please contact Jack Delany at jjdelany@daylight.com with your title and abstract to schedule your participation. MUG 2003 will be held at the Eldorado Hotel, 309 W. San Francisco St., Santa Fe, NM 87501 (http://www.eldoradohotel.com/). Please call the Eldorado directly at 1-800-955-4455 for room reservations. Ask for the Daylight MUG Meeting special rate of $141 (single or double) which will be available until January 9, 2003. Each year we have a banquet on Wednesday evening. This year it will be held at The Bishop's Lodge (http://www.bishopslodge.com). Preceding the banquet we will host a one-hour horseback excursion through the hills surrounding Bishop's Lodge. Those able to join us will be charged an additional $45 by Bishop's Lodge for the ride. You will be riding at your own risk; neither Daylight nor the Bishops Lodge assume any liability. Remember to pack some warm clothes. Santa Fe is a 1 hour drive from the Albuquerque airport (ABQ). The Santa Fe airport (SAF) is restricted to commuter flights, accessible only from Denver and a few other cities. Airport shuttle reservations from Albuquerque can be made in advance with Sandia Shuttle (http://www.sandiashuttle.com) at 1-888-775-5696. Registration fee is $390 for all four days. Prices include breakfast and lunch each day and the banquet Wednesday evening. Please pre-register on-line via the Daylight meetings page at http://www.daylight.com/meetings/mug03/. (You will still need to send your fee to be officially registered). Alternatively, you may complete and e-mail the form below to info@daylight.com. We accept payments by check, VISA, MC or American Express. Mail registration and fees to: Daylight CIS Inc. 27401 Los Altos, Suite 360 Mission Viejo, CA 92691 or fax to 1-949-367-0990 For further information, please e-mail info@daylight.com, or call the Corporate Office at 949-367-9990 or Peter Nielsen, Director of Marketing and Business Development at 802-223-9831. See you at MUG 2003!!! - The Daylight Krewe Daylight MUG 2003 Registration Form ----------------------------------- Name ___________________________________________________ Organization ___________________________________________________ Email ___________________________________________________ Address ___________________________________________________ ___________________________________________________ ___________________________________________________ Phone ___________________________________________________ FAX ___________________________________________________ Payment: ___ Check ___ VISA ___ MasterCard ___ American Express Credit Card Number: ___________________________________________ Expiration Date: _______________________ Your affiliation: ___ Corporate ___ Academic ___ Government ___ Nonprofit Your department: ___ Scientific R&D ___ Corporate IT ___ Business Dev. ___ Other Daylight Software Used: _____________________________________________________________________ What do you hope to gain from this meeting? _____________________________________________________________________ Would you like to give a talk? ___ Yes ___ No or poster? ___ Yes ___ No If yes, please give a title: _____________________________________________________________________ and abstract: _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Planned days of attendance (check all days that you will attend): ___ Tue 25 FEB ___ Wed 26 FEB ___ Thu 27 FEB ___ Fri 28 FEB Any dietary restrictions? ___ Vegetarian ___ Other (please tell us) Horseback Ride ___ Yippy! Count me in. ___ No thanks, I'll sit by the fireplace. Comments: _____________________________________________________________________ Send this completed form with payment to: Daylight CIS Inc. 27401 Los Altos Ave., Suite 360 Mission Viejo, CA 92691 or fax to 1-949-367-0990 THANK YOU From chemistry-request@server.ccl.net Tue Jan 14 20:11:37 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0F1Bb425098 for ; Tue, 14 Jan 2003 20:11:37 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0F1Bbj10734 for ; Tue, 14 Jan 2003 20:11:37 -0500 (EST) Date: Tue, 14 Jan 2003 20:11:37 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: 03.08.25 Int.Conf: Appl.Stat.Phys. ASTATPHYS-2003, Puerto Vallarta, MX (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 14 Jan 2003 17:29:33 -0600 From: Yosadara Ruiz-Morales Reply-To: yruiz@www.imp.mx To: jkl@ccl.net Subject: 03.08.25 Int.Conf: Appl.Stat.Phys. ASTATPHYS-2003, Puerto Vallarta, MX Second International Conference on Applied Statistical Physics: Molecular Engineering (ASTATPHYS-MEX- 2003) August 25-29, 2003 in Puerto Vallarta, Mexico. Dear Colleagues, This is to invite you to contribute with an oral or poster presentation in the "Statistical Physics: Molecular Engineering Conference (ASTATPHYS-MEX-2003)", which will be held on August 25-29, 2003 in Puerto Vallarta, Jalisco, Mexico. The Applied Statistical Physics: Molecular Engineering Conference (ASTATPHYS-MEX-2003) will be the second international meeting of its kind. The ASTATPHYS-MEX-2001 was focused on Molecular Engineering where over 350 participants from the Americas, Europe and Asia attended. The conference proceedings were published by Molecular Physics. The ASTATPHYS-MEX-2003 Conference will focus on exciting topics of Molecular Engineering, with high level scientific content. Also, a social program with the traditional warmth and hospitality of Latin American people is being planned. The aim of the Conference is to gather applied and basic scientists interested in the design and understanding of nanostructured materials and their applications. The Conference topics will be: molecular design of catalysts and nano-catalysts, nano-tubes and fullerenes; magnetic nano-structures, nano-circuits, microlithography, supramolecular chemistry, nano-biotechnology, petroleomics; quantum engineering, electrokinetic phenomena, biological tissue reconstruction, polymers, gene-delivery, molecular self assembling, confined complex fluids, ionic channels, dynamics of confined fluids, phase transitions and other aspects of molecular engineering. What these topics have in common is the self-assembling of supramolecular species and/or molecular confinement, at micro or nano-scale level. The approach can be, for example, chemical synthesis, ATM, electronic microscopy, characterization, evaluation and prospective experiments, solid and soft condensed matter physics, quantum physics and chemistry, and equilibrium and non-equilibrium statistical mechanics. We hope that the various Conference sessions will promote fruitful discussions among pure and applied scientists and technologists > from all over the world. We all can help to identify key areas of opportunity to enhance our understanding of nano-science. The program will have both invited and contributed presentations. During the Conference, there will be a Technological Exhibition, EXPO-ASTATPHYS-MEX-2003, where state-of-the-art experimental equipment, computer software and diverse products will be exhibited. The excellent facilities of the Nh Krystal Hotel in Puerto Vallarta will offer a natural frame to all of the above activities. Please check the Conference Web Site: http://www.amim.org/astatphys2003 where submission deadlines, registration costs and all related information on this event can be found. Please If you have any question do not hesitate to contact me. Looking forward with pleasure seeing you in Puerto Vallarta in August. Dr. Marcelo Lozada-Cassou Mexican Petroleum Institute (IMP) ASTATPHYS-MEX-2003 Conference Chairman e-mail: astatphys2003@amim.org From chemistry-request@server.ccl.net Thu Jan 16 10:00:05 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GF05V00721 for ; Thu, 16 Jan 2003 10:00:05 -0500 Received: from attglobal.net (dhcp065-029-080-040.indy.rr.com[65.29.80.40]) by prserv.net (asmtp2) with SMTP id <20030116150003252016f26he> (Authid: jmmckel); Thu, 16 Jan 2003 15:00:03 +0000 Message-ID: <3E2683D0.BC1C9667@attglobal.net> Date: Thu, 16 Jan 2003 10:05:04 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Chemistry@ccl.net Subject: TDDFT Symposium at New Orleans ACS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings! There will be a 3 1/2 day symposium on TDDFT and related methods at the ACS meeting in New Orleans from Mar 23-Mar 26. There are 28 speakers including many from leading DFT groups from Europe, Canada, and the US. Talks will include ab initio and semiempirical methods. The speakers include Speaker Institution Frank Neese Max Planck Stefan Grimme U. Muenster E. J. Baerands Vrije University Filipe Furche U. Karlsruhe Kenneth Wiberg Yale University P. J. Hay Los Alamos John Jean Washington U. Kieron Burke Rutgers