From CCLSurv@redvax1.dgsca.unam.mx Fri Jun 3 02:43:29 1994 Received: from redvax1.dgsca.unam.mx for CCLSurv@redvax1.dgsca.unam.mx by www.ccl.net (8.6.4/930601.1506) id BAA18774; Fri, 3 Jun 1994 01:50:44 -0400 Received: from standard-input by redvax1.dgsca.unam.mx; Thu, 2 Jun 94 23:44:37 CST Sender: CCLSurv@redvax1.dgsca.unam.mx Date: Thu, 2 Jun 1994 23:38:08 -0600 (CST) From: Pisanty Baruch Alejandro Subject: Survey on weekend! To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear fellow netters, replies to the recently posted Survey on the Impact of the CCL have been coming in steadily! As I read them I can only wish for more, because of the enormous richness and variety of the points of view. As the week comes to a close in most of the world, do allow me to ask those who have not yet responded to do so! It may be a good way to step down from a hard week of Chemical Computing. I will be glad to re-post it or to mail it to anyone who may have (inadvertently?) deleted the questionnaire. Your contribution to the statistical soundness of this study will be most welcome. Be well! Alejandro . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Secretary of the Advisory Council on Computing, UNAM, and Head of the Graduate Division, Faculty of Chemistry, UNAM Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico City DF MEXICO Tel. (+52-5) 622 4181, 616 1649; Fax 550 0904, 616 2010 . . . . . . . . . . . . . . . . . . . . . . . . . . From vkitzing@sunny.mpimf-Heidelberg.mpg.de Fri Jun 3 04:43:34 1994 Received: from foxy.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-Heidelberg.mpg.de by www.ccl.net (8.6.4/930601.1506) id EAA19559; Fri, 3 Jun 1994 04:40:52 -0400 Received: from sunny.mpimf-heidelberg.mpg.de by foxy.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA01220; Fri, 3 Jun 94 10:40:27 +0200 Received: from [192.109.43.34] (mac10) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA21352; Fri, 3 Jun 94 10:35:47 +0200 Date: Fri, 3 Jun 94 10:35:46 +0200 Message-Id: <9406030835.AA21352@sunny.mpimf-Heidelberg.mpg.de> To: CHEMISTRY@ccl.net (Computational Chemistry List) From: vkitzing@sunny.mpimf-Heidelberg.mpg.de (Eberhard von Kitzing) X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Subject: Experimental Hydrophobicities and partial charges Dear colleges, in our lab we are estimating the radius of biological ion channels by means of organic cations (for instance see David J. Adams, Terry M. Dwyer and Bertil Hille (1980). "The Permeability of Endplate Channels to Monovalent and Divalent Metal Cations." The Journal of General Physiology 75: 493-510). To better understand the measurements it would be interesting if there are some experimental values for their hydrophobicities. Additionally, for model building studies I would like to know whether people did calculations on the partial charges on these molecules. The molecules are: NH4 Methylamine Dimethylamine Trimethylamine Tetramethylamine Hydrazine (NH2)2-C-C(NH2)2 Choline (Ch3)3-N-CH2-CH2-OH Tris-(hydroximethyl)-aminomethane (CH2OH)3-N-CH3 Thanks for your help in advance. I will compile a summary. ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de From toukie@zui.unizh.ch Fri Jun 3 05:43:30 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.4/930601.1506) id FAA19824; Fri, 3 Jun 1994 05:16:27 -0400 Received: from rzurs5.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA29262; Fri, 3 Jun 94 11:11:14 +0200 Received: by rzurs5.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA17971; Fri, 3 Jun 1994 11:11:11 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9406030911.AA17971@rzurs5.unizh.ch> Subject: Modelling hydrophobic interactions To: chemistry@ccl.net Date: Fri, 3 Jun 1994 11:11:11 +0100 (MEST) Cc: toukie@zui.unizh.ch, haney@netcom.com, hyperchem@hyper.com X-Mailer: ELM [version 2.4 PL13] Content-Type: text Content-Length: 856 Dear colleagues; I am interested in examining the interactions between biological mem- branes and hydrophobic weak acids in order to better understand why some of these acids are toxic towards cells and others are not. The molecular modelling software I have at my immediate disposal are Hyperchem 3.0 and MOPAC 6.0. Can anyone suggest how these programmes might be used to examine prospective interactions between biomembranes and small molecular weight com- pounds? Would anyone care to recommend _other_ programmes which can be used to accomplish this? Thanks in advance to all respondents. Sincerely, S. Shapiro Internet: toukie@zui.unizh.ch P.