From chemistry-request@server.ccl.net Fri May 14 07:03:17 1999 Received: from mailhost.rdg.ac.uk (exim@sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA01216 for ; Fri, 14 May 1999 07:03:15 -0400 Received: from suma3 ([134.225.16.13]) by mailhost.rdg.ac.uk with esmtp (University of Reading Email Service) id {10iFgl-0001p8-00} for CHEMISTRY@ccl.net; Fri, 14 May 1999 11:59:35 +0100 Date: Fri, 14 May 1999 11:59:35 +0100 (BST) From: "l.r.cooper" To: CCL Subject: GROMOS96 parallelisation & glycosylated residue topologies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id HAA01218 after many a month i have managed to simulate the dynamics of a native protein with g96. my parallel implementation does not work with data sets and switch values which do work in a scalar version. any suggestions? nonbpl array size? the error message relates to a shake failure- which doesn't occur in scalar. i want to describe this modified glycine residue po3-o-ch2-ch2o-ch2o-ch2o-ch2o-ch=nh-ch2-co-amino acid2-aa3- ^ ^ schiff's base alpha carbon of glycine and the circularized amadori product. i have abandoned trying to do this by hand. prodrg_serv at embl creates a gromos87 topology, which i have in hand. in the /contrib/ directory of gromos96 there is a routine which translates G87 topologies to G96. the problem is it doesn't get past reading NRATT number of atoms without an error. has anyone had a similar experience? do you have a work around? °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` //=\Mr. Lee R. Cooper Bsc(Hons) MSc, Parallel, Emergent//=\evolution, \=//& Distributed Architechture Laboratory, Dept. of \=//creationists //=\Comp. Science, University of Reading, Whiteknights //=\have argued, \=//PoBox 225, Reading, Berkshire. RG6 6AY (UK) \=/was as likely //=\Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax //=to have made \=//Tel +44 (0)118 931 8188 x7817 (1900-2300)|0118 975 \=//man as a //=\http://www.rdg.ac.uk/~ssr97lrc/ 1994 //=\monkey..., °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` randomly typing the bible without error. with natural selection acting as an eraser of mistakes; assuming thirteen mistakes for every correct character & a rate of 1 keystroke per second, the 6 million characters of the holy script could be typed in 13x6e6 s, or <3 yrs. From chemistry-request@server.ccl.net Fri May 14 10:10:52 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA02934 for ; Fri, 14 May 1999 10:10:52 -0400 Received: from NIH2WAAF (smtp6.site1.csi.com [149.174.183.75]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA18278 Fri, 14 May 1999 10:07:11 -0400 (EDT) Received: from mail pickup service by csi.com with Microsoft SMTPSVC; Fri, 14 May 1999 10:06:33 -0400 Sender: tony@acdlabs.com Received: from noteb-tony.acdlabs.com (ppp01.acdlabs.com [207.176.233.41]) by hil-img-10.compuserve.com (8.8.6/8.8.6/IMS-1.7) with SMTP id KAA06925; Fri, 14 May 1999 10:06:16 -0400 (EDT) Message-Id: <3.0.6.32.19990513135713.0088aba0@mail.acdlabs.com> X-Sender: tony@mail.acdlabs.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 13 May 1999 13:57:13 -0700 To: "COMP-CHEM-LIST (CCL)" From: Tony Williams Subject: Vapor pressure predicter Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA02935 [Edited by CCL Censor -- Jan Labanowski] Dear Merethe, Advanced Chemistry Development (www.acdlabs.com) has a boiling point predictor and VP predictor for PC, Mac with Virtual PC, ISIS integrated. Details are found on the website. Please contact me with any questions. Boiling Point & VP Pro ACD/Boiling Point & Vapor Pressure is a program to calculate the boiling point for a compound, from 0.001 torr to 10 atm. Our predictions are normally accurate to within ± 5oC for structures with fewer than two polar groups, and to within ± 10o for structures with more polar groups. It will also calculate the flash point, and vapor pressure as a function of temperature, and will calculate the enthalpy of vaporization at the boiling point. The Pro version handles structures containing up to 255 heavy atoms and H, B, C, N, O, F, Cl, Br, I, Si, P, S, Ge, As, Se, Sn, or Pb. The economy version is restricted to 50 atoms including H, and 8 elements. Select the graph and table output you desire: boiling point vs. pressure or vapor pressure vs. temperature. Select the units for these, and also for the enthalpy of vaporization. You can choose to print out any or all of this information. Flash point Protocol window shows you how the value was estimated. To determine constants and relationships, our algorithm uses an internal database which contains boiling points for 10 000 compounds—6 000 of which have a boiling point at 760 mm Hg. Additive increments of atoms and groups for our function K and force increments of interactions between groups and atoms were calculated from this database. Your compound does not have to be in the data base in order to have its boiling or flash point calculated. At 10:14 AM 4/22/1999 -0600, Merethe Sjovoll wrote: >Hi everybody, > >is there a way of estimating in a crude way the vapour pressure of organic >liquids and solids? I have a whole bunch of molecules and I don't need absolute >values, just look for tendencies. So I imagine some calculation formula which >perhaps contains temperature, possibly boiling point and melting point, or >perhaps dipole moment, molecular weight etc. (easily accessible quanities). > >Is this wishful thinking? > >Best regards > >Merethe Sjovoll > >-- > >******************************************************** >Merethe Sjovoll, Ph.D. * * >Senior Research Scientist * * >Norsk Hydro a.s Research Center * * > * * >P.O.Box 2560 * HYDRO * >N-3907 Porsgrunn, * RESEARCH * >Norway * * > * ((( * >email: Merethe.Sjovoll@hre.hydro.com * (=====) * >Phone:+47 35 56 48 97 * * >Fax :+47 35 56 27 22 * * >******************************************************** From chemistry-request@server.ccl.net Fri May 14 16:18:18 1999 Received: from kodakr.kodak.com (kodakr.kodak.com [192.232.119.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA10786 for ; Fri, 14 May 1999 16:18:18 -0400 Received: from mail.rl.kodak.com (mail.rl.kodak.com [150.220.10.53]) by kodakr.kodak.com (8.9.1/8.9.1) with ESMTP id QAA26749 for ; Fri, 14 May 1999 16:14:35 -0400 (EDT) Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id QAA12001; Fri, 14 May 1999 16:38:34 -0400 (EDT) Received: from mozart.rl.kodak.com (berlioz [150.220.89.22]) by mozart.rl.kodak.com (980427.SGI.8.8.8/950213.SGI.AUTOCF) via ESMTP id PAA30853 for ; Fri, 14 May 1999 15:47:37 -0400 (EDT) Sender: giesen@kodak.com Message-ID: <373C7C90.A6C5B67A@mozart.rl.kodak.com> Date: Fri, 14 May 1999 15:42:08 -0400 From: David Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP25) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Gallium and Indium calculations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm sorry for the bandwidth of the non-contributing type, but I would appreciate hearing experiences from anyone who has run calculations on Ga(III) or In(III) complexes with organic ligands. Particularly, what basis sets/levels of theory/ECP's did you find useful? A search of the CCL archives and and ACS journals through their website turned up nothing of interest, perhaps due to incompetent searching on my part... Plain old HF and B3LYP/3-21g* and PM3(tm) calculations gave non-useful results, and before I slide down the slope of simply ramping up the level of calculation on reasonably large systems until I get something I like, I'd like the input of more experienced users in the field. As usual, I'll be thrilled to advertise your research to the list if you reply usefully... Dave Giesen -- Dr. David J. Giesen Eastman Kodak Company giesen@kodak.com 2/83/RL MC 02216 (ph) 1-716-58(8-0480) Rochester, NY 14650 (fax)1-716-722-2327 From chemistry-request@server.ccl.net Sat May 15 04:59:51 1999 Received: from CHEMNA.DICHI.UNINA.IT (chemna.dichi.unina.it [192.135.165.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA17762 for ; Sat, 15 May 1999 04:59:50 -0400 From: ENZO@CHEMNA.DICHI.UNINA.IT Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V5.2-29 #30460) id <01JB82HT6YRK0005ZK@CHEMNA.DICHI.UNINA.IT> for CHEMISTRY@ccl.net; Sat, 15 May 1999 10:56:18 CET Date: Sat, 15 May 1999 10:56:17 +0100 (CET) Subject: DFT and PCM in G98 To: CHEMISTRY@ccl.net Message-id: <01JB82HT93XE0005ZK@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: text/plain; CHARSET=US-ASCII Dear Colleagues, there have been some queries about both new Density Functionals and PCM in G98. Being among the authors of both parts of the program, I would like to clarify matters. 1) Concerning DFT, only the very recent PBE0 model and those containing the Laplacian of the density or the kinetic energy are not yet available in G98. 2) Concerning PCM, all the three models, D-PCM (the original one), C-PCM (very close to COSMO and essentially identical at least for the electrostatic part using XCOSMO=0.5) and IEF-PCM are available at the HF and DFT levels for energy and analytical gradients (both RHF and UHF and, possibly, including pseudopotentials). Correlated computations (not yet MC-SCF) of energies can be also performed. 3) The problem with this part of the program is that it is rapidly evolving and that the number of options is so large that it is impossible to summarize them in the manual. 4) Another recent question is that giving EPS=XX.XXX in the input of PCM, the output of the program still says that the solvent is water. While it is true that water parameters are used for the non electrostatic part (since they have not been updated from input) the dielectric constant becomes that given from input. The value is written giving the keyword DUMP to PCM. I remain at the disposal of the CCL community for further clarifications. Best regards Vincenzo Barone -------------------------------------------------------------------------- Prof.Vincenzo Barone, full Professor of Physical Chemistry Dipartimento di Chimica | phone: +39-81-5476503 Universita' Federico II | fax: +39-81-5527771 via Mezzocannone 4 | e-mail: enzo@chemna.dichi.unina.it I-80134 Napoli, Italy | enzo@napo.dichi.unina.it -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Sat May 15 06:04:53 1999 Received: from handel.RZ-Berlin.MPG.DE (handel.RZ-Berlin.MPG.DE [141.14.128.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA18503 for ; Sat, 15 May 1999 06:04:51 -0400 Received: (from hermann@localhost) by handel.RZ-Berlin.MPG.DE (8.8.8/8.8.8) id MAA51578 for CHEMISTRY@ccl.net; Sat, 15 May 1999 12:01:00 +0200 From: Klaus Hermann Message-Id: <199905151001.MAA51578@handel.RZ-Berlin.MPG.DE> Subject: Decomposition of Ca(HCO3)2 To: CHEMISTRY@ccl.net Date: Sat, 15 May 1999 12:01:00 +0200 (MSZ) X-Mailer: ELM [version 2.4ME+ PL32 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear collegues, a company claims that the calciumbicarbonate decomposition Ca(HCO3)2 -> CaCO3 + CO2 + H2O can be facilitated by strong magnetic fields which I think is nonsense. Did anyone hear anything about this phenomenon? Are there any explanations arund that may prove that I am ignorant? Thanks for your help. I will summarize. -- Klaus Hermann Berlin, May 15, 1999 =========================================================================== Prof.Dr. K. Hermann Tel.: [+49]-30-8413-4812/3 (office) Abt. Theorie, Fritz-Haber-Institut [+49]-30-8413-4702 (secrt.) Faradayweg 4-6 Fax.: [+49]-30-8413-4701 D-14195 Berlin Germany e-mail: hermann@FHI-Berlin.MPG.DE WWW: http://www.fhi-berlin.mpg.de/th/member/hermann_k.html ===========================================================================