U. Weitao Yang Duke U. Sergei Tretiak Los Alamos Tom Ziegler U. Calgary Jochen Autschbach Erlangen Richard L. Martin Los Alamos Martin Head-Gordon Berkley U. R. R. Burnette U. Wisconsin Mark Casida Grenoble, FR Paul Day Wright Patterson AFB Fan Zhang Rutgers U. A. Wasserman Rutgers U. K. Nguyen Wright Patterson AFB Gary Trucks Gaussian, Inc. K. Krogh-Jespersen Rutgers U. N. T. Maitre Rutgers U. Mel Levy N. Carolina A&T R. J. Bartlett U. Florida J. McKelvey Indianapolis Roberto Car Princeton U. Todd Martinez U. Illinois Enjoy! John McKelvey Kieron Burke From chemistry-request@server.ccl.net Thu Jan 16 08:53:23 2003 Received: from mailserv.unb.ca ([131.202.3.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GDrNV31538 for ; Thu, 16 Jan 2003 08:53:23 -0500 Received: from pop.unb.ca (root@newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h0GDrKTi004654; Thu, 16 Jan 2003 09:53:20 -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 h0GDrKC14290; Thu, 16 Jan 2003 09:53:20 -0400 (AST) X-WebMail-UserID: l72k6 Date: Thu, 16 Jan 2003 09:53:19 -0400 Sender: Robert Flight From: Robert Flight To: Antonio Lavecchia , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:Non integral total charge in Autodock Message-ID: <3E29BFB0@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: Hi Antonio, I'm assuming that the "molecule" in question is a protein. This message means there was a problem with the partial charges on a residue in the protein somewhere. AutoDock likes everything to have integer charges (-1, 0, +1) and it acts as a check to make sure there are no major problems with the structure. If you are using AutoDock Tools, you can check the partial charges on the protein and it will tell you where the problem is. In my experience the charge problem results from incomplete or improperly modeled residues (missing atoms, problems with bond order, etc). Depending on the method of calculating the charges (MMFF94, Gasteiger-Marsili, Amber) you may likely find that there are more problems with the structure. As a last resort, you can always modify the charges in the *.PDBQS file manually, this shouldnt be a problem if the residue in question is far from the region you are docking to. If the problem is with the ligand (and it is not a protein) try calculating your partial charges with another force field or method, and double check the structure. Good luck. I hope this helps. Cheers, Robert >===== Original Message From Antonio Lavecchia ===== >Dear All, >when starting an autodock job, I receive the following warning message: >"non integral total charge (-0,014e) on molecule". >Does anyone know what does it mean and how to avoid it? >Thanks for the attention. > >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: robert.flight@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 From chemistry-request@server.ccl.net Thu Jan 16 13:41:30 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GIfTV09931 for ; Thu, 16 Jan 2003 13:41:29 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18ZExF-0001K1-00; Thu, 16 Jan 2003 19:41:29 +0100 Message-ID: <3E26FCD5.6060306@mpi-bpc.mpg.de> Date: Thu, 16 Jan 2003 19:41:25 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: chemistry@ccl.net, amber Subject: MEAD help---still hope for an answer Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to use MEAD for the first time. Since the documentation is very scarce I would like to ask somebody that has already calculated electrostatic potentials on macromocules using "potential" from MEAD suite to give me some hints. I am refering here to a simple basic calculation. I tried to look at the examples in the distribution but there is no examples for how to take a structure from the pdb and calculate the potential and visualizing it. All the examples deal with more advanced stuff. I tried "potential -epsin 1.0 -CoarseFieldOut file molname" on a pqr file created with ambpdb (AMBER) and a ogm file that looks like below ON_GEOM_CENT 41 1.0 ON_GEOM_CENT 41 0.25 I got some warnings and errors that look like this: WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice, WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 1 WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the lattice, WARINING from potential main program: Could not open field point file, comp_test.fpt, for reading. Exiting