-S.: Of course, references and citations are also useful. From noy@tci002.uibk.ac.at Fri Jun 3 05:51:06 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id FAA19670; Fri, 3 Jun 1994 05:02:46 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA00489 (5.65c/IDA-1.4.4 for ); Fri, 3 Jun 1994 11:02:37 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA33480; Fri, 3 Jun 1994 11:02:34 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9406030902.AA33480@tci002.uibk.ac.at> Subject: Hyperchem is not for research purposes To: chemistry@ccl.net Date: Fri, 3 Jun 1994 11:02:34 +0200 (DFT) In-Reply-To: <9406012249.AA00127@atp.biochem.su.oz.au> from "andrey@atp.biochem.su.oz.au" at Jun 2, 94 08:46:53 am X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1942 : Dear CCL readers, : : Due to current interest to HyperChem I decided to add my 0.02c. : : Last year we had a chance to try HyperChem v 3.0. This programs has : good graphics and very good molecular editor/builder. Unfortunately, it : is very slow, at least for semiempirical calculations. For example, : it takes 35 min. on 486DX2 50MHz with 16 MB of memory to do MNDO 1SCF : and gradients for C60 (compare to Sibiq - 10 min.). We send to HyperChem : mail list a question 'why it is slow?', and the answer was "HyperChem : have not been optimized for speed". The second thing, which surprised us, : was that the best geometry optimization method we could choose was : conjugated gradients. This method not only 2-10 times more slow then : ordinary used in semiempirical calculation qusi-newton methods, but, : also, it may has a problem with convergence for a flat potential surface. I would completely agree with you. No matter how hard Autodesk is trying to improve the speed of Hyperchem, they will never get close to the true speed of 486. The problem is that Hyperchem is still on the Windows and it will suffer the bottle-neck speed of Windows. : If someone is looking for program to do demonstration or teaching, HyperChem : is, probably, a way to go. I don't think that it is (sorry, was, : I am not sure that version 3 is the last version) a right choice to do : semiempirical calculations. It is, of course, my personal opinion. Hyperchem is only a toy. Molecular builder and visualization are perfect if we forget the price. If you want to do the real researches that people believe in your results, go Gaussian or else. I usually find people who suffer finding how to avoid mentioning that they used Hyperchem when they want to publish the works. It's hard at least now to believe what is in this blackbox package. So, most of my colleague use it as a front-end. sincerely, Teerakiat From leif@MPA-Garching.MPG.DE Fri Jun 3 06:43:33 1994 Received: from ibm-1.MPA-Garching.MPG.DE for leif@MPA-Garching.MPG.DE by www.ccl.net (8.6.4/930601.1506) id GAA20306; Fri, 3 Jun 1994 06:22:24 -0400 Received: (leif@localhost) by ibm-1.MPA-Garching.MPG.DE (8.6.8.1/8.6) id MAA108018; Fri, 3 Jun 1994 12:20:45 +0200 Date: Fri, 3 Jun 1994 12:20:45 +0200 (MDT) From: Leif Laaksonen Subject: HyperChem and software in general... To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers, This HyperChem discussion takes incredible stupid forms. I have always been in the (stupid) believe that science is independent of the software or hardware which produced it. I can hardly believe that supercomputers produce better science than PC:s. But with supercomputers one can tackle more difficult problems. All computational chemistry software is based on some sort of approximations. Depending on the level of approximations and size of system it can be run on different levels of hardware. In fact it's good policy to run a particular problem on the lowest level of hardware which can handle the problem. Quite many write the final manuscript on a PC or on a Mac. Does this mean that a manuscript produced on a PC or Mac is worse than a manuscript produced using LaTex on a