From owner-chemistry@ccl.net Wed Jan 10 01:32:16 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id BAA00120; Wed, 10 Jan 1996 01:29:38 -0500 Received: from Ladyhawk.Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by bedrock.ccl.net (8.7.1/950822.1) id BAA28532; Wed, 10 Jan 1996 01:29:32 -0500 (EST) From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HZUPAYYG4090NKQ8@Levels.UniSA.Edu.Au> for chemistry@ccl.net; Wed, 10 Jan 1996 16:58:23 +0930 Date: Wed, 10 Jan 1996 16:58:23 +0930 Subject: problems with the number of atoms in COSMO To: chemistry@ccl.net Message-id: <01HZUPAYZSCI90NKQ8@Levels.UniSA.Edu.Au> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear All, I think a question similar to this came up recently but I can't remember the answer. We recently installed COSMO onto MOPAC 93. On trying to refine a system containing 123 atoms (previously succesfully carried out using only MOPAC) we obtained the error parameter CENABL is to small for this system. On reducing the number of atoms to 57 the system refined. Can sombody tell my what the problem is? Thanks Andy From owner-chemistry@ccl.net Wed Jan 10 03:47:18 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA01438; Wed, 10 Jan 1996 03:42:55 -0500 Received: from netcom9.netcom.com for javito@netcom.com by bedrock.ccl.net (8.7.1/950822.1) id DAA29106; Wed, 10 Jan 1996 03:42:53 -0500 (EST) Received: by netcom9.netcom.com (8.6.12/Netcom) id AAA11765; Wed, 10 Jan 1996 00:42:34 -0800 From: javito@netcom.com (James Vito) Message-Id: <199601100842.AAA11765@netcom9.netcom.com> Subject: FWD: Antimatter (fwd) To: chemistry@ccl.net Date: Wed, 10 Jan 1996 00:42:34 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Forwarded message: From marcus.pasram@reuters.com Tue Jan 9 08:55:57 1996 Mr-Received: by mta RIT.MUAS; Relayed; Tue, 09 Jan 1996 11:56:33 -0500 Mr-Received: by mta RIT1; Relayed; Tue, 09 Jan 1996 16:57:00 -0500 Mr-Received: by mta RITIG4; Relayed; Tue, 09 Jan 1996 16:56:05 -0500 Disclose-Recipients: prohibited Date: Tue, 09 Jan 1996 11:56:33 -0500 (EST) From: "Marcus Pasram (516) 233-6869" Subject: FWD: Antimatter To: Sean Logan , simeon Fishman , Michael Kraizman , Ian Koenig , javito@netcom.com, David Schleifer Message-Id: <2733561109011996/A13933/RIT1/11A14AF81D00*@MHS> Autoforwarded: false Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="Boundary (ID JbQGAXPq5h6oiUaI6cmBhQ)" Importance: normal Priority: normal Sensitivity: Company-Confidential Ua-Content-Id: 11A14AF81D00 X400-Mts-Identifier: [;2733561109011996/A13933/RIT1] Hop-Count: 2 --Boundary (ID JbQGAXPq5h6oiUaI6cmBhQ) Content-type: TEXT/PLAIN; CHARSET=US-ASCII --Boundary (ID JbQGAXPq5h6oiUaI6cmBhQ) MIME-version: 1.0 Content-type: MESSAGE/RFC822 Received: from DIRECTORY-DAEMON by RITIG4.RIT.REUTERS.COM (PMDF V4.3-10 #7805) id <01HZNGFZNLHS000D40@RITIG4.RIT.REUTERS.COM>; Fri, 05 Jan 1996 12:28:37 -0500 (EST) Received: from ritig1.rit.reuters.com (RITIG1) by RITIG4.RIT.REUTERS.COM (PMDF V4.3-10 #7805) id <01HZNGFW0L1S000DLZ@RITIG4.RIT.REUTERS.COM>; Fri, 05 Jan 1996 12:28:35 -0500 (EST) Received: from relay5.UU.NET by ritig1.rit.reuters.com; (5.65v3.2/1.1.8.2/14Sep94-0947PM) id AA06271; Fri, 5 Jan 1996 12:30:02 -0500 Received: from uucp1.UU.NET by relay5.UU.NET with SMTP id QQzxfp08542; Fri, 5 Jan 1996 12:26:34 -0500 (EST) Received: from ppllc.UUCP by uucp1.UU.NET with UUCP/RMAIL ; Fri, 5 Jan 1996 12:27:42 -0500 Received: from laguardia.ppllc.com by washington.ppllc.com (5.x/SMI-SVR4) id AA10115; Fri, 5 Jan 1996 12:23:38 -0500 Received: by laguardia.ppllc.com (5.x/SMI-SVR4) id AA18436; Fri, 5 Jan 1996 12:21:08 -0500 From: Salvatore Saieva Subject: Antimatter To: Friends -- Alan Rothstein , Alan Boord , Angella Chin , Jon Leong , Takamitsu Yanagihashi , Marcus Pasram , Al Perez , Robert Pescinski , Dave Richards , James Romano Message-id: X-Envelope-to: marcus.pasram@RIT.REUTERS.COM Autoforwarded: false MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Delivery-date: Fri, 5 Jan 1996 12:29:58 EST Importance: normal By MALCOLM W. BROWNE c.1996 N.Y. Times News Service Physicists at the European Laboratory for Particle Physics announced on Thursday that they had created, for 40 billionths of a second, the first complete atoms of antimatter ever made by human beings or seen in nature. In an anti-atom, the antimatter equivalent of an ordinary atom, the electrical charges of all the component particles are reversed; while an ordinary atom has a positively charged nucleus with one or more negatively charged electrons orbiting it, the antimatter atom has a negatively charged nucleus with positively charged orbiting electrons. An ordinary atomic nucleus contains positively charged protons, while its antimatter counterpart contains negatively charged anti-protons. Unless an antimatter atom is kept from coming into contact with an ordinary atom, the two atoms annihilate each other in a violent flash of energy _ a fact that may explain the apparent absence of antimatter in the natural universe. Anti-protons are routinely made in physics laboratories, as are anti-electrons, which are also called positrons. But no one had heretofore succeeded in nudging a positron into orbit around an anti-proton, making an atom of antimatter. The announcement on Thursday by the European laboratory near Geneva, known by its former acronym, CERN, establishes that this bizarre kind of atom can actually exist. Physicists hope one day to make comparative measurements of the properties of atoms and anti-atoms in terms of their gravitational attraction, their interactions with light, and other features. Subtle differences between atoms and their antimatter counterparts may shed light on the origin and evolution of the universe and help solve the puzzle as to why we are made of matter instead of antimatter. Although most physicists discount the idea that anti-hydrogen might one day be developed as a very high potency fuel for interstellar rockets or superbombs, some scientists have not abandoned the dream of exploiting antimatter as a propellant. When combined with ordinary matter it annihilates, converting mass to energy far more efficiently than does a nuclear bomb. Dr. Walter Oelert of the Juelich Institute for Nuclear Physics Research in Germany and his German and Italian colleagues reported that they created the 11 atoms of anti-hydrogen during a three-week experiment at CERN last September, but withheld the news until they and independent experts had thoroughly checked their results, which will be published in a forthcoming issue of the journal Physical Review B. ``We're absolutely sure now,'' he said in an interview, ``and the experiment shows without doubt that anti-hydrogen can exist. No one really doubted it, but it's nice to have the experimental proof.'' The anti-hydrogen atoms created in the experiment were moving at nearly the speed of light and survived only some 40 billionths of a second before colliding with atoms of ordinary matter and annihilating themselves. But from the pattern and types of debris created by these collisions, the scientists were able to establish the identity of the projectiles as anti-hydrogen atoms. Dr. John Eades, the British coordinator of experiments at CERN, said that the real challenge had been in producing enough of the right kind of collisions between ordinary particles to create a few anti-hydrogen atoms. To do this, anti-protons from one of CERN's accelerators were boosted to very high energy and hurled into a target of xenon atoms, Some of the anti-protons survived and passed through, while others collided with xenon nuclei, converting part of their collision energy into the creation of anti-electrons (also called positrons). In a few very rare cases, the speeds and directions of the newly born anti-electrons and the surviving anti-protons coincided enough that the anti-electrons were captured into orbits around the anti-protons, thus forming anti-hydrogen atoms. These atoms, like ordinary hydrogen atoms, are electrically neutral, since the charges of their components cancel each other. nn But the neutrality of anti-hydrogen, like that of ordinary hydrogen, renders it impossible to contain or manipulate using magnetic fields. Moreover, an anti-atom cannot be contained in an ordinary vessel, since the slightest contact with the container's wall causes it to annihilate. Consequently, other groups are developing enormously sophisticated methods, including interacting lasers, to manipulate and secure anti-particles inside vacuum chambers. Oelert acknowledges that the anti-hydrogen atoms his group made cannot be used as the basis of far-reaching experiments in the fundamental interactions of physics, including such cosmological questions as to why the universe seems to consist entirely of matter rather than antimatter. ``We just wanted to have fun and see if you could make anti-hydrogen,'' he said. ``It maybe is not such a great scientific achievement in itself, because our anti-hydrogen atoms are moving around much too fast to study in detail before they annihilate.'' Meanwhile, physicists at Harvard University, Pennsylvania State University, Los Alamos National Laboratory, and other groups are attempting to create, capture, and control anti-hydrogen in a more useful form. Their efforts focus on ``cooling'' anti-protons and anti-electrons using lasers and other tools, and assembling atoms not by violent collisions but by manipulation. Such atoms, when they are eventually made, will be held almost motionless in their chambers, isolated from contact with ordinary matter while their gravitational, spectral, charge-conjugation, parity, and other characteristics are measured. ``Everyone makes shrewd guesses about the probable behavior of anti-hydrogen and other anti-atoms,'' Eades said, ``and we don't really expect a big surprise _ that an atom of antimatter would fall up instead of down, for instance. But there may be subtle differences of great importance. For instance, an atom and an anti-atom might fall at slightly different speeds toward a gravitating object like the sun. Our orbit around the sun is elliptical, so the sun's gravitational pull on the Earth varies slightly over a year, and by observing its effect on an anti-hydrogen atom, we might learn interesting things.'' In principle, scientists believe that atoms larger than anti-hydrogen _ the simplest possible atomic form of antimatter _ might be created. But each increase in the size and complexity of an atom complicates the assembly problem. Anti-helium, the least complicated atom after hydrogen, would have a nucleus of two anti-protons and two anti-neutrons, with two orbiting anti-electrons. ``We're especially interested in hydrogen and anti-hydrogen,'' Eades said, ``not only because of their structural simplicity, but because 90 percent of the mass of the universe is hydrogen. Even slight differences in the properties of hydrogen and anti-hydrogen could help explain why the universe, as we know it, consists entirely of matter rather than antimatter.'' Dr. Gerald Gabrielse of Harvard University, whose research group is working to slow down particles of antimatter contained in special traps, commented that the CERN synthesis of anti-hydrogen ``is an important experiment demonstrating that it can be done. The payoff will be down the road, when one is eventually able to study the properties of these atoms.'' --Boundary (ID JbQGAXPq5h6oiUaI6cmBhQ)-- From JDA03546@niftyserve.or.jp Wed Jan 10 06:17:20 1996 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by www.ccl.net (8.6.10/950822.1) id GAA02535; Wed, 10 Jan 1996 06:03:15 -0500 Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id UAA06404; Wed, 10 Jan 1996 20:04:41 +0900 Message-Id: <199601101104.UAA06404@inetnif.niftyserve.or.jp> Date: Wed, 10 Jan 1996 17:29:00 +0900 From: "JDA03546@niftyse" Subject: [Summary]Standard Basis Set for Lanthani To: chemistry@www.ccl.net Dear all, I asked about the basis set for lanthanide atoms last week and I got only one answer from Dr. Laurent. His message was: >I'm also doing calculations on lanthanides (Nd) with Gaussian 94. >Effectively, the ECP included in G94 doesn't accept lanthanides. >So you have to specify your own basis. >Here are two papers about it : >T.R. Cundari and W.J.Stevens (J.Chem.phys. 98(7) April 1993) >and >M.Dolg, H.Stoll, A.Savin and H.Preuss (Theor.Chim.Acta (1989) 75:173-194) > >I had many problems with them. > >So, I'm very interested by your calculations. >Could you tell me if you have any results with your ECP ?? > >P.S. : the first ECP (Cundari) is included in Gamess with the keyword ECP=SBK >I'm now working with Gamess. > >Laurent Joubert > >---------------------------------------------------------------- > Joubert laurent (Doctoral Grant) > > Ecole Nationale Superieure de Chimie de Paris > > ( New Website : ) > ( http://www.enscp.jussieu.fr ) > > Laboratoire de Modelisation Appliquee a la Chimie (M.A.C.) > Tel : 44-27-66-94 > E-Mail : joubert@idf.ext.jussieu.fr >---------------------------------------------------------------- Thank you. ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <01/10 09:47> ** From zuegg@fochsg03.tu-graz.ac.at Wed Jan 10 06:47:25 1996 Received: from fochsg03.tu-graz.ac.at for zuegg@fochsg03.tu-graz.ac.at by www.ccl.net (8.6.10/950822.1) id GAA02634; Wed, 10 Jan 1996 06:32:35 -0500 Received: by fochsg03.tu-graz.ac.at id AA01485 (5.67b/IDA-1.5t for chemistry@www.ccl.net); Wed, 10 Jan 1996 12:29:06 -0800 Date: Wed, 10 Jan 1996 12:29:00 -0800 (PST) From: Johannes Zuegg X-Sender: zuegg@fochsg03.tu-graz.ac.at To: Osc - CompChemList Subject: Q: Surface presentations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Net, I am nearly at the end of my PhD project and now I am working on publishing my results but run into some problems you may help with : I wanted to display a own-calculated property (like pharmacophor interests or by GRID interaction energies) on a surface of the binding site of an enzyme and add calculated substrates as line presentations. I used MOLCAD within SYBYL by generating a Connolly surface only for the interesting part of the enzyme and tried to color it by using the program as I have been told by the Tripos support but got only colors by deepness and not by property. After no responce from the main author in Germany I tried to color the corresponding atoms and using the command in MolCad but with the result that the color on some areas were not the same as for the corresponding atom. The result was not unique color areas, and additionally I had only 8 colors (values) to choose from. My question is (to Sybyl-User and others): Does anyone have a suggestions or reference or something on how generating a surface-presentation of a part of an enzyme and color it by own properties? I know Grasp but, apart that it is quite expensive, Can Grasp do it? Are there other low budget programs ? Many thanks in advanve for the help Johannes Zuegg --------------------------------------------------------------------- Institute for Organic Chemistry Tel : +43 [0]316 873-8746 University of Technology Graz 8939 Stremayrgasse 16 Fax : +43 [0]316 873-8740 A-8010 Graz EMail: Zuegg@orgc.tu-graz.ac.at Austria Http : www-orgc.tu-graz.ac.at --------------------------------------------------------------------- From 94970459@vax1.dcu.ie Wed Jan 10 09:17:22 1996 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.6.10/950822.1) id JAA03770; Wed, 10 Jan 1996 09:15:44 -0500 Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01HZUJK5JE0099E8Q5@vax1.dcu.ie>; Wed, 10 Jan 1996 14:14:36 GMT Date: Wed, 10 Jan 1996 14:14:35 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Chiral Selectivity To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@www.ccl.net Message-id: <01HZUJK5KQ8299E8Q5@vax1.dcu.ie> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"hyperchem@hyper.com", IN%"support@hyper.com" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, Happy New Year. I am a HyperChem user and I wish to study the chiral selectivity of some molecules. I wish to study why some chiral substrates of a given configuration are more selective towards eithier the R- or S- forms of for example, phenylethylamine. Firstly, can anyone point me to some general references on this subject. Secondly, Can anyone advise me on the best way to model such interactions with HyperChem. More specifically, I would like to know: a) how I should initially place the phenylethylamine molecule. Presumably, I should place the chiral region of the phenylethylamine molecule near the chiral region of the substrate but can anyone be more specific than this. b) should I model such interactions with bond dipoles or atomic charges Kind regards, Paddy Paddy Kane 94970459@vax1.dcu.ie From tamasgunda@tigris.klte.hu Wed Jan 10 10:47:23 1996 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id KAA04692; Wed, 10 Jan 1996 10:38:36 -0500 Message-Id: <199601101538.KAA04692@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Wed, 10 Jan 1996 16:39:41 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Wed, 10 Jan 1996 16:39:37 +1 Subject: unknown file format Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Hi Netters, Some days ago Konstantin Momot send to the list a molecule file with unknown format. The coordinates are Carthesian ones, but the full format itself is its own. I could input the molecules with Mol2mol, the second one without problems, the first after some manual pre-editing. They are transformed now into Sybyl mol2 format. Nice molecules! Tamas E. Gunda PS: I hope that the mailer program will not cut the lines ------------------------------------------------ # Name: first molecule # Created by Mol2Mol 3.1 # Creation time: Wed Jan 10 15:27:39 1996 # from ZMAT2.Z of type SYBYL_2 # first molecule @MOLECULE first molecule 67 74 1 0 0 SMALL NO_CHARGES @ATOM 1 **** 0.0000 0.0000 0.0000 Fe 1 <1> 0.0 2 **** -1.9332 0.0000 0.0000 N.pl3 1 <1> 0.0 3 **** 0.0003 -1.9420 0.0000 N.pl3 1 <1> 0.0 4 **** 1.9374 0.0000 0.0000 N.pl3 1 <1> 0.0 5 **** -0.0003 1.9523 0.0000 N.pl3 1 <1> 0.0 6 **** -2.7347 1.0316 -0.2946 C.2 1 <1> 0.0 7 **** -2.7240 -1.0117 0.3863 C.2 1 <1> 0.0 8 **** -1.0378 -2.7190 0.3616 C.2 1 <1> 0.0 9 **** 1.0010 -2.6733 -0.3519 C.2 1 <1> 0.0 10 **** 2.7332 -1.0057 -0.3925 C.2 1 <1> 0.0 11 **** 2.7427 1.0253 0.3064 C.2 1 <1> 0.0 12 **** 1.0054 2.6866 0.3283 C.2 1 <1> 0.0 13 **** -1.0453 2.7320 -0.3331 C.2 1 <1> 0.0 14 **** -4.0203 0.7014 -0.1364 C.2 1 <1> 0.0 15 **** -4.0114 -0.6547 0.3548 C.2 1 <1> 0.0 16 **** -0.6135 -4.1073 0.2218 C.2 1 <1> 0.0 17 **** 0.6287 -4.0777 -0.2423 C.2 1 <1> 0.0 18 **** 4.1341 -0.5989 -0.3367 C.2 1 <1> 0.0 19 **** 4.1411 0.6486 0.1213 C.2 1 <1> 0.0 20 **** 0.6300 4.0913 0.2359 C.2 1 <1> 0.0 21 **** -0.6214 4.1207 -0.2015 C.2 1 <1> 0.0 22 **** -2.2818 -2.3675 0.7145 C.2 1 <1> 0.0 23 **** 2.3536 -2.2496 -0.7166 C.2 1 <1> 0.0 24 **** 2.3675 2.2640 0.6507 C.2 1 <1> 0.0 25 **** -2.2993 2.3813 -0.6474 C.2 1 <1> 0.0 26 **** -4.9133 1.3278 -0.2938 H 1 <1> 0.0 27 **** -4.8970 -1.2602 0.6073 H 1 <1> 0.0 28 **** -1.2034 -5.0156 0.4262 H 1 <1> 0.0 29 **** 1.2584 -4.9549 -0.4624 H 1 <1> 0.0 30 **** 5.0233 -1.1988 -0.5906 H 1 <1> 0.0 31 **** 5.0365 1.2704 0.2844 H 1 <1> 0.0 32 **** 1.2624 4.9690 0.4459 H 1 <1> 0.0 33 **** -1.2170 5.0293 -0.3885 H 1 <1> 0.0 34 **** -2.9833 -3.0931 1.1073 H 1 <1> 0.0 35 **** 3.0592 -2.9693 -1.1128 H 1 <1> 0.0 36 **** 3.0833 2.9826 1.0305 H 1 <1> 0.0 37 **** -3.0114 3.1044 -1.0253 H 1 <1> 0.0 38 **** -0.0912 0.0664 2.0089 N.2 1 <1> 0.0 39 **** 0.0764 -0.2421 4.2071 N.pl3 1 <1> 0.0 40 **** 0.4543 -0.6872 2.9963 C.2 1 <1> 0.0 41 **** -0.8197 0.9904 2.6759 C.2 1 <1> 0.0 42 **** -0.7257 0.8123 4.0083 C.2 1 <1> 0.0 43 **** 0.4459 -0.7953 5.5388 C.3 1 <1> 0.0 44 **** 1.3899 -1.8497 2.8128 C.3 1 <1> 0.0 45 **** -1.4182 1.7826 2.2026 H 1 <1> 0.0 46 **** -1.2158 1.4175 4.7881 H 1 <1> 0.0 47 **** 1.5320 -0.6395 5.7296 H 1 <1> 0.0 48 **** -0.1212 -0.2983 6.3583 H 1 <1> 0.0 49 **** 0.2165 -1.8843 5.5834 H 1 <1> 0.0 50 **** 1.9301 -2.1020 3.7513 H 1 <1> 0.0 51 ** 52 **** 2.1711 -1.6038 2.0655 H 1 <1> 0.0 53 **** 0.0904 0.0709 -2.0095 N.2 1 <1> 0.0 54 **** -0.0795 -0.2331 -4.2084 N.pl3 1 <1> 0.0 55 **** -0.4545 -0.6817 -2.9979 C.2 1 <1> 0.0 56 **** 0.7225 0.8211 -4.0083 C.2 1 <1> 0.0 57 **** 0.8178 0.9962 -2.6757 C.2 1 <1> 0.0 58 **** -1.3860 -1.8480 -2.8174 C.3 1 <1> 0.0 59 **** -0.4495 -0.7849 -5.5406 C.3 1 <1> 0.0 60 **** 1.2118 1.4277 -4.7876 H 1 <1> 0.0 61 **** 1.4177 1.7873 -2.2021 H 1 <1> 0.0 62 **** -1.9540 -2.0738 -3.7463 H 1 <1> 0.0 63 **** -0.8183 -2.7632 -2.5411 H 1 <1> 0.0 64 **** -2.1454 -1.6232 -2.0422 H 1 <1> 0.0 65 **** 0.1306 -0.2995 -6.3579 H 1 <1> 0.0 66 **** -0.2372 -1.8775 -5.5809 H 1 <1> 0.0 67 **** -1.5319 -0.6127 -5.7381 H 1 <1> 0.0 @BOND 1 1 2 1 2 1 3 1 3 1 4 1 4 1 5 1 5 2 6 1 6 2 7 1 7 3 8 1 8 3 9 2 9 4 10 1 10 4 11 1 11 5 12 2 12 5 13 1 13 6 14 2 14 6 25 1 15 7 15 2 16 7 22 1 17 8 16 1 18 8 22 2 19 9 17 1 20 9 23 1 21 10 18 1 22 10 23 2 23 11 19 1 24 11 24 2 25 12 20 1 26 12 24 1 27 13 21 1 28 13 25 2 29 14 15 1 30 14 26 1 31 15 27 1 32 16 17 2 33 16 28 1 34 17 29 1 35 18 19 2 36 18 30 1 37 19 31 1 38 20 21 2 39 20 32 1 40 21 33 1 41 22 34 1 42 23 35 1 43 24 36 1 44 25 37 1 45 38 40 2 46 38 41 1 47 39 40 1 48 39 42 1 49 39 43 1 50 40 44 1 51 41 42 2 52 41 45 1 53 42 46 1 54 43 47 1 55 43 48 1 56 43 49 1 57 44 50 1 58 44 51 1 59 44 52 1 60 53 55 2 61 53 57 1 62 54 55 1 63 54 56 1 64 54 59 1 65 55 58 1 66 56 57 2 67 56 60 1 68 57 61 1 69 58 62 1 70 58 63 1 71 58 64 1 72 59 65 1 73 59 66 1 74 59 67 1 @SUBSTRUCTURE 1 **** 67 TEMP 0 **** **** 0 ROOT ---------------------------cut here --------------- # Name: second molecule # Created by Mol2Mol 3.1 # Creation time: Wed Jan 10 15:27:39 1996 # from ZMAT2.Z of type SYBYL_2 # second molecule @MOLECULE second mol 67 74 1 0 0 SMALL NO_CHARGES @ATOM 1 **** 0.0000 0.0000 0.0000 Fe 1 <1> 0.0 2 **** -1.9205 0.0000 0.0000 N.pl3 1 <1> 0.0 3 **** -0.0113 -1.9437 0.0000 N.pl3 1 <1> 0.0 4 **** 1.9476 0.0033 -0.0021 N.pl3 1 <1> 0.0 5 **** 0.0075 1.9341 -0.0080 N.pl3 1 <1> 0.0 6 **** -2.7408 1.0108 0.4389 C.2 1 <1> 0.0 7 **** -2.7421 -1.0233 -0.4191 C.2 1 <1> 0.0 8 **** -1.0317 -2.7498 -0.4358 C.2 1 <1> 0.0 9 **** 1.0157 -2.7526 0.3879 C.2 1 <1> 0.0 10 **** 2.7621 -1.0371 0.3417 C.2 1 <1> 0.0 11 **** 2.7469 1.0290 -0.4426 C.2 1 <1> 0.0 12 **** 1.0372 2.7572 -0.3783 C.2 1 <1> 0.0 13 **** -1.0120 2.7397 0.4436 C.2 1 <1> 0.0 14 **** -4.0982 0.5927 0.3257 C.2 1 <1> 0.0 15 **** -4.1105 -0.6207 -0.2596 C.2 1 <1> 0.0 16 **** -0.6273 -4.1264 -0.3213 C.2 1 <1> 0.0 17 **** 0.6152 -4.1269 0.2368 C.2 1 <1> 0.0 18 **** 4.1248 -0.6545 0.1380 C.2 1 <1> 0.0 19 **** 4.1152 0.5912 -0.3907 C.2 1 <1> 0.0 20 **** 0.6428 4.1221 -0.1824 C.2 1 <1> 0.0 21 **** -0.5883 4.1083 0.3610 C.2 1 <1> 0.0 22 **** -2.3107 -2.3045 -0.7583 C.cat 1 <1> 0.0 23 **** 2.3283 -2.3329 0.6474 C.cat 1 <1> 0.0 24 **** 2.3132 2.3273 -0.7125 C.cat 1 <1> 0.0 25 **** -2.3054 2.2981 0.7369 C.cat 1 <1> 0.0 26 **** -4.9574 1.1421 0.6494 H 1 <1> 0.0 27 **** -4.9777 -1.1798 -0.5430 H 1 <1> 0.0 28 **** -1.1997 -4.9811 -0.6155 H 1 <1> 0.0 29 **** 1.1854 -4.9897 0.5113 H 1 <1> 0.0 30 **** 4.9906 -1.2400 0.3671 H 1 <1> 0.0 31 **** 4.9675 1.1524 -0.7126 H 1 <1> 0.0 32 **** 1.2228 4.9884 -0.4234 H 1 <1> 0.0 33 **** -1.1490 4.9644 0.6736 H 1 <1> 0.0 34 **** -3.0281 -2.9764 -1.2060 H 1 <1> 0.0 35 **** 3.0264 -3.0453 1.0616 H 1 <1> 0.0 36 **** 3.0172 3.0396 -1.1167 H 1 <1> 0.0 37 **** -3.0251 3.0114 1.1107 H 1 <1> 0.0 38 **** 0.1308 -0.1027 -1.9967 N.2 1 <1> 0.0 39 **** 0.0236 0.1439 -4.1608 N.pl3 1 <1> 0.0 40 **** -0.4404 0.5488 -2.9754 C.2 1 <1> 0.0 41 **** 0.9802 -0.8468 -3.9256 C.2 1 42 **** 1.0452 -0.9957 -2.6121 C.2 1 <1> 0.0 43 **** -1.4671 1.5989 -2.8588 C.3 1 <1> 0.0 44 **** -0.3038 0.6032 -5.4840 C.3 1 <1> 0.0 45 **** 1.5478 -1.3787 -4.6603 H 1 <1> 0.0 46 **** 1.6862 -1.6737 -2.0884 H 1 <1> 0.0 47 **** -1.7528 1.9651 -3.8449 H 1 <1> 0.0 48 **** -2.3436 1.1976 -2.3501 H 1 <1> 0.0 49 **** -1.0540 2.4283 -2.2849 H 1 <1> 0.0 50 **** 0.2773 0.0365 -6.2115 H 1 <1> 0.0 51 **** -1.3667 0.4457 -5.6672 H 1 <1> 0.0 52 **** -0.0688 1.6633 -5.5788 H 1 <1> 0.0 53 **** 0.0725 0.1018 2.0003 N.2 1 <1> 0.0 54 **** -0.1397 -0.0402 4.1768 N.pl3 1 <1> 0.0 55 **** -0.5616 -0.4765 2.9796 C.2 1 <1> 0.0 56 **** 0.9987 1.0546 2.6406 C.2 1 <1> 0.0 57 **** 0.8501 0.9217 3.9346 C.2 1 <1> 0.0 58 **** -0.5638 -0.4024 5.5002 C.3 1 <1> 0.0 59 **** -1.5960 -1.4832 2.8503 C.3 1 <1> 0.0 60 **** 1.6790 1.7153 2.1449 H 1 <1> 0.0 61 **** 1.3908 1.4662 4.6803 H 1 <1> 0.0 62 **** 0.0123 0.1668 6.2298 H 1 <1> 0.0 63 **** -1.6274 -0.1922 5.6121 H 1 <1> 0.0 64 **** -0.3961 -1.4653 5.6742 H 1 <1> 0.0 65 **** -1.9357 -1.7883 3.8401 H 1 <1> 0.0 66 **** -2.4314 -1.0802 2.2778 H 1 <1> 0.0 67 **** -1.1865 -2.3552 2.3404 H 1 <1> 0.0 @BOND 1 1 2 1 2 1 3 1 3 1 4 1 4 1 5 1 5 2 6 1 6 2 7 1 7 3 8 1 8 3 9 1 9 4 10 1 10 4 11 1 11 5 12 1 12 5 13 1 13 6 14 2 14 6 25 1 15 7 15 2 16 7 22 1 17 8 16 1 18 8 22 2 19 9 17 1 20 9 23 2 21 10 18 2 22 10 23 1 23 11 19 2 24 11 24 1 25 12 20 1 26 12 24 2 27 13 21 1 28 13 25 2 29 14 15 1 30 14 26 1 31 15 27 1 32 16 17 2 33 16 28 1 34 17 29 1 35 18 19 1 36 18 30 1 37 19 31 1 38 20 21 2 39 20 32 1 40 21 33 1 41 22 34 1 42 23 35 1 43 24 36 1 44 25 37 1 45 38 40 2 46 38 42 1 47 39 40 1 48 39 41 1 49 39 44 1 50 40 43 1 51 41 42 2 52 41 45 1 53 42 46 1 54 43 47 1 55 43 48 1 56 43 49 1 57 44 50 1 58 44 51 1 59 44 52 1 60 53 55 2 61 53 56 1 62 54 55 1 63 54 57 1 64 54 58 1 65 55 59 1 66 56 57 2 67 56 60 1 68 57 61 1 69 58 62 1 70 58 63 1 71 58 64 1 72 59 65 1 73 59 66 1 74 59 67 1 @SUBSTRUCTURE 1 **** 67 TEMP 0 **** **** 0 ROOT ------------------------------------------------- ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From JF@ctch20.itc.tu-clausthal.de Wed Jan 10 12:32:24 1996 Received: from ctch02.itc.tu-clausthal.de for JF@ctch20.itc.tu-clausthal.de by www.ccl.net (8.6.10/950822.1) id MAA06366; Wed, 10 Jan 1996 12:16:29 -0500 Received: from ctch20.itc.tu-clausthal.de by ctch02.itc.tu-clausthal.de (AIX 3.2/UCB 5.64/4.03) id AA11610; Thu, 11 Jan 1996 00:56:55 +0100 Received: from VARRAN/MAIL by ctch20.itc.tu-clausthal.de (Mercury 1.21); 10 Jan 96 18:13:28 +1 Received: from MAIL by VARRAN (Mercury 1.21); 10 Jan 96 18:09:40 +1 From: "J. Fleischhauer" To: chemistry@www.ccl.net, pwalters@portal.vpharm.com, gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.), Paul van Maaren Date: Wed, 10 Jan 1996 18:09:36 GMT+1 Subject: SUMMARY Charge Equilibration Priority: normal X-Mailer: Pegasus Mail v3.1 (R1a) Message-Id: <277999A495E@ctch20.itc.tu-clausthal.de> Dear CClers, Some time ago I posted a question concerning the (QEq) of Rappe and Goddard. Thanks to all who replayed I received the following answers : ===================================================================== My original question : Dear Netters In our approach to describe charge influences in Force Field calculations, we want to try the an empirical method so called (QEq), described in A. K. Rappe, W. A. Goddard, J. Phys. Chem., 95, 3358, 1991. This method is also available in the commercial CERIUS2 package. Our problem is that there is no detailed description of the algorithm. Does anybody knows other sources of information dealing with the charge equilibration algorithm? Especially we can't find an mathematical expression used for the calculation of the coulomb potential between center A and B = Jab(R). The Problem is the following : The simple coulomb expression between unit charges on center A and B separated by the distance R is : (14) Jab(R) = 14.4 / R 14.4 conversion factor, R in Angstroem, Jab in eV Equation (14) is no longer valid for atoms with overlapping charge distributions (e.g. mostly bonded atoms). For R = 0 (14) leads to an infinite value whereas Jab(R=0) should reach a finite value Jaa instead. Like described in the reference, they use a shielding corrections to (14). The shielding to (14) will be quite large for bonded atoms (small R). The shielding correction to (14) were described in terms of a coulomb integral between atomic densities witch are expressed in form of slater orbitals. (eq.15) (15) Phi_slater = Nn * r power( n-1 ) * exp(-zeta*r) Nn normalisation Constant n long periodic row zeta Slater Exponent r distance The diatomic Coulomb integral Jab is evaluated exactly. Our question : 1) Witch is the correct mathematical expression to describe the coulomb interaction Jab(R) to get a potential with a finite value for R=0 ? ================================================================== First answer: > Dear Juergen, > I don't have the reference at hand. but what I think they did is > just integrating the expression. > Also take a look the following reference: > | AUTHOR: Rick, S. W.; Stuart, S. J.; Berne, B. J. > | TITLE: Dynamical fluctuating charge force fields: Application to > | liquid water > | JOURNAL NAME: The Journal of chemical physics. > | VOL, ISSUE: Volume 101, Number 7 > | PAGES: 6141 > | YEAR: 1994 > They used the Rappe & Goddard approach and did what I said above > (eqn 2.11, in the rick et al > article) > Hope this helps, > Paul van Maaren ================================================================== In the above article they describe the form of the coulomb overlap integral as follows : Jab(r) = INT dri drj |SQR(Phi_slater_ni(ri) )| * 1 / (ri -rj -r) * |SQR(Phi_slater_nj(rj) )| ni, nj principal quantum number eg. H = 1, O = 2 .. INT means integral Phi_slater_ni, Phi_slater_nj see above Phi_slater The problem is now the mathematical solution of the integral. Does anybody knows it ??????????????????? ================================================================== Second answer: > Hi! > I would be interested in the summary to your request. I tried > implementing this algorithm on > my own several years ago, but ran into many problems. Most annoying > is that certain atomic > parameters were not included in the paper and have never been > published in the literature ( as of > that time!). > Good Luck! > Gustavo A. Mercier, Jr. M.D.-Ph.D. ================================================================== Indeed, I found in the CCL archive the following question, but without any answer : From the CCL Archive : Date: Sun, 13 Jun 1993 08:38:16 -0400 (EDT) From: Gustavo Mercier Subject: Goddard's Modified Mulliken - Pauling electronegativities To: chemistry@ccl.net Message-Id: Hi, Netters! Does any body know the reference for the Mulliken - Pauling electonegativities as Modified by Rappe and Goddard for the construction of charges using the Charge Equilibration Method? The Charge Equilibration Method generates charges for MM/MD simulations that depend on the atomic geometry without having to perform QM computations. Ref: Rappe and Goddard (1991) J. Phys. Chem. 95, 3358-3363. In this paper they refer to a modified set of electronegativities necessary for the computations (see ref. 9, Rappe and Goddard Generalized Mulliken -Pauling Electronegativities. I. Main Group Elements (Groups 1, 13-17). J. Phys. Chem., submitted for publication.). A subsequent paper describing their UFF potential (UFF=Universal force field; ref: Rappe et. al. (1992) JACS 114, 10024- 10035), also makes reference to the GMP electronegativities, but again states "submitted for publication". I cannot find the reference in SCI. Was it ever published? Gus Mercier,jr It is interesting to know, that the < 1991 Annual Report of the Materials & Molecular Simulation Center from Beckman Institute, California Institute of Technology > refers 3) G. H. Miller, N. Karasawa and W. A. Goddard III. Charge Equilibration for Crystals, to be submitted 4) a) Rappe and Goddard III , Generalized Mulliken -Pauling Electronegativities. I. Main Group Elements. J. Phys. Chem., submitted for publication.) and b) Rappe and Goddard III , Generalized Mulliken -Pauling Electronegativities. II. Transition Metals, Lanthaanides, Actinides, and Groups 2, 12, and 18 , J. Phys. Chem., submitted for publication.) The Director and one of the authors of the report is W. A. Goddard III. An extensive search in the CA database for this articles or any other publication of the authors and the charge equilibration algorithm was without a hit. It seems the above references where never published. This means that only parameter for 16 elements were published (A. K. Rappe, W. A. Goddard, J. Phys. Chem., 95, 3358, 1991.) So I wrote an E- Mail request to W. A. Goddard III., more than 2 months ago, dealing with our problems with the charge equilibration algorithm but there was no responce. I wrote that charge equilibration is also available in the commercial CERIUS2 and POLYGRAF software packages. In the case of CERIUS2, there is a parameter file in /home/msi/cerius2_dir/res/CHARGE/QEq_neutral . (cerius_dir depends on the version , may be cerius2_1.6.2) If you are a CERIUS2 user it would be nice to have a look to the file, it contains parameters for all elements of the periodic system. In the case of POLYGRAF there should be a equal one. J. Fleischhauer ====================================================================== Third answer > I am also interested in implementing this method. Would you please > send me a copy of any replies you receive. > Thank you, > Patrick Walters ====================================================================== Any further comments are welcome Thanks, Juergen Fleischhauer _________________________________________________ Dipl. Chem. Juergen Fleischhauer Technical University Clausthal Dept. of Technical Chemistry Erzstr. 18 D-38678 Clausthal Zellerfeld Germany Tel. : 05323-72-2647 Fax. : 05323-72-3655 E-Mail : jf@ctch20.itc.tu-clausthal.de __________________________________________________ From jalaie@chem.iupui.edu Wed Jan 10 14:17:25 1996 Received: from sos1.chem.iupui.edu for jalaie@chem.iupui.edu by www.ccl.net (8.6.10/950822.1) id OAA07991; Wed, 10 Jan 1996 14:13:10 -0500 Received: from sos1 by sos1.chem.iupui.edu (940816.SGI.8.6.9/MSU-2.04) id TAA03409; Wed, 10 Jan 1996 19:10:40 GMT Message-Id: <199601101910.TAA03409@sos1.chem.iupui.edu> Date: Wed, 10 Jan 96 14:10:40 -0500 Sender: jalaie@chem.iupui.edu From: Mehran Jalaie X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: unit cell replication routine X-URL: http://www.ccl.net/ccl/welcome.html#2 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii I am looking for a Fortran code that takes in crystallographic specification of a molecule and replicates a sufrface from that. Please let me know if you come across any program which is capable of such a task. Thanks Mehran Jalaie From owner-chemistry@ccl.net Wed Jan 10 14:24:44 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA08039; Wed, 10 Jan 1996 14:16:37 -0500 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by bedrock.ccl.net (8.7.1/950822.1) id OAA04481; Wed, 10 Jan 1996 14:16:32 -0500 (EST) From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01HZUJN10SL09KOC2P@neu.edu>; Wed, 10 Jan 1996 14:20:39 EST Date: Wed, 10 Jan 1996 14:20:38 -0500 (EST) Subject: supercomputer center question To: chemistry@ccl.net Message-id: <01HZUJN11BVQ9KOC2P@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello everybody Can somebody please point me in the right direction? What supercomputer centers are currently active and offer time to those outside (e.g by proposal)? How can I find out about the centers (type of system, software, support, etc.)? I would also be interested in the recent experiences of supercomputer users. Was the system accessible and reasonably easy to use? Thanks very much, Mary Jo Ondrechen From profeta~s@glaxo.com Wed Jan 10 19:17:29 1996 Received: from gatekeeper.glaxo.com for profeta~s@glaxo.com by www.ccl.net (8.6.10/950822.1) id TAA11488; Wed, 10 Jan 1996 19:03:57 -0500 Received: by gatekeeper.glaxo.com (5.65/fma-120691); id AA29396; Wed, 10 Jan 96 19:03:54 -0500 Received: by us0u31.glaxo.com (5.65/DEC-Ultrix/4.4) id AA06384; Wed, 10 Jan 1996 19:08:06 -0500 Received: from umc by us0u31.glaxo.com via MR/USAV00 with conversational-MRIF; Wed, 10 Jan 96 19:08:05 -0500 Posted: Wed, 10 Jan 96 23:59:01 -0500 Date: Wed, 10 Jan 96 23:46:01 -0500 Sender: profeta~s@glaxo.com From: "Sal Profeta, Jr. [SP4087]" Message-Id: <31200011106991/353998@USA> To: "Peter Shenkin" Cc: chemistry@www.ccl.net, "Per-Ola Norrby" Subject: RE: CCL:M:? re partial atomic charges Msg-Class: ALL-IN-1 V2.4 BL8 27-Apr-1990 + WPS-PLUS V4.0 [This message is converted from WPS-PLUS to ASCII] Recently, there has been a question regarding establishing "partial charge" values for lone pairs on atoms such as phenolic oxygens, in the context of force field calculations. This is actually an old but still bothersome aspect to dealing with FF calculations which explicitly use lone pairs. As the individual who parameterized MM2 for aliphatic nitrogen systems, I faced a similar problem 20 years ago. Peter Shenkin's suggestion to evaluate the bond moment and proceed from there is a conservative but effective means to attack the problem. I have used this also to parameterize MM2 for quaternary amines, relying on ESP- derived charges from MP2/6-31G**//6-31G** or similar calculations to do the bond moment scaling. Presumably, this can be done as readily with MOPAC ESP charges. There may, in fact, be programs to do this automatically out there - I know that several years ago, Chandra Singh, when he was at Scripps worked on such a scheme. Others who may have also done so include the compchem folks at many of the large drug firms, like Merck, Pfizer, Lilly, Vertex (Mark - do you have one?) - who may be able to share this 'piece' of software with the academic community. Also, the folks at the SW vendors, such as Tripos, Biosym/MSI or SPARTAN might have a solution. Hope this helps. Cheers, Sal Profeta, Jr. ++++++De mortuis nil nisi bonum.++++++++++* Dr. Salvatore Profeta, Jr. Research Computing & Consulting 104 Cottage Lane Durham, NC 27713-9387 (919) 544-2299/5304 (Fax) email: sal@rti.org (neutral zone) email: profeta~s@glaxo.com (courtesy acct) ++++++Sic transit gloria mundi++++++++++++ From MARYJO@neu.edu Wed Jan 10 20:02:30 1996 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by www.ccl.net (8.6.10/950822.1) id TAA11735; Wed, 10 Jan 1996 19:58:33 -0500 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01HZUVQERL8G9OCVM7@neu.edu>; Wed, 10 Jan 1996 20:02:55 EST Date: Wed, 10 Jan 1996 20:02:55 -0500 (EST) Subject: Thanks! - Supercomputing summary To: chemistry@www.ccl.net Message-id: <01HZUVQETGR69OCVM7@neu.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Thanks to those who answered my question about supercomputer centers. Some people requested a summary, so here it is. Mary Jo ____________________________________________________________________ From Janet Del Bene: Mary Jo, My understanding is that the national NSF centers (Pittsburgh, San Diego, Cornell, etc.) are open to all by proposal. So, checking with one of these would be a good starting point. My experience is with the Ohio Supercomputer Center which is not in this group, and requires some type of "Ohio" affiliation as a prerequisite for access. Regards, Janet ___________________________________________________________________ Reply-to: Jeffrey.Nauss@UC.edu You might want to check out our WWW page at URL http://www.che.uc.edu/supercomputer.html. It is a brief list of the three centers we found most useful plus a link to Cal Tech for a more comprehensive list. > How can I find out about the centers (type of system, > software, support, etc.)? Follow the links in the above URL. > I would also be interested in the recent experiences > of supercomputer users. Was the system accessible > and reasonably easy to use? If you are doing biomedical applications, we found the Biomedical Supercomputing Center in Frederick, MD, very helpful. The connection to the site was fast with minimal interuptions and the staff were extremely helpful. Fo non-medical applications, the Pittsburgh Supercomputing Center has also been helpful. Feel free to contact me if you do not have WWW access. -- Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * **************************************************************************** From: "Petety V. Balaji" Hi, >What supercomputer centers are currently active and >offer time to those outside (e.g by proposal)? > >How can I find out about the centers (type of system, >software, support, etc.)? Contact the Biomedical Supercomputing Center (BSC) at 301-846-5555 (or http://www.ncifcrf.gov) for details. It is part of the National Cancer Institute, NIH. Balaji _________________________________________________________________________ From: crowley@mantis.psc.edu (Michael Crowley) Pittsburgh Supercomputing Center is alive and well and has the following web pages to help you out in your efforts: http://www.psc.edu http://www.psc.edu/grants/grants.html If you need other phone numbers or contacts to this place, feel free to send me a message and I'll get the right people in contact with you. You probably want to look into the "starter grants" that you'll see in the second http page. Good luck, Michael Crowley ____________________________________________________________________ From: bender@ccl.net (Charlie Bender) Mary Jo, Take a look at http://www.ccl.net/casc.html a list most US based supers -- Charlie Bender Charlie Bender Director, Ohio Supercomputer Center Professor of Chemistry, Ohio State University 1224 Kinnear Rd. Columbus, OH 43212-1163 _________________________________________________________________________ From: "Michael D. Bartberger" Dear Mary Jo: Hiya! Funny you should post that question just now.... I just handed over a proposal to my research director, that I just now finished up. We are going to try to get some time at the San Diego Supercomputing Center. There are a few NSF-supported supercomputing centers in the US. You might be interested in SDSC (try www.sdsc.edu), NCSA at Urbana-Champagne (www.ncsa.uiuc.edu), Pennsylvannia (www.psc.edu, I think), and the Cornell Theory Center (which I can't remember off hand.) :) These web sites will tell you about installed software, application policies, etc. Anyway, there's a start. If I may ask, what kinds of systems are you working on? I'd love to talk more about the kind of research we have going on. Hope to hear from you soon, and I hope this helps. Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (352) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (352) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From: bernhold@npac.syr.edu (David E. Bernholdt) The NSF centers grant time based on proposals. Their web pages will probably give you all the info you need: http://www.tc.cornell.edu http://www.sdsc.edu http://www.ncsa.uiuc.edu http://www.psc.edu If you have funding from other agencies (i.e. DoE, DoD), you may be able to get access to some of their centers either by proposal, or via your program manager. Many states now have centers, but typically are open only to local researchers. I'm not aware of a center in MA. Good luck! -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu ________________________________________________________________________ From: rbw@msc.edu (Richard Walsh) Mary Jo, Minnesota Supercomputer Center, Inc. (MSCI) has been providing high-performance scientific computing services to academic and commercial users since the early 1980's. One of our largest current customers uses MSCI for both applications in computational chemistry and computational engineering and fluid dynamics. We support a wide range of third-party applications (I just installed the new version of ACESS II 2.0 today) and have an experienced scientific and technical staff. As a wholly owned subsidiary of CRAY Research we also have access to their applications support people. Please feel free to call me at 612-337-3467 and/or visit our web site at http://www.msc.edu for further information. Sincerely, Richard Walsh rbw@msc.edu Project Manager Chemistry Applications Support ____________________________________________________________________ From: Jie Yuan They all have web pages on the net. Do a web search and you can find all of them :-) I have used NCI's center in Frederick, MD, and Ohio Superc. Center (where CCL resides). I know Pitts., SanDiego and UIUC centers, but never used them. Jie ____________________________________________________________________ From: Anita Ilze Zvaigzne Try the following URLs: http://www.psc.edu/ Pittsburgh Supercomputing Center http://www.sdsc.edu/ San Diego Supercomputing Center Good luck! Anita Zvaigzne From owner-chemistry@ccl.net Wed Jan 10 20:17:30 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id UAA11845; Wed, 10 Jan 1996 20:15:48 -0500 Received: from ultrix.uor.edu for bmurray@ultrix.uor.edu by bedrock.ccl.net (8.7.1/950822.1) id UAA29262; Wed, 10 Jan 1996 20:15:45 -0500 (EST) Received: by ultrix.uor.edu (5.65/DEC-Ultrix/4.4) id AA03081; Wed, 10 Jan 1996 17:13:45 -0800 Date: Wed, 10 Jan 1996 17:13:42 -0800 (PST) From: Barbara Murray To: MARYJO@neu.edu Cc: chemistry@ccl.net Subject: Re: CCL:supercomputer center question In-Reply-To: <01HZUJN11BVQ9KOC2P@neu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You can get alot of information about the various supercomputer centers from the web. There are four national sites, plus many other state ones. If you go to Webcrawler (http://webcrawler.com) and search for supercomputer, you should get more information. ***************************************************************************** Barbara Murray bmurray@ultrix.uor.edu Chemistry Department (909) 793-2121 ext 2374 University of Redlands PO Box 3080 Redlands, CA 92373-0999 ***************************************************************************** From pvrossem@vnet3.vub.ac.be Mon Jan 8 05:48:09 1996 Received: from rc4.vub.ac.be for pvrossem@vnet3.vub.ac.be by www.ccl.net (8.6.10/950822.1) id FAA10557; Mon, 8 Jan 1996 05:48:05 -0500 Received: from vnet3.vub.ac.be (vnet3.vub.ac.be [134.184.15.13]) by rc4.vub.ac.be (8.6.10/3.4.2.ap (rc4)) id LAA17546; Mon, 8 Jan 1996 11:51:11 +0100 Received: by vnet3.vub.ac.be (SMI-8.6/VUB-SOLARIS.920228) id LAA18638; Mon, 8 Jan 1996 11:47:31 +0100 Received: from rc4 by fse.vub.ac.be (5.61/BFUCC-920211) id AA00158; Fri, 29 Dec 95 03:53:06 +0100 Received: from vnet3.vub.ac.be (vnet3.vub.ac.be [134.184.15.13]) by rc4.vub.ac.be (8.6.10/3.4.2.ap (rc4)) id DAA22801; Fri, 29 Dec 1995 03:56:37 +0100 Received: from fse.vub.ac.be by vnet3.vub.ac.be (SMI-8.6/VUB-SOLARIS.920228) id DAA08813; Fri, 29 Dec 1995 03:53:03 +0100 Received: from rc4 by fse.vub.ac.be (5.61/BFUCC-920211) id AA00154; Fri, 29 Dec 95 03:53:03 +0100 Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by rc4.vub.ac.be (8.6.10/3.4.2.ap (rc4)) id DAA22797; Fri, 29 Dec 1995 03:56:32 +0100 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id VAA04631; Thu, 28 Dec 1995 21:26:16 -0500 Received: from tammy.harvard.edu for paul@tammy.harvard.edu by www.ccl.net (8.6.10/950822.1) id VAA04544; Thu, 28 Dec 1995 21:04:46 -0500 Received: by tammy.harvard.edu (5.64/10.0) id AA16198; Thu, 28 Dec 95 21:07:58 -0500 Date: Thu, 28 Dec 95 21:07:58 -0500 From: paul@tammy.harvard.edu (Paul Lyne) Message-Id: <9512290207.AA16198@tammy.harvard.edu> To: chemistry@www.ccl.net Subject: CCL:CADPAC on the HP Cc: paul@tammy.harvard.edu Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Status: RO Hi, I am using CADPAC at the moment and I am trying to run it on a HP. I get an executable that does not work properly. After many hours debugging I still have not got a proper executable. Among some compiler specific problems, the main seems to be that the HP does not recognise the INTEGER*1 declaration. This is used in the pack.F routines that are used to store the indices of the integrals. Has anybody managed to run CADPAC on a HP and if so how did you do it? Thanks for your help, Paul -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: paul@tammy.harvard.edu -- Original Sender From: Address: paul@tammy.harvard.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From owner-chemistry@ccl.net Wed Jan 10 06:42:56 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA02661; Wed, 10 Jan 1996 06:42:55 -0500 Received: from Mailer.Uni-Marburg.DE for STAHL@ps1515.chemie.uni-marburg.de by bedrock.ccl.net (8.7.1/950822.1) id GAA29436; Wed, 10 Jan 1996 06:42:40 -0500 (EST) Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA70097; Wed, 10 Jan 1996 12:42:13 +0100 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 10 Jan 96 12:43:53 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 10 Jan 96 12:43:27 GMT+2 To: chemistry@ccl.net From: "Martin Stahl" Date: Wed, 10 Jan 1996 12:43:24 MDT Subject: CCL:MM3 parameters for O-C-C-C(sp2) X-Pmrqc: 1 Priority: normal X-Mailer: WinPMail v1.0 (R1) Message-Id: Status: R Dear subscribers, I have been doing calculations on some rather simple organic compounds containing an alcoholic OH-group in 3-position to an sp2-hybridized carbon atom (a phenyl or a vinyl group, for example). I do the conformational analyses with macromodel and recalculate all energies by means of MM3(94). For such molecules, the energetic order of the low energy conformers is not confirmed by experiment, wehereas for the pure unsaturated hydrocarbons results agree very well with measured data. My first suspicion is that the weak hydrogen bond -like interaction between the acidic proton and the double bond, which is possible in some conformers, might play a role here. Has anyone come across a problem like this or even treated it within a force field? I am grateful for any hint. Martin Stahl