without giving any potentials. Woould I ask too much if I ask somebody to shortly explain these? About the last one in the README file it is said that an .fpt file is not mandatory with the option "-CoarseFieldOut file" so I used the flag but still it gave me the error. If this file .fpt is mandatory could somebody tell me what is the ".fpt" file and can I get a file like this for a molecule....it is not explain in the README file from MEAD distribution Thanks a lot in advance for any help. Hope I did not ask too much Best wishes, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Thu Jan 16 13:43:03 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GIh2V10002 for ; Thu, 16 Jan 2003 13:43:03 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18ZEyk-0001bQ-00; Thu, 16 Jan 2003 19:43:02 +0100 Message-ID: <3E26FD33.4010407@mpi-bpc.mpg.de> Date: Thu, 16 Jan 2003 19:42:59 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL , amber Subject: MEAD help-----still hope for at least one short answer Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to use MEAD for the first time. Since the documentation is very scarce I would like to ask somebody that has already calculated electrostatic potentials on macromocules using "potential" from MEAD suite to give me some hints. I am refering here to a simple basic calculation. I tried to look at the examples in the distribution but there is no examples for how to take a structure from the pdb and calculate the potential and visualizing it. All the examples deal with more advanced stuff. I tried "potential -epsin 1.0 -CoarseFieldOut file molname" on a pqr file created with ambpdb (AMBER) and a ogm file that looks like below ON_GEOM_CENT 41 1.0 ON_GEOM_CENT 41 0.25 I got some warnings and errors that look like this: WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice, WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 1 WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the lattice, WARINING from potential main program: Could not open field point file, comp_test.fpt, for reading. Exiting without giving any potentials. Woould I ask too much if I ask somebody to shortly explain these? About the last one in the README file it is said that an .fpt file is not mandatory with the option "-CoarseFieldOut file" so I used the flag but still it gave me the error. If this file .fpt is mandatory could somebody tell me what is the ".fpt" file and can I get a file like this for a molecule....it is not explain in the README file from MEAD distribution Thanks a lot in advance for any help. Hope I did not ask too much Best wishes, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Thu Jan 16 12:32:25 2003 Received: from sal.ahpcrc.org ([144.34.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GHWOV08058 for ; Thu, 16 Jan 2003 12:32:24 -0500 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h0GHWOR08723 for ; Thu, 16 Jan 2003 11:32:24 -0600 Received: (from rbw@localhost) by mycroft.ahpcrc.org (8.11.6/8.11.6) id h0GHWJa03798 for Chemistry@ccl.net; Thu, 16 Jan 2003 11:32:19 -0600 Date: Thu, 16 Jan 2003 11:32:19 -0600 From: Richard Walsh Message-Id: <200301161732.h0GHWJa03798@mycroft.ahpcrc.org> To: Chemistry@ccl.net Subject: Gaussian 98 on Linux clusters and SGE ... All, Has anyone had a successful experience using Sun's Grid Engine product (available free under a GPL-like license) as the batch queueing system for Gaussian 98 in a RedHat Linux cluster context. Most folks seem to use PBS, but SGE has a number of features that are generally attractive that PBS does not have. I have heard that there may be problems handling Gaussian's need to run in serial-parallel-serial mode as the code moves through its links. The queueing system must retain the requested number of processors for the life of the batch job for a typical parallel G98 run to complete. Some guidance based on experience here would be very helpful. Regards, rbw #--------------------------------------------------- # Richard Walsh # Project Manager, Cluster Computing, Computational # Chemistry and Finance # netASPx, Inc. # 1200 Washington Ave. So. # Minneapolis, MN 55415 # VOX: 612-337-3467 # FAX: 612-337-3400 # EMAIL: rbw@networkcs.com, richard.walsh@netaspx.com # rbw@ahpcrc.org # #--------------------------------------------------- # "What you can do, or dream you can, begin it; # Boldness has genius, power, and magic in it." # -Goethe #--------------------------------------------------- # "Without mystery, there can be no authority." # -Charles DeGaulle #--------------------------------------------------- # "Why waste time learning when ignornace is # instantaneous?" -Thomas Hobbes #--------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 16 10:46:59 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GFkxV02327 for ; Thu, 16 Jan 2003 10:46:59 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18ZCEM-0000IC-00 for chemistry@ccl.net; Thu, 16 Jan 2003 16:46:58 +0100 Message-ID: <3E26D3EF.7070107@mpi-bpc.mpg.de> Date: Thu, 16 Jan 2003 16:46:55 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL Subject: [Fwd: MEAD help]--this is the last message ..hope this time I will get some short advices Content-Type: multipart/alternative; boundary="------------030605040206060503000202" --------------030605040206060503000202 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit -------- Original Message -------- Subject: MEAD help Date: Wed, 15 Jan 2003 18:01:58 +0100 From: Vlad Cojocaru To: CCL Dear CCLers, I am trying to use MEAD for the first time. Since the documentation is very scarce I would like to ask somebody that has already calculated electrostatic potentials on macromocules using "potential" from MEAD suite to give me some hints. I am refering here to a simple basic calculation. I tried to look at the examples in the distribution but there is no examples for how to take a structure from the pdb and calculate the potential and visualizing it. All the examples deal with more advanced stuff. I tried "potential -epsin 1.0 -CoarseFieldOut file molname" on a pqr file created with ambpdb (AMBER) and a ogm file that looks like below ON_GEOM_CENT 41 1.0 ON_GEOM_CENT 41 0.25 I got some warnings and errors that look like this: WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice, WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 2 WARNING: SAVanal_calc: vertex found with count = 1 WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the lattice, WARINING from potential main program: Could not open field point file, comp_test.fpt, for reading. Exiting without giving any potentials. Woould I ask too much if I ask somebody to shortly explain these? About the last one in the README file it is said that an .fpt file is not mandatory with the option "-CoarseFieldOut file" so I used the flag but still it gave me the error. If this file .fpt is mandatory could somebody tell me what is the ".fpt" file and can I get a file like this for a molecule....it is not explain in the README file from MEAD distribution Thanks a lot in advance for any help. Hope I did not ask too much Best wishes, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 --------------030605040206060503000202 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

-------- Original Message --------
Subject: MEAD help
Date: Wed, 15 Jan 2003 18:01:58 +0100
From: Vlad Cojocaru <Vlad.Cojocaru@mpi-bpc.mpg.de>
To: CCL <chemistry@ccl.net> 


Dear CCLers,
   I am trying to use MEAD for the first time. Since the documentation 
is very scarce I would like to ask  somebody that has already calculated 
electrostatic potentials on macromocules using "potential" from MEAD 
suite to give me some hints.
   I am refering here to a simple basic calculation. I tried to look at 
the examples in the distribution but there is no examples for how to 
take a structure from the pdb and calculate the potential and 
visualizing it. All the examples deal with more advanced stuff.
   I tried "potential -epsin 1.0 -CoarseFieldOut file molname" on a pqr 
file created with ambpdb (AMBER) and a ogm file  that looks like below
ON_GEOM_CENT 41 1.0
ON_GEOM_CENT 41 0.25
   I got some warnings and errors that look like this:

WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice,
WARNING: SAVanal_calc: vertex found with count = 2
WARNING: SAVanal_calc: vertex found with count = 2
WARNING: SAVanal_calc: vertex found with count = 1
WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the 
lattice,
WARINING from potential main program:
Could not open field point file, comp_test.fpt, for reading.  Exiting 
without giving any potentials.

   Woould I ask too much if I ask somebody to shortly explain these? 
About the last one in the README file it is said that an .fpt file is 
not mandatory with the option "-CoarseFieldOut file" so I used the flag 
but still it gave me the error. If this file .fpt is mandatory could 
somebody tell me what is the ".fpt" file and can I get a file like this 
for a molecule....it is not explain in the README file from MEAD 
distribution

Thanks a lot in advance for any help. Hope I did not ask too much
Best wishes,
vlad

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de
home tel: ++49-551-9963204  





-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de
home tel: ++49-551-9963204
--------------030605040206060503000202-- From chemistry-request@server.ccl.net Thu Jan 16 10:24:30 2003 Received: from 01mail.PghMail.com ([216.151.83.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GFOUV01798 for ; Thu, 16 Jan 2003 10:24:30 -0500 Received: from DJM.gaussian.com (unverified [63.113.39.156]) by 01mail.PghMail.com (Vircom SMTPRS 5.3.232) with ESMTP id for ; Thu, 16 Jan 2003 10:24:29 -0500 Message-Id: <5.1.0.14.2.20030116102116.00bd3008@mail.pghmail.com> X-Sender: tripletdad@mail.pghmail.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 16 Jan 2003 10:24:01 -0500 To: chemistry@ccl.net From: Gaussian Subject: Gaussian Workshop at University of Ulm Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE Gaussian, Inc., in conjunction with the Center of Excellence (COE) for Computational Chemistry at the University of Ulm and SUN Microsystems is pleased to announce a workshop that will cover the features of Gaussian's popular electronic structure programs. ____________________________________________________________________ Date: April 1-4, 2003 Location: University of Ulm April 1-4, 2003 Abteilung Organische Chemie I Albert Einstein Allee 11, O26 / 4405 Universitaet Ulm D-89069 Ulm GERMANY Academic Registration Fee: $430 Commercial Registration Fee: $580 Application deadline: "Introduction to Gaussian: Theory and Practice." will be presented by representatives of Gaussian, Inc. The workshops will cover the full range of methods available in the Gaussian package with emphasis on new methods and features which make Gaussian applicable to an ever-widening spectrum of research applications. The workshop is structured to provide an introduction to electronic structure theory as well as a hands-on review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of a workstation to complete exercises, experiment and/or conduct short research topics. The GaussView user interface will be used to perform visualization of results and to facilitate calculation setup. Each workshop participant will also be provided a copy of the lecture notes, a copy of Exploring Chemistry with Electronic Structure Methods and a Gaussian User's Reference. For an Application please contact: Workshop Coordinator Gaussian, Inc. Carnegie Office Park, Bldg. 6 Pittsburgh, PA 15106 Additional information can be obtained from: Telephone: 412 279 6700 Fax: 412 279 2118 email: info@gaussian.com Travel information and hotel accommodations may be found at: http://www.uni-ulm.de/coe/comingevents.html Lunch and breaks will be provided to all registrants. Hotel accommodations and other meals will be the responsibility of each participant. DEADLINES: Receipt of Registration Materials along with the registration fee must be received by the specified deadlines. **************************************************************************** This notice is sent without warranty of any kind, expressed or implied by Gaussian Inc., or Sun Microsystems. Gaussian is a registered trademark of Gaussian, Inc. From chemistry-request@server.ccl.net Thu Jan 16 13:11:35 2003 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GIBYV09168 for ; Thu, 16 Jan 2003 13:11:34 -0500 content-class: urn:content-classes:message Subject: Conferences ... MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2BD8A.82147CF4" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Thu, 16 Jan 2003 13:10:10 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Conferences ... Thread-Index: AcK9iq0y8qhk3ZYhQ96kdx/GaB15Xg== From: "Axel Mathieu" To: This is a multi-part message in MIME format. ------_=_NextPart_001_01C2BD8A.82147CF4 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings everybody, =20 I'm wondering if any of you have suggestions for a molecular = modeling/computational chemistry conferencesto which I (or others with = similar interests) could attend. Since my previous entourage was not = drug design, I'm not aware of the conferences are out there on that = subject; I'm looking for a good conference on computer aided drug = design. Last year I attended the Structure-Based Drug Design conference = in Boston. I really enjoyed this conference and is exaclty the kind of = conference I wish to attend again this year. On the other hand, since = this conference is based on idustrial applications of computer-aided = drug design, I do not feel that the content will change much with = respect to last year (obviously due to the confidential nature of = industrial research). I've looked around on the net and found a few = conferences that may seem interesting (for ex: Gordon conference on = Comp-Aided Drug Design) but many others include too much ab initio for = my own practical use at the moment. Any suggestions? I'll summarize if I = get enough answers. =20 Axel ------_=_NextPart_001_01C2BD8A.82147CF4 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
Greetings=20 everybody,
 
I'm = wondering if any=20 of you have suggestions for a molecular modeling/computational chemistry = conferencesto which I (or others with similar interests) could attend. = Since my=20 previous entourage was not drug design, I'm not aware of the = conferences=20 are out there on that subject; I'm looking for a good conference on = computer=20 aided drug design. Last year I attended the Structure-Based Drug Design=20 conference in Boston. I really enjoyed this conference and=20 is exaclty the kind of conference I wish to attend again this = year. On=20 the other hand, since this conference is based on idustrial applications = of=20 computer-aided drug design, I do not feel that the content will change = much with=20 respect to last year (obviously due to the confidential nature of = industrial=20 research). I've looked around on the net and found a few conferences = that may=20 seem interesting (for ex: Gordon conference on Comp-Aided Drug Design) = but many=20 others include too much ab initio for my own practical use at = the=20 moment. Any suggestions? I'll summarize if I get enough=20 answers.
 
Axel
------_=_NextPart_001_01C2BD8A.82147CF4-- From chemistry-request@server.ccl.net Thu Jan 16 10:22:44 2003 Received: from chem-mail.chemistry.gatech.edu ([130.207.35.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0GFMhV01726 for ; Thu, 16 Jan 2003 10:22:44 -0500 Received: from aurelius.chemistry.gatech.edu (aurelius.chemistry.gatech.edu [130.207.35.94]) by chem-mail.chemistry.gatech.edu (8.9.0/8.9.0) with ESMTP id KAA16861 for ; Thu, 16 Jan 2003 10:27:38 -0500 (EST) Date: Thu, 16 Jan 2003 10:23:03 -0500 (EST) From: David Sherrill To: chemistry@ccl.net Subject: Georgia Tech Summer Theory Program 2003 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Georgia Tech will host its third annual Summer Theory Program as part of its National Science Foundation Research Experiences for Undergraduates program in chemistry and biochemistry. During the ten week REU program, students will conduct research in the groups of Georgia Tech Chemistry faculty. The program is open to students who will be in their junior or senior years during the 2003-2004 academic year. Successful applicants will receive a stipend of $3500, a travel allowance, on-campus dormitory housing, and health insurance coverage. More information on the Georgia Tech REU program may be found at http://www.chemistry.gatech.edu/Undergraduate/summerprogram.html. REU students who are interested in theoretical chemistry will take part in the Summer Theory Program, which supplements the research experience with a a series of introductory lectures in theoretical chemistry at the undergraduate level. Summer research projects in the areas of dynamics and electronic structure theory are available in the groups of Professors Rigoberto Hernandez and David Sherrill. Students will have access to a 72-processor IBM SP2 parallel supercomputer in the Center for Computational Molecular Science & Technology for their computations. -- C. David Sherrill, Ph.D. sherrill@chemistry.gatech.edu Blanchard Assistant Professor of Chemistry School of Chemistry and Biochemistry Phone: (404) 894-4037 Georgia Institute of Technology Fax: (404) 894-7452 http://www.chemistry.gatech.edu/faculty/sherrill/ From chemistry-request@server.ccl.net Thu Jan 16 19:38:24 2003 Received: from sciences.sdsu.edu ([130.191.226.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0H0cOV21023 for ; Thu, 16 Jan 2003 19:38:24 -0500 Received: from localhost (jcuervo@localhost) by sciences.sdsu.edu (8.10.2+Sun/8.8.8/SCEC-8.8.8-AS.AR.S5) with ESMTP id h0H0cFl25726 for ; Thu, 16 Jan 2003 16:38:23 -0800 (PST) Date: Thu, 16 Jan 2003 16:38:15 -0800 (PST) From: Javier Cuervo To: chemistry@ccl.net Subject: Dissociation Constant Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I'm looking for Dissociation Constant (Kd) of protein-protein complex, If anyone knows about a public database or publication that has this information of as many complex as possible, I will really appreciate it. Thanks in advance Javier Cuervo Graduate student Computational Sciences Program SDSU