workstation? C'mon an paper is good or bad depending on its scientific value! I can still remember a few years ago when Apple was drumming that they were using a Cray to design the next Macintosh. Then S. Cray told that he was using a Macintosh to design the nect Cray. Peace, -leif laaksonen Ps. I don't know hardly anything about HyperChem. I'm not even a happy user so I don't know if the software is good or bad. I just don't like the way this discussion is going. ****************************************************************************** Leif Laaksonen * On loan at: * Phone: 49 89 3299???? * Max-Planck-Institute for Astrophysics Fax: 49 89 32993235 * Karl-Schwarzschild-Strasse 1 * D-85740 Garching * Germany * --------URL: http://www.csc.fi/lul/leif/leif.laaksonen.html-------- Who has seen the wind? Neither you nor I: But when the trees bow down their heads The wind is passing by. Christina Rossetti ****************************************************************************** From DSMITH@uoft02.utoledo.edu Fri Jun 3 10:44:50 1994 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id JAA22348; Fri, 3 Jun 1994 09:53:20 -0400 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.3-7 #5345) id <01HD3MWPX30G000K7K@UOFT02.UTOLEDO.EDU>; Fri, 3 Jun 1994 09:53:06 EST Date: Fri, 03 Jun 1994 09:53:06 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Hyperchem and good science To: chemistry@ccl.net Message-id: <01HD3MWPXVYA000K7K@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT Leif Laaksonen writes: >This HyperChem discussion takes incredible stupid forms. I have always >been in the (stupid) believe that science is independent of the software >or hardware which produced it. I can hardly believe that supercomputers >produce better science than PC:s. But with supercomputers one can tackle >more difficult problems. All computational chemistry software is based on >some sort of approximations. Depending on the level of approximations >and size of system it can be run on different levels of hardware. In fact >it's good policy to run a particular problem on the lowest level of >hardware which can handle the problem. Quite many write the final >manuscript on a PC or on a Mac. Does this mean that a manuscript produced >on a PC or Mac is worse than a manuscript produced using LaTex on a >workstation? Here, here! This is not the place to discuss Windows vs. System 7 vs. UNIX, nor FORTRAN vs. C, nor anything else that silly. Let's talk CHEMISTRY. Neil Ostlund is an excellent scientist who has been involved in MO methods for longer than some people on this exploder have been alive. I have no problems with his science, done years ago with Pople or independently, or with his current science (which seems to be primarily implemented in HyperChem). I know some of the others at Hypercube - they are not a gang of fly-by-night computer jockeys either! I have been involved with HyperChem as a beta tester and documentation editor/proofreader since version 2.0, first with Autodesk and most recently with Hypercube. I have also worked with some of their other products. While I am not the world's greatest theoretician (far from it!), I have not found any reason to complain about the science in the products or the results produced. I use HyperChem when it is appropriate for my research; I use MOPAC, AMPAC, Gaussian, GAMESS, MacroModel, SYBYL, and more the same way - when the software/methods are appropriate and the available combination of software and hardware is sufficient to solve the problem at hand. >C'mon an paper is good or bad depending on its scientific value! Exactly! And we use peer review to judge that value, although that system is also far from perfect. HyperChem is no more black box than Gaussian! Many people do not have source code access to Gaussian any more. And even for those who do, how many of you know the meaning of "iop(4/20=7)", which John McKelvey recently suggested as a keyword when choosing initial Hessian force constants? (Please don't waste bandwidth telling me you know the meaning -- many more people don't than do.) The HyperChem manuals provide an excellent theoretical description and background for the calculations the program performs, which is more than many, more acceptible (or accepted?) academic codes provide. Let's not be hardware or software snobs. Instead, let us applaud the use of the proper tool for a problem, and encourage our peers, students, colleagues and chemists (and even physicists and biologists) to use computational chemistry as much as possible. Then, let us all help them to use it properly and effectively. Who knows, you may get your name in the author list. Douglas A. Smith Assistant Professor, Department of Chemistry Center for Drug Design and Development and Chairman-elect, ACS Division of Computers in Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From SHYAMAL@tifrvax.tifr.res.in Fri Jun 3 13:44:01 1994 Received: from tifrvax.tifr.res.in for SHYAMAL@tifrvax.tifr.res.in by www.ccl.net (8.6.4/930601.1506) id NAA26403; Fri, 3 Jun 1994 13:24:55 -0400 Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01HD4EZ77QJ400441U@tifrvax.tifr.res.in>; Fri, 3 Jun 1994 22:54 +0530 Date: Fri, 3 Jun 1994 22:54 +0530 From: SHYAMALAVA MAZUMDAR Subject: Hyperchem To: IN%dsmith@uoft02.utoledo.edu, chemistry@ccl.net Message-id: <01HD4EZ77QJ400441U@tifrvax.tifr.res.in> X-VMS-To: IN%"IN%dsmith@uoft02.utoledo.edu",IN%"chemistry@ccl.net" Hi, I am interested in the hyperchem program. Can you please send me some information regarding this program and a possible source (preferably some ftp site) where from one can get it. Many thanks in advance. S. Mazumdar Shyamal@tifrvax.tifr.res.in From jle@world.std.com Fri Jun 3 13:52:59 1994 Received: from ftp.std.com for jle@world.std.com by www.ccl.net (8.6.4/930601.1506) id MAA25846; Fri, 3 Jun 1994 12:45:04 -0400 Received: from world.std.com by ftp.std.com (8.6.8.1/Spike-8-1.0) id MAA00689; Fri, 3 Jun 1994 12:45:02 -0400 Received: by world.std.com (5.65c/Spike-2.0) id AA07997; Fri, 3 Jun 1994 12:45:00 -0400 Date: Fri, 3 Jun 1994 12:45:00 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199406031645.AA07997@world.std.com> To: chemistry@ccl.net Subject: MM3(92) Saunders' stochastic search author(s) sought... If the author(s) of this portion of MM3(92) are on the net, please contact me! I am looking for information regarding the implementation of this code and how the increasing number of MM3 atom types might/does affect it. THanks in advance! Joe Leonard jle@world.std.com From friedman@tammy.harvard.edu Fri Jun 3 13:59:41 1994 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.4/930601.1506) id NAA26447; Fri, 3 Jun 1994 13:28:29 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA26633; Fri, 3 Jun 94 13:29:30 -0400 Date: Fri, 3 Jun 94 13:29:30 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9406031729.AA26633@tammy.harvard.edu> To: chemistry@ccl.net Subject: hyperchem for heterocycle mos? Cc: friedman@tammy.harvard.edu Mel Schriver asks (specifically): > >What it boils down to for me is wether >I can use AM1 or PM3 to calculate the orbitals of a heterocycle that >contains S and/or P. > Short answer: yes. In terms of orbital energies, you will not get anything like the absolute energies you get with ab initio methods. But your relative energies will be very useful. We have just calculated HOMO-LUMO energy gaps for an extensive series of heterocycles and heterocyclic oligomers containing S, using PM3 in Hyperchem (and in G92) as well as ab initio calculations at STO-3G* and 3-21G*. The absolute values of the HOMO-LUMO gaps are very different at PM3, but the ordering is the same, and the correlation with an experimental variable is almost identical. So I would say that relative orbital energies of related compounds at PM3 (PM3 because of the sulfur parametrization) can be valuable. As to whether PM3 orbitals look like STO-3G* or 3-21G* orbitals -- in a general sense, yes; that is, trends are reproduced. But for more details, well, I'll be looking into it myself... -- Dawn friedman@tammy.harvard.edu From mckelvey@Kodak.COM Fri Jun 3 14:06:25 1994 Received: from Kodak.COM for mckelvey@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id MAA25845; Fri, 3 Jun 1994 12:45:03 -0400 From: Received: from NTPROF.DECnet MAIL11D_V3 by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA14588; Fri, 3 Jun 94 12:47:46 -0400 Date: Fri, 3 Jun 94 12:47:45 -0400 Reply-To: mckelvey@Kodak.COM Message-Id: <9406031647.AA14588@Kodak.COM> To: osc@Kodak.COM Subject: HYPERCHEM, CACHE, GAUSSIAN< ROCKET-SCIENCE Netters: Re:HYPERCHEM It's a great package in my opinion. It's not perfect in my view, but for the PC enviroment it does more than most others I am familiar with. I would compare it against George Purvis' Mac CACHE package at Tektronix. Two very good packages! I would like to see a bit more flexibility in some of HYPERCHEM's approach to some of its features. I share the concern related to conjugate gradient optimisation for semi-empirical, and in cartesian coordinates. When such an approach is taken for floppy molecules such as dyes, a lot of cpu time gets used! Internal coordinates using a Newton-Raphson approach is more powerful than anything we have used for the past 10 years. Baker's EF routine, particularly in MOPAC-93, is hard to beat in our experience on PC's and work stations. Now in good fun, I have to take a friendly poke about the recent comment about what IOP(4/20=7) means in Gaussian: 1) Most places have source. 2) All places SHOULD have documentation. I realise things are getting to "If I have to read the documentation, the program's not well written," but you gotta do it! IOP(4/20=N) is described therein, though not explicitly for N=6,7,8. The documenation is a bit behind, as it usually reflects the text at the beginning of each block of Links for the source....so Rocket-Science is not required, just a little logic. John McKelvey Eastman Kodak From mckelvey@Kodak.COM Fri Jun 3 14:13:02 1994 Received: from Kodak.COM for mckelvey@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id MAA25954; Fri, 3 Jun 1994 12:48:07 -0400 From: Received: from NTPROF.DECnet MAIL11D_V3 by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA14675; Fri, 3 Jun 94 12:50:44 -0400 Date: Fri, 3 Jun 94 12:50:43 -0400 Reply-To: mckelvey@Kodak.COM Message-Id: <9406031650.AA14675@Kodak.COM> To: osc@Kodak.COM Subject: HYPERCHEM, CACHE, GAUSSIAN92, CEREBELLA, ROCKET-SCIENCE Netters: Re:HYPERCHEM It's a great package in my opinion. It's not perfect in my view, but for the PC enviroment it does more than most others I am familiar with. I would compare it against George Purvis' Mac CACHE package at Tektronix. Two very good packages! I would like to see a bit more flexibility in some of HYPERCHEM's approach to some of its features. I share the concern related to conjugate gradient optimisation for semi-empirical, and in cartesian coordinates. When such an approach is taken for floppy molecules such as dyes, a lot of cpu time gets used! Internal coordinates using a Newton-Raphson approach is more powerful than anything we have used for the past 10 years. Baker's EF routine, particularly in MOPAC-93, is hard to beat in our experience on PC's and work stations. Now in good fun, I have to take a friendly poke about the recent comment about what IOP(4/20=7) means in Gaussian: 1) Most places have source. 2) All places SHOULD have documentation. I realise things are getting to "If I have to read the documentation, the program's not well written," but you gotta do it! IOP(4/20=N) is described therein, though not explicitly for N=6,7,8. The documenation is a bit behind, as it usually reflects the text at the beginning of each block of Links for the source....so Rocket-Science is not required, just a little logic. John McKelvey Eastman Kodak From thep@risc1.lrm.fi.cnr.it Fri Jun 3 14:43:38 1994 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.4/930601.1506) id OAA27700; Fri, 3 Jun 1994 14:17:20 -0400 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA38642; Fri, 3 Jun 1994 20:18:18 +0200 Date: Fri, 3 Jun 1994 20:18:18 +0200 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9406031818.AA38642@risc1.lrm.fi.cnr.it> To: chemistry@ccl.net Subject: problem on the selection of the residue's name Dear Netters; Please forgive me if this message interupts you. Since I have a doubt about some typical data sets from the DG (Distance Geometry) calculation. The program provides the library in which contains several data sets. I was looking at it and I found that some residues which are different in term of the charges, for example ARG/ARG+ or GLU/GLU- etc., are provided in order to choose as the kind of residue be considering. I afraid that if I define the wrong one in the input file (for instance, instead of ARG+ , I use ARG), it will be a big problem. And then I will get the different structure. Therefore, I have some question are; - Are there any serious problem if I define the wrong residue's name which is not corresponded to the real system? (As far as I looked the library, there are just a few differences in term of proton donor/acceptor.) - These problem can be corrected by the molecular dynamic calculation. Is that right? - Are there any pKa value of the amino acids which consist of labile proton? How can I get them? or, does anybody have this value in hand? Please inform me. I will be appreciate if I get any response. Thank you very much Pornthep From KGRAFTON@aardvark.ucs.uoknor.edu Fri Jun 3 17:44:12 1994 Received: from aardvark.ucs.uoknor.edu for KGRAFTON@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id RAA00775; Fri, 3 Jun 1994 17:08:53 -0400 From: Message-Id: <199406032108.RAA00775@www.ccl.net> Date: Fri, 3 Jun 94 16:09 CDT Subject: AMBER 4.0 Energies. What are they? To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" AMBER 4.0 purports to output energies from MD runs in Kcals (pg 79 of the manual). This energy does not seem to be kcals/mol, as a box of 200 water molecules gives twice the energy as a box of 100 molecules. My best guess is that since the AMBER code accepts a 'built-in' solvent such as TIP3p water as a single 'molecule' built up of many residues, the energies are reported in (kcal)/(mol of boxes of whatever). Is this true? Also, has anyone had any difficulty using TIP4p water in AMBER? The pure solvent that I have run drops dramatically (~400 kcal) in energy after about 30-40ps, and from there on fluctuates only about 1 kcal up or down in total energy. It seems to have formed some type of rigid 'polywater'structure. It has been suggested to me that this is caused by the charge center being given a mass of ~12amu, and that it might be corrected by setting this mass to zero, but AMBER will not accept a zero mass. I would be very interested to hear about other experiences with TIP4p in AMBER. Please feel free to e-mail me at Kgrafton@aardvark.ucs.uoknor.edu. I will post a short summary of responses if the infomation gained warrants it. K. Grafton Department of Chemistry University of Oklahoma at Norman, USA. From jkl@ccl.net Fri Jun 3 17:51:38 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id QAA00584; Fri, 3 Jun 1994 16:46:47 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id QAA00542; Fri, 3 Jun 1994 16:46:46 -0400 Date: Fri, 3 Jun 1994 16:46:46 -0400 Message-Id: <199406032046.QAA00542@krakow.ccl.net> To: chemistry@ccl.net Subject: Survey and going places Forwarding: Mail from 'Mail Delivery Subsystem ' dated: Fri, 3 Jun 1994 15:02:33 -0400 Cc: jkl@ccl.net Dear netters, I know how you hate doing this, but we really need your answers to the survey. The survey questions can be accessed in a number of ways: 1) via e-mail. You can retrieve the survey questions and instructions by sending a message: select chemistry cd instructions get survey quit to MAILSERV@ccl.net 2) via ftp, as follows: ftp www.ccl.net or ftp 128.146.36.5 Name: anonymous Password: Your_e-mail_address ftp> cd pub/chemistry/instructions ftp> get survey ftp> quit 3) via gopher: gopher www.ccl.net 73 instructions survey 4) via WWW form (USE IT IF YOU CAN, IT IS THE EASIEST WAY) http://www.ccl.net/cgi-bin/survey Thank you in advance. Please be reminded that I will not see your id's (names or e-mail addresses), however, at some point, I will read all your anonimized answers --- as dumm as I am, I will not be able to figure our who bitched the most {:-)}. The second thing. I will be out of town for over 3 weeks. I am going to 3 conferences: DFT in Cracow, Poland Quantum Chemistry in Prague, Czech Republic Computational Chemistry, Wroclaw, Poland. See some of you there. During this time, I may be kept incommunicado (though I will try to peek and poke whenever I can) and the list will be in good hands of Robby Berry. Jan Labanowski Your coordinator jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET