From Ales.Zupan@ijs.yu Thu Sep 24 10:50:07 1992 Date: Thu, 24 Sep 1992 08:50:07 +0200 From: Ales.Zupan@ijs.yu To: CHEMISTRY@ccl.net Subject: CRYSTAL 92 again Dear netters, I am sorry for the wrong info I sent around a few days ago. The address for info on CRYSTAL92 is: bitnet : CRYSTA92@ITOCSIVM internet: CRYSTA92@itocsivm.csi.it My message was definitely not the official announcement of the new version of the programme. When it is time for it, it will be released by the authors and we hope also through the Chemistry mail box. +--------------------------------+-----------------------------------------+ | Ales Zupan | Internet address: | | Jozef Stefan Institute | Ales.Zupan@ijs.ac.mail.yu | | Jamova 39 | | | 61111 Ljubljana | We are being switched to new contry | | SLOVENIA | code, so please try also: | | | Ales.Zupan@ijs.ac.mail.SI | | | and inform your sysmanager, if it fails | +--------------------------------+-----------------------------------------+ From E702BS@FRCCSC21.bitnet Thu Sep 24 05:51:40 1992 Date: Thu, 24 Sep 92 11:48 FST From: "BIOSTRUCTURE SA" To: "Computer Chemistry List" Subject: ND-NMR BIOSTRUCTURE is now distributing N-DEE, a package from treatment and analysis of NMR data developped in Germany with the help of BRUKER Spectrospin. N-DEE runs under X11 on E&S, DEC, SUN and SGI Workstations. 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Euclide F-67400 Illkirch, FRANCE Phone : (33) 88 67 98 00 Fax: (33) 88 67 98 01 ------------------------------------------------------------------------------- From reinert@VAX.MPIZ-KOELN.MPG.dbp.de Thu Sep 24 20:06:23 1992 Date: Thu, 24 Sep 1992 18:06:23 +0200 From: reinert@VAX.MPIZ-KOELN.MPG.dbp.de To: chemistry@ccl.net Subject: Reply to Molecular Modeling question Ravi, Some of theses books and articles might be useful to You: REVIEWS IN COMPUTATIONAL CHEMISTRY by D.B. Boyd and K.B. Lipkowitz (Vol. 1+2), VCH Publishers, Inc. A HANDBOOK OF COMPUTATIONAL CHEMISTRY by Tim Clark, John Wiley And Sons 1985 PROTEIN ARCHITECTURE by A. M. Lesk, Oxford University Press 1991 COMPUTER AIDED MOLECULAR MODELING: RESEARCH STUDY OR RESEARCH TOOL by A. Dearing, J. Comput.-Aided Mol. Design, 2, 179-189 (1988) Peter Reinert From NEELY@AUDUCVAX.bitnet Thu Sep 24 03:20:00 1992 Date: Thu, 24 Sep 92 08:20 CDT From: Subject: UHF FORCE with MOPAC/AMPAC To: chemistry@ccl.net I'd like to thank everyone who sent me suggestions. These included using LET to force use of the persent structure for the FORCE computation, which pointed out that the program was starting with a much higher gradient than the previous run completed with. Which in turn made suggestions I improve the optimization most pertinent. I was also advised to try TS; I neglected to mention in my original posting that TS with this system seems always to lead to a structure with no negative eigenvalues. I was also advised to try RECALC=3. I'm trying these suggestions, and seem to be making progress. Irene Newhouse From NEELY@AUDUCVAX.bitnet Thu Sep 24 03:20:00 1992 Date: Thu, 24 Sep 92 08:20 CDT From: Subject: UHF FORCE with MOPAC/AMPAC To: chemistry@ccl.net I'd like to thank everyone who sent me suggestions. These included using LET to force use of the persent structure for the FORCE computation, which pointed out that the program was starting with a much higher gradient than the previous run completed with. Which in turn made suggestions I improve the optimization most pertinent. I was also advised to try TS; I neglected to mention in my original posting that TS with this system seems always to lead to a structure with no negative eigenvalues. I was also advised to try RECALC=3. I'm trying these suggestions, and seem to be making progress. Irene Newhouse From zjtg05@nap.amoco.com Thu Sep 24 03:32:55 1992 Date: Thu, 24 Sep 1992 08:32:55 -0500 From: zjtg05@nap.amoco.com To: chemistry@ccl.net Subject: Re: PaintJet config question I think that Joao