From chemistry-request@server.ccl.net Tue Feb 27 04:16:31 2001 Received: from yangtze.hku.hk (IDENT:root@yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1R9GPw30775 for ; Tue, 27 Feb 2001 04:16:26 -0500 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.9.3/8.9.3) with ESMTP id RAA17217 for ; Tue, 27 Feb 2001 17:27:32 +0800 Date: Tue, 27 Feb 2001 17:27:32 +0800 (HKT) From: Ng Man Fai To: Subject: Indo/s parameter for TDHF In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, May I ask is there any people have tried to reparameterize the Indo/s parameters for TDHF method for calculating the absorption spectrum? Thanks a lot. Andy From chemistry-request@server.ccl.net Tue Feb 27 07:56:23 2001 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RCuNw32175 for ; Tue, 27 Feb 2001 07:56:23 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Tue, 27 Feb 2001 13:52:30 +0100 Message-ID: <000701c0a0bc$f206c680$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <157A51F55AAAD3119CD70008C7B1629DDAACDB@lvlxch01.unitedcatalysts.com> Subject: Re: CCL:Mott insulators and DFT & viruses Date: Tue, 27 Feb 2001 13:58:13 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f1RCuNw32176 > I'm afraid to open attachments I didn't expect, with all the viruses > floating around. Please use plain text whenever possible. (Artem, I'm > sorry about cc'ing this to the list, but you're not the only "offender" > here). > > --David Shobe It is understandable. However, some advices: If it is a text (txt) or image (.jpg, .gif etc) file, you can open it without problem. Html format is also quite safe. If it is a doc file, save it and do not open immediately from the mailing program. When opening this separate doc file with the Word, press the shift button simultaneously. In this case Word does not start automatically macros or scripts. Or open it with WordPad, which is a stupid simple program and it has no built-in scripting features. Resave it in Word format, if want to keep the letter. This may feel a bit complicated, but that is the price for more security. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Tue Feb 27 09:16:34 2001 Received: from mx1.ustc.edu.cn ([61.132.182.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1REGXw32553 for ; Tue, 27 Feb 2001 09:16:33 -0500 Received: from BOC4 ([202.38.66.112]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id WAA06123 for ; Tue, 27 Feb 2001 22:55:45 -0800 Message-ID: <005c01c0a0c8$2b3daee0$704226ca@ustc.edu.cn> Reply-To: "benny" From: "benny" To: Subject: How to deal with large rwf file? Date: Tue, 27 Feb 2001 22:18:34 +0800 Organization: ustc Dear CCL Members: I use Gaussian A.7 to do MP2 frequency calculation.My workstation's configuration is 30G hard disk and 780M memory. However,when I calculate a system with 7 heavy atoms using MP2/6-31+g**, The calcualtion will stop with the following message: Erroneous write during file extend. write 114687 instead of 4096 Probably out of disk space. ****** I have split the scratch file as the following: %rwf=f1,2GB,f2,2GB However,the calculation still stop after the first file(f1) exceed 2.1G,while f2 do not contain any data. Does anyone have the similar experience and how to deal with the problem? Thanks a lot! Yours From chemistry-request@server.ccl.net Tue Feb 27 11:38:48 2001 Received: from mail.iwr.uni-heidelberg.de (mail.iwr.uni-heidelberg.de [129.206.104.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RGcmw00856 for ; Tue, 27 Feb 2001 11:38:48 -0500 Received: from kenzo.iwr.uni-heidelberg.de (IDENT:root@kenzo.iwr.uni-heidelberg.de [129.206.120.29]) by mail.iwr.uni-heidelberg.de (8.11.1/8.11.1) with ESMTP id f1RGch606089; Tue, 27 Feb 2001 17:38:43 +0100 (MET) Received: from iwr.uni-heidelberg.de (ficus.iwr.uni-heidelberg.de [129.206.120.39]) by kenzo.iwr.uni-heidelberg.de (8.9.3/8.9.3) with ESMTP id RAA24709; Tue, 27 Feb 2001 17:38:43 +0100 Sender: matthias.ullmann@iwr.uni-heidelberg.de Message-ID: <3A9BD813.BB935D43@iwr.uni-heidelberg.de> Date: Tue, 27 Feb 2001 17:38:43 +0100 From: Matthias Ullmann X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.17-14 i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Analytical solution of the PBE for charge in a membrane Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, does anyone of you know if there exists a analytical solution of the Poisson-Boltzmann equation for a charge in a membrane (dielectric plate with epsilon_1) in a solution with the ionic streng I and epsilon_2. Any hints are very much apprechiated. All the best, Matthias -- G. Matthias Ullmann IWR - Biocomputing University Heidelberg Im Neuenheimer Feld 368 69120 Heidelberg Germany Telephone: +49-6221-54-8806 Fax: +49-6221-54-8868 e-mail: Matthias.Ullmann@iwr.uni-heidelberg.de http://www.iwr.uni-heidelberg.de/groups/biocomp/ullmann From chemistry-request@server.ccl.net Tue Feb 27 11:03:45 2001 Received: from gate.syntem-sa.fr (gate.syntem-sa.fr [146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RG3iw00631