From gadre@chem.unipune.ernet.in Mon Mar 17 09:29:57 1997 Received: from sangam.ncst.ernet.in for gadre@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id IAA12717; Mon, 17 Mar 1997 08:35:01 -0500 (EST) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id TAA25516 for ; Mon, 17 Mar 1997 19:10:12 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA08876; Mon, 17 Mar 1997 19:01:48 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.7.5/SMI-SVR4.1.0) id TAA02895; Mon, 17 Mar 1997 19:02:28 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id UAA02294; Mon, 17 Mar 1997 20:04:39 -0500 Date: Mon, 17 Mar 1997 20:04:39 -0500 From: gadre@chem.unipune.ernet.in (Prof. Shridhar R. Gadre) Message-Id: <199703180104.UAA02294@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Meaning of RMP2 parameter in GAUSSIAN Dear Sirs : Could someone clarify the following point. If we optimize the geometry using RMP2 parameter, are all the orbitals (occ+vir) treated by GAUSSIAN package OR does it do some frozen core approximation? Thanks....Shridhar Gadre From jz_guo@f18.hotmail.com Tue Mar 18 09:02:26 1997 Received: from f18.hotmail.com for jz_guo@f18.hotmail.com by www.ccl.net (8.8.3/950822.1) id IAA22719; Tue, 18 Mar 1997 08:22:11 -0500 (EST) Received: (from root@localhost) by f18.hotmail.com (8.7.5/8.7.3) id FAA16916; Tue, 18 Mar 1997 05:21:41 -0800 (PST) Date: Tue, 18 Mar 1997 05:21:41 -0800 (PST) Message-Id: <199703181321.FAA16916@f18.hotmail.com> Received: from 202.194.10.200 by www.hotmail.com with HTTP; Tue, 18 Mar 1997 05:21:41 PST X-Originating-IP: [202.194.10.200] From: " Jingzhong Guo" To: chemistry@www.ccl.net Subject: questions Content-Type: text/plain Hello CCL: Recently, we are interested in the reactions of some diatomic species such as NH, NF, PH, PF, etc. For these species with pi-2 confuguration, the ground state is 'X triplet-SIGMA', the lowest singlet state is 'a singlet-DELTA'. When computing the singlet state using Gaussian92 program directly, it seems that the state we obtained is the second singlet state ('b singlet-SIGMA'). I would like to know the calculating method to obtain the geometries and energies of these species in the lowest singlet state ('a singlet-DELTA'). Can I use Gaussian-2 theory to deal with these singlet states? What is input for such a calculatin? Dr. Jingzhong GUO Department of Chemistry Shandong University Jinan 250100 P. R. China Email: guojz@sdunetsv2.sdu.edu.cn or jz_guo@hotmail.com --------------------------------------------------------- Get Your *Web-Based* Free Email at http://www.hotmail.com --------------------------------------------------------- From ivsc@ufba.br Wed Mar 19 07:30:22 1997 Received: from canudos.ufba.br for ivsc@ufba.br by www.ccl.net (8.8.3/950822.1) id HAA09792; Wed, 19 Mar 1997 07:18:06 -0500 (EST) Received: from localhost by canudos.ufba.br (AIX 4.1/UCB 5.64/4.03) id AA65960; Wed, 19 Mar 1997 09:16:03 -0300 Date: Wed, 19 Mar 1997 09:16:03 -0300 (GRNLNDST) From: Ivan Souza Costa To: chemistry@www.ccl.net Subject: dipole momement Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm trying to determine the dipole moment of molecules using semi-empirical methods and have obtained good results, with the MNDO and AM1, for those containg H,B,C,N,O,F and Cl.To complete my work I would like to extended to molecules with the atoms Si,P and S.In order to finish my work I need to Know the experimental value of the dipole moment and the bondlenght of the following compoud: HSi, HP and HS, for using in my parametrization. Should anyone have these please e-mail them ASAP. Ivan From fgonzale@lauca.usach.cl Thu Mar 20 07:44:49 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id GAA17713; Thu, 20 Mar 1997 06:32:02 -0500 (EST) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.7.4/8.7.3) with ESMTP id HAA02375 for ; Fri, 21 Mar 1997 07:35:56 -0400 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id IAA21720; Thu, 20 Mar 1997 08:33:23 -0400 Date: Thu, 20 Mar 1997 08:33:22 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: CHEMISTRY@www.ccl.net cc: Fdo Danilo Gonzalez Nilo Subject: Summary: Water Box (MD) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! It's the summary of the answers, about the following question: ************************************************************************** We are runnig a dynamic Calculation of a macroion with 8 positive charges in a water box, using PBC and a 30x30x30 cell, T=300 K, 50ps. We observe many water molecules going out from the box, during the process. We don't use any counterion. Is it normal that in the PBC condition, water molecules go out the cell? if not.... How can that be controlled? *********************************************************************** THANK YOU VERY MUCH to all the CCL is GREAT! ANSWERS: 1------------------------------------------------------------------ Hi, I'm a bit confused as to what you are asking. If you are using periodic boundary conditions then when the water molecules leave one side of the box they just return on the other side. When using PBC it should make no difference where you put the 'walls' of your box as you are hoping to simulate a bulk fluid. If I am misinterpreting your question please let me know and I'll try to answer it again. good luck, Marcus Martin Graduate Student Department of Chemistry, University of Minnesota marti108@gold.tc.umn.edu http://siepmann6.chem.umn.edu/~marcus 2-------------------------------------------------------------------- It all could depend on what software you're using. Bill Ross 3-------------------------------------------------------------------- Hi, PBC ensures the conserved number of particles and if it works correctly, the leaving water will enter from the opposite side of the box with the identical momentum. I am wondering which software are you using. One important thing doing simulation with the unbalancing chared system is the calculation of long-range interactions. For yours, Ewald summation must not be used. Usually, I used reaction-field method to cope with the long-range interactions if unbalance charge is present in the box. take care, Noy ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Profession: Lecturer and Information Technology Consultant Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: 2461381 FAX 2461381 Cellular: 01-4906089 E-mail: noy@einstein.sc.mahidol.ac.th, noy@atc.atccu.chula.ac.th Homepage: http://www.sc.mahidol.ac.th/noy/ Research: Computer Aided Molecular Design (CAMD) ----------------------------------------------------------------------------- 3----------------------------------------------------------------------- Hi!! Yes, this is perfectly normal - as long as the water molecules come in again from the opposite side. And how could you prevent the water molecules from leaving the cell, anyway? You would have to make the cell boundary some kind of wall, where the molecules would be reflected. But this is exactly what you are trying to prevent with periodic boundary conditions - namely, a finite system that is influenced by boundary effects! On the other hand: If you are not applying any external force to the system, all molecules should leave the box in any direction with the same probability. SO if you have the impression that the molecules stream out through one side (and come in from the opposite side), then there is something wrong with your simulation. If you want to be sure about this, I think you should calculate the velocity auto-correlation function of the water molecules, which has to vanish within 1ps or so. If it does not, you are wittnessing this 'streaming effect'. good luck, gerald Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA 4-------------------------------------------------------------------- Dear Mr Gonzalez, what program do you use? I know this problem from SYBYL 6.1 on Sun. There it was a bug. Within SYBYL 6.2 for Sun it is removed. But there exist other possibilities for the observed behaviour: 1. PBC allows a few water molecules to run a bit out of the box under one special condition. It depends on the minimum image convention normally used within PBC. However, this effects only less then 5 solvent molecules at one simulation step (from my observations), which leave the box only up to a distance lower than their molecular size. In a following step they return to their old place inside the box or are switched to the opposite side inside the box, if you watch a replay of the trajectories. 2. I guess you do the simulation within an NPT ensemble. Therefore the size of the box must be adjustable, it changes at everey simulation step. If you have the box dimension frozen, but you request an NPT ensemble, then many programs are confused. One possible result would be like you observed. 3. The box size should be related to the NBC. NBC should be not greater than 1/2 x boxlength. If your box is too small in relation to the NBC, it depends on the program how this is handled. Within SYBYL the box size will be enlarged without changing the number of particles, when NBC is greater than allowed. Sincerely yours B. Kallies ----------------------------------------------------- Dr. Bernd Kallies Institut fuer Physikalische und Theoretische Chemie Universitaet Potsdam Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm Tel : [+49] (0)331 / 977-1313 Fax : [+49] (0)331 / 977-1315 ----------------------------------------------------- 5---------------------------------------------------------------------- I'm not sure I understand the question. If you mean they go out one side of the cell and come in the other, then yes that is normal. That is why you use periodic boundary conditions. If you mean they go out and don't come back, then no that is not normal, and you are doing something wrong with your boundary conditions. Have I misunderstood the question? ------------- Visiting Research Instructor Steven J. Stuart U.S. Naval Academy stuart@brass.nadn.navy.mil 572 Holloway Rd., Mail Code 9B (410) 293-6636 Annapolis, MD 21402 fax: (410) 293-2218 6--------------------------------------------------------------------- What software are you running? I have had similiar problems before and it turned out that I had not defined something correctly. If you are using CHARMM I may be able to help. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** 7-------------------------------------------------------------------------- Hi, If you have water molecules comming in from the opposite direction, everything is fine. Istvan -- ************************************************* Istvan Enyedy The Catholic University of America Chemistry Department/ Malloney Hall Washington DC 20064 email istvan@bioorg.ee.cua.edu phone 202-319-5707 or 5349 fax 202-319-5381 ************************************************** ---------------------------------------------------------------------- Thanks a lot ... again Fernando Danilo Gonzalez N. University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago, Chile fono: (562) 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quimbio.usach.cl URL : http://quimbio.usach.cl/~danilo/ *************************************************************************x From me00007@cc.uoi.gr Fri Mar 21 06:30:47 1997 Received: from cc.uoi.gr for me00007@cc.uoi.gr by www.ccl.net (8.8.3/950822.1) id FAA26469; Fri, 21 Mar 1997 05:56:39 -0500 (EST) Received: from persefoni.cc.uoi.gr (persefoni.cc.uoi.gr [193.92.4.148]) by cc.uoi.gr (8.8.4/8.8.3) with ESMTP id OAA00391 for ; Fri, 21 Mar 1997 14:59:14 +0200 (GMT+0200) Message-ID: <33326908.4D56@cc.uoi.gr> Date: Fri, 21 Mar 1997 12:55:06 +0200 From: Nikos Kourkoumelis X-Mailer: Mozilla 4.0b2 (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Mopac 93-R2 MO symmetry X-Priority: 3 (Normal) Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=iso-8859-7 Is it possible using Mopac93 R2 to incule the MO's symmetries in the output file ? The "Eigenvectors" matrix does not contain this information. Is it something wrong with the compilation or with the keywords ? Thank you in advance. Nick Kourkoumelis University of Ioannina - Greece e-mail: me00007@cc.uoi.gr From bruce@cosy.utmb.edu Fri Mar 21 09:30:49 1997 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.8.3/950822.1) id IAA27324; Fri, 21 Mar 1997 08:32:46 -0500 (EST) Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id HAA11686; Fri, 21 Mar 1997 07:33:33 -0600 From: "Bruce A. Luxon" Message-Id: <9703210733.ZM11684@cosy.utmb.edu> Date: Fri, 21 Mar 1997 07:33:26 -0600 Organization: Sealy Center for Structural Biology Reply-To: bruce@nmr.utmb.edu X-Phone: (409) 747-6802 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Structural Biology and Virology Positions Available Cc: virus@nmr.utmb.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Positions in Virology and Structural Biology University of Texas Medical Branch at Galveston * * * * * * * * * * * * * * * * * * * * * * * Postdoctoral and research technician positions are available to carry out structure-based design of antiviral agents directed against cell attachment and replication of alphaviruses, flaviviruses and arenaviruses. This project, funded by the Defense Advanced Research Projects Agency (DARPA; see Science, 275, pp. 744-746), provides unique opportunities to participate in a highly focused interdisciplinary approach bringing together internationally recognized structural biologists from the Sealy Center for Structural Biology and virologists from the World Health Organization Collaborating Center for Tropical Diseases. Facilities include state-of-the-art Biosafety level 3 laboratories, automated sequencing and molecular biology imaging equipment. Instrumentation available for structural studies includes Varian UNITYplus 750 (4 channel), 600 and wide-bore 400 MHz spectrometers, Cray J90 supercomputer, SGI Power Challenge and graphics workstations, MacScience imaging plate detectors and rotating anode X-ray generators, and a Pharmacia DNA synthesizer. We also have our own fully-equipped graphics and multimedia preparation system. Both postdoctoral (Ph.D. degree) and technician (BS or MS degree) candidates are encouraged to apply for positions in the following areas: Structural and Molecular Biology: 1. Expression, purification and X-ray crystallography of viral molecules. 2. Drug development using phage display techniques. 3. Biomolecular NMR spectroscopy (protein and nucleic acid structures), backbone modified aptamer oligonucleotide synthesis, molecular biology, combinatorial chemistry, computational biology and computer-aided drug design. 4. Production, purification and testing of recombinant NFkB proteins, and testing of decoy oligonucleotides using recombinant NFkB proteins in vitro and in cell culture systems. Structural Biology Faculty: David G. Gorenstein (david@nmr.utmb.edu) Robert O. Fox (fox@bloch.utmb.edu) Bruce A. Luxon (bruce@nmr.utmb.edu) Stanley J. Watowich (watowich@bloch.utmb.edu) Virology: 1. Assay development and testing of decoy oligonucleotides in animal systems. Experience in tissue and virus culture, animal infections, cytokine bioassays and immunoasssays is required. 2. Mapping of RNA packaging signals and other conserved sequence elements in alphavirus genomes; testing of decoy oligonucleotides in cell culture and animal models. Experience in molecular virology and animal infections is required. Virology Faculty: Judy F. Aronson (jaronson@mspo6.med.utmb.edu) Alan D. T. Barrett (abarrett@mspo5.med.utmb.edu) Norbert K. Herzog (nherzog@mspo4.med.utmb.edu) Robert E. Shope (rshope@mspo6.med.utmb.edu) Scott C. Weaver (sweaver@marlin.utmb.edu) Please send CV, statement of research interests and career goals, and the names, addresses and telephone numbers of three references to: Dr. Robert E. Shope, Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555-0609; FAX (409) 747-2429; Email: robert.shope@utmb.edu. Further information can also be obtained by contacting me or any of the faculty listed above. -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From boufer@cennas.nhmfl.gov Fri Mar 21 11:30:52 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id KAA28323; Fri, 21 Mar 1997 10:33:14 -0500 (EST) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id KAA26754 for ; Fri, 21 Mar 1997 10:33:14 -0500 (EST) Date: Fri, 21 Mar 1997 10:33:14 -0500 (EST) From: Ahmed Bouferguene X-Sender: boufer@cennas To: CHEMISTRY@www.ccl.net Subject: HONDO Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I would appreciate receiving any information about how the guess density matrix is initialized in HONDO. Thanks >From jkl@ccl.net Fri Mar 21 11:22 EST 1997 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id LAA24934; Fri, 21 Mar 1997 11:22:30 -0500 (EST) Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id LAA06810; Fri, 21 Mar 1997 11:22:27 -0500 (EST) From: Jan Labanowski Date: Fri, 21 Mar 1997 11:22:27 -0500 (EST) Message-Id: <199703211622.LAA06810@krakow.ccl.net> To: chemistry@www.ccl.net Subject: CCL Administrator speaking Cc: jkl@ccl.net Dear CCL subscribers, First, I need to remind you all to read rules and regulations of the list before posting. They are accessible from CCL home page: http://www.ccl.net/chemistry.html You can also get it via e-mail by sending a message: help chemistry to MAILSERV@www.ccl.net Specifically, job ads and solicitations should not appear on the list. We have a job section in CCL Archives, and I am told that it is very successful. Please submit job offers (or CVs) to me and I will place them in the archives. Please check: http://www.ccl.net/ccl/jobs.html Please limit your posting on CCL to good computational chemistry stuff (encouraged topics are listed in CCL help file accessible from our home page). Until the time when we install the option for individual subscriber's filters, it is important to keep CCL traffic focused, since it is already too heavy for some subscribers. Sorry for this reminder, but I am doing my job... On the brighter site, we already installed new Web server on our Pentiums and CCL has even its own subdomain. We are totally rehabbing the archives and test new modes of distribution. It will not be ready tomorrow, but it is coming. I also attach here an appeal to deposit software and materials to CCL archives. WE WILL ALSO BE VERY HAPPY TO MIRROR YOUR CCL RELATED WEB SITE!!! With the fluidity of Web, it may be a good idea to have your site "eternalized" {:-)} To upload the material to CCL, just deposit it in the incoming directory on the anonymous ftp www.ccl.net and send me a short notice. To have your Web site mirrored in CCL, please send me the URL, and permission to mirror it. Thank you for your patience. Jan Labanowski jkl@ccl.net From meylan@syrres.com Fri Mar 21 12:30:53 1997 Received: from syrres.syrres.com for meylan@syrres.com by www.ccl.net (8.8.3/950822.1) id MAA29511; Fri, 21 Mar 1997 12:19:54 -0500 (EST) Message-ID: <9703211217.AA06757@syrres.syrres.com> Received: from syrres.com by syrres.syrres.com; Fri, 21 Mar 97 12:17 EST From: "William Meylan" To: Subject: LogP FDOPA Date: Fri, 21 Mar 1997 12:18:30 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit In response to Dr. Ilonka Guenther's request for a logP value for FDOPA: Although I do not have an experimental value for FDOPA, a logP is easily calculated. L-DOPA has an experimentally measured logP of -2.39 (Sangster Database of Evaluated LogKow Values, 1994). Using Syracuse Research Corp's KOWWIN Program, the logP of the fluoro derivative of L-DOPA is calculated to be -2.19 using the program's Experimental Value Adjusted method (which uses the experimental L-Dopa value and then adjusts for the fluoro-substitution). Estimating the logP from structure alone, the KOWWIN Program gives a value of -2.04. The ClogP for Windows Program (BioByte Corp) gives a value of -2.29. The ACD/LogP Program (ACD/Labs) estimates 0.46 and the PrologP51 Program (CompuDrug Corp) estimates 0.12. The ACD/LogP and PrologP programs do not consider the zwitterionic nature of the compound. *********************************** Bill Meylan Syracuse Research Corp e-mail: meylan@syrres.com phone: 315 426-3303 fax: 315 426-3429 *********************************** >Dear Colleagues, >I am looking for the logP value of FDOPA. >Does anyone has calculated it once or know where to find this value either >calculated or measured? >Thanks for any help. >Kind regards, > Ilonka Guenther