needs to put some virtual paper in the HP's paper tray and then put on some virtual reality goggles. Everything should work fine after that... I've written some of my best proposals this way! ;-) :Joe jtgolab@nap.amoco.com From tudor@wucmd.wustl.edu Thu Sep 24 05:57:17 1992 Date: Thu, 24 Sep 92 10:57:17 -0500 From: tudor@wucmd.wustl.edu (Tudor Oprea) To: CHEMISTRY@ccl.net Subject: Computational Chemistry on PCs Answering to the request of G. Ravishanker >from 09/24/92 There is a paper called Computational Chemistry on a PC by G. Naray-Szabo et.al Int.J.Quantum Chem. XXXVIII 163-171 that deals with SOME of this stuff. G.N-S has a program called PCMODEL[TM] - you'll find his address in his paper. Then, there is ALCHEMYII and ALCHEMYIII >from Tripos Associates, StL. There is a molecular graphics program called HAMOG (HAlle MOlecular Graphics) that originates from the former DDR. It runs with 10000 atoms and does MEP calculations (no molecular mechanics, though). I lost track of the address of the company, but I guess I would be able to find it in 2 weeks or so, if you are REALLY interested. Graphics are good, MEP are based on electronegativities. A program that does real modelling on a PC is COSMIC (2.0) - which is developed by J.G. Vinter (see Morley et.al, J. Comput.-Aided Mol. Design 5:475-504 for the latest version). This runs on ATs with 386/387 OR 486 & 4 megs of RAM, and is supported by Nothingam U., & Salford U. (last one for the FTN77 Fortran compiler). It performs rigid docking, torsional minimisations (from 5 degrees up), CNDO/2, docking with H+, HO-, and a hydrophobic probe (gets minima/maps), interface with CCDC, entropy (like Williams, JACS 113:7020-7030), and usual molecular mechanics stuff. Charges with CHARGE3 Abraham et.al J. Comput.-Aided Mol. Design 6:273-286, good combination of Hinze-Jaffe stuff & iterative Huckel. As far as I know, no papers are published on COSMIC for PC. Then there is Oxford Molecular Design, which took Chem-X to the PC. For these proprietary products, better ask the owners for more details. P.S. I no not too much of the Mac, but COSMIC on the Mac is called NEMESIS. This is all that I have been in contact with. I worked with ALCHEMYII, COSMIC 1.02 & 2 and I've seen the Demo of HAMOG back in Romania (where I come from) - and I was particularly interested in the problem. I know that a compilation of software incl. PCs is given by Donald Boyd at the end of Reviews in Computational Chemistry II VCH New York 1991 - which does NOT mention COSMIC. For other details, contact me at ____________________________________________ Tudor Ionel Oprea Washington University Center for Molecular Design Lopata Hall, Box 1099, One Brookings Drive St.Louis MO 63130 Tel:(1-314) 935 4672 Fax:(1-314) 935 4979 Email: tudor@wucmd.wustl.edu ____________________________________________ Bye, T. From ssidner@unmc.edu Thu Sep 24 06:11:53 1992 Date: Thu, 24 Sep 92 11:11:53 CDT From: ssidner@unmc.edu (Steve Sidner) To: chemistry@ccl.net Subject: Converting PostScript to EPS I recently received a newsletter from Qualix, a vendor of Unixware (The Qualix Group, 1-800-245-UNIX, info@qualix.com). In it was a tip on converting PostScript files to Encapsulated PostScript files by hand. I haven't tried it yet - Caveat programmer! I quote: The top of a regular PostScript file looks something like this: %!PS-Adobe-2.0 %%Creator: NiftyZap %%Title: Resource Histogram %%CreationDate: %%Pages: (atend) %%BoundingBox: 36.000 36.000 720.000 540.000 %%EndComments The top of an Encapsulated PostScript file looks like this: %!PS-Adobe-2.0 EPSF-1.0 %%Creator: NiftyZap %%Title: Resource Histogram %%CreationDate: %%Pages: (atend) %%BoundingBox: 36 36 720 540 %%EndComments To make your PostScript file look like an Encapsulated PostScript file: 1. Make a backup of your PostScript output. 2. Open your PostScript file in a text editor. 3. Add the characters "EPSR-1.0" to the end of the first line. 4. If necessary, change the bounding box numbers to integers instead of floating-point numbers. 5. Save your modified file. Now try importing the file as an Encapsulated PostScript file into your word processor. Ninety-nine times out of a hundred, you'll discover that, in this case, cheating isn't all bad. End quote. Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805 (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From CUNDARIT@MEMSTVX1.bitnet Thu Sep 24 06:20:00 1992 Date: Thu, 24 Sep 92 11:20 CDT From: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: MOPAC and charges To: chemistry@ccl.net Fellow Netters, A colleague of mine is researching the metabolites of various psychoactive drugs using theory and experiments. He is using MOPAC to compare the geometry of various metabolite structures, and from their electronic structure try to predict potential reactivity. Since the most pertinent reactions are charge-controlled, he would like to know which of the various MOPAC Hamiltonians (AM1, PM3, MNDO) is most suitable for calculating Mulliken atomics charges. Of course, there are philosophical problems with using the Mulliken versus the other schemes, but we want to keep it simple here. I have seen much discussion about one of the MOPAC Hamiltonians giving spurious results for nitrogen compounds (which these molecules have), and I don't remember which, if any, was the offending culprit. Thanks. Tom Cundari Assistant Professor Department of Chemistry Memphis State University Memphis, TN 38152 From cabku01@mailserv.zdv.uni-tuebingen.de Thu Sep 24 20:11:44 1992 Date: Thu, 24 Sep 92 18:11:44 +0200 From: cabku01@mailserv.zdv.uni-tuebingen.de (Hartwig Kuehbauch) To: chemistry@ccl.net Subject: CFV: sci.chem.organomet Dear netters! This is a Call For Votes for : "sci.chem.organomet" The proposed newsgroup would support all kind of discussion related to organometallic chemistry. The voting period will end at october, 18, 1992. Only votes received 'til this date (incl.) will be counted. VOTING INSTRUCTIONS: -------------------- To vote for or against this newsgroup, you must send an e-mail-message to cabku01@mailserv.zdv.uni-tuebingen.de Posted votes will not be counted. Your vote has to be clear. Something like: I vote for sci.chem.organomet I vote against sci.chem.organomet sci.chem.organomet yes sci.chem.organomet no will do it. ABOUT THE PROPOSED NEWSGROUP: ----------------------------- The newsgroup sci.chem.organomet would be unmoderated. The main purpose of this newsgroup would be to give organometallic chemists all over the world the chance to communicate with each other. That means no chatter about irrelevant (to a scientist doing research in organometallic chemistry) things, but serious discussion with people of the same interest. Everything that has to do with organometallic chemistry in a wide range would be welcome. That would also include analytical methods like NMR, IR and so on, computational problems, or things like postdoc positions. This newsgroup would be one more source of information for the researcher --- and possibly one of the best. Thank you for reading. Hartwig Kuehbauch +----------------------------------------------------------------+ | cabku01@mailserv.zdv.uni-tuebingen.de (Hartwig Kuehbauch) | +-------------------------------+--------------------------------+ | Hartwig Kuehbauch | Tel.: | | Inst. f. Anorg. Chemie II | | | AK Lindner | +49 7472 25484 (privat) | | Auf der Morgenstelle 18 | +49 7071 292448 (office) | | 7400 Tuebingen (Germany) | | +-------------------------------+--------------------------------+ From d3f012@gator.pnl.gov Thu Sep 24 02:34:00 1992 Date: Thu, 24 Sep 92 09:34:00 PDT From: d3f012@gator.pnl.gov Subject: Disclaimer on platform survey To: chemistry@ccl.net Dear OSC readers: A short time ago I conducted an informal survey on user's opinions on hardware platforms for computational chemistry. I subsequently posted the responses to this forum. I have since had some requests from both industry and private researchers to allow them to disseminate the results. To all of these requests, I must answer with the disclaimer below. The survey and its results are not condoned or sponsored in any way by Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. As I stated in the survey results, the survey and it's results are not statistically significant. No statistical significance should be placed on the results, nor can the results be used in any statistically meaningful way. Neither my name, Battelle Memorial Institute, Pacific Northwest Laboratory, or any of Battelle's clients' names may be associated with any reproduction or reporting of the results of the survey. I conducted the survey solely as an individual, and do not represent anyone other than myself. Mark Thompson PNL From U32472@UICVM.UIC.EDU Thu Sep 24 16:51:58 1992 Date: 24 September 1992 15:05:00 CDT From: "Alan Hinds 6-4541" To: Subject: G88 and G90 startup time on IBM mainframes G88 and G90 begin their execution by initializing a large direct-access file (the RWF file) that is used to hold many logical files over the course of the run. The RWF initialization takes little CPU time, but it takes from 20 to 30 minutes wall-clock time in VM/ESA CMS release 8 on the IBM 3090-300J at this site. This is a terrible burden, and makes running more than a small sample of the test jobs shipped with the installation package a painful chore. I have attempted to get G90 to run with an RWF file created and initialized by a different program, but I have failed in my various attempts with STOP 300 or STOP 400 errors. Does anyone know a way to get G90 to accept an RWF file that has been created outside G90? If affirmative, does anyone have handy a program to quickly generate the RWF file? Or, has anyone modified G90 to expedite the creation of the RWF file? Even in multihour batch G90 jobs, this 30 minute initialization represents considerable lost opportunity to do useful work. (I am aware that the G90 user can specify a smaller RWF file size, but this feature is rarely used at this site, since the initialization time is almost invisible to batch G90 users.) - Alan Hinds U32472@UICVM.UIC.EDU From chemistry-request@ccl.net Thu Sep 24 18:26:45 1992 From: burton@hyper.com (Ian Burton) Subject: Re: FAQ: description of pdb format To: CHEMISTRY@ccl.net Date: Thu, 24 Sep 1992 16:14:02 -0400 Richard, In response to your question: > >Hi, does anyone know where I can find a description of the >brookhaven pdb file format? > >Thanks > >Richard Gillilan >Visualization Specialist >Cornell Theory Center > If you are a HyperChem user, there is a brief description of Brookhaven PDB file format in Chapter 9 of the reference manual. Otherwise you could contact Brookhaven National Laboratory at: Protien Data Bank Brookhaven National Laboratory Chemistry Department, Bldg. 55 Upton, NY, USA 11973 Telephone: (516)-282-3629 Facsimile: (516)-282-5751 e-mail: pdb@bnlchm.bitnet pdb@chm.chm.bnl.gov Cheers, Ian. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2 From wsonnen@alnitak.usc.edu Thu Sep 24 08:15:23 1992 Date: Thu, 24 Sep 92 15:15:23 PDT From: wsonnen@alnitak.usc.edu (Wayne Sonnen) To: chemistry@ccl.net Subject: base-pair stacking Dear netters, I am asking if any of you have any good references on base pair stacking interactions. The book by: W. Saenger 'Principles of Nucleic Acid Structure' gives several references up until about 1980. I am particularly interested in any references (possibly preprints?) on this subject from the point of view of moleculer modeling/simulations (especially free energy calculations) and ab initio or semi-emperical energy calculations. In addition, if there are any thoughts on this subject that you would like share, i would like to hear (read) them. I have only begun studing base-pair interactions, therefore have nothing much to say. Thanks very much, Wayne sonnen wsonnen@alnitak.usc.edu P.S. If there is enough interest on the net, i will summarize references and any communications. If you wish to express your interest in this subject, it would be best to send me e-mail directly to me. From d3f012@gator.pnl.gov Thu Sep 24 08:52:53 1992 Date: Thu, 24 Sep 92 15:52:53 PDT From: d3f012@gator.pnl.gov Subject: Rotational invariance? and help with data deck To: chemistry@ccl.net ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 108 Regarding the earlier discussion on discrepancy between MOPAC and G90: I responded with a query that perhaps rotational invariance in the MNDO-family of methods may play a role (note, we saw that different values of physical constants was the cause of that specific example). However, my questions about invariance remain unresolved. Mike Frisch writes: > Mark Thompson suggest that a lack of rotational invariance might > account for the descrepancy. Nice try, but that's not it. The > difference between using the standard and z-matrix orientations in > Gaussian 92 is 5x10^-7 kcal/mole. Similarly, using two different > orientations in MOPAC 6.0 produces no change in the 5 decimal places > printed in the energy. ok...so I tried two different orientations in MOPAC 6.0 using formaldehyde. No matter how I place the x,y,z coordinates, the program rotates the molecule into some "standard" orientation before performing the calculation. Putting two different orientations into MOPAC actually generates the exact same set of cartesian coordinates used internally for the calculation. I would like to run these calcs using the absolute coordinates I type in. Is this possible?...can anyone help me with this? Am I building the data deck incorrectly? Anyway, whatever help I could get with these data decks would be helpful. Thanks in advance. Mark Thompson *********************** case 1 ************************* Here is my data deck form.dat: PRECISE FOCK 1SCF GEO-OK ITRY=100 1ELECTRON DENSITY VECTORS LARGE formaldehyde DATE: Thu May 14 16:03:43 1992 C 0.000000 0 0.578379 0 0.000000 0 O 0.000000 0 -0.629421 0 0.000000 0 H -0.920165 0 1.146823 0 0.000000 0 H 0.920165 0 1.146823 0 0.000000 0 Here is the geometry that MOPAC generates to perform the calc. (from the output file) CARTESIAN COORDINATES NO. ATOM X Y Z 1 C 0.0000 0.0000 0.0000 2 O 1.2078 0.0000 0.0000 3 H -0.5684 0.9202 0.0000 4 H -0.5684 -0.9202 0.0000 (molecule has been rotated onto the xy plane along the x-axis) ********************** case 2 ***************************** Here is the same geometry in another orientation: (rotated 90 deg. about y-axis and displaced 5 angs. along x) PRECISE FOCK 1SCF GEO-OK ITRY=100 1ELECTRON DENSITY VECTORS LARGE formaldehyde DATE: Thu May 14 16:03:43 1992 C 5.000000 0 0.578379 0 0.000000 0 O 5.000000 0 -0.629421 0 0.000000 0 H 5.000000 0 1.146823 0 -0.920165 0 H 5.000000 0 1.146823 0 0.920165 0 Here is the geometry that MOPAC generates to perform the calc. CARTESIAN COORDINATES NO. ATOM X Y Z 1 C 0.0000 0.0000 0.0000 2 O 1.2078 0.0000 0.0000 3 H -0.5684 0.9202 0.0000 4 H -0.5684 -0.9202 0.0000 (same as case 1) ********************************************************** Reordering the atoms in the data deck does give different coordinates in MOPAC. However, since the molecule is still lined up on the x-axis and in the xy plane, the rotational invariance of the two-electron integrals method will not be observed. ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 14 ---------------------------------------------------------------- Mark A. Thompson email: d3f012@pnlg.pnl.gov Sr. Research Scientist voice: 509-375-6734 Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ---------------------------------------------------------------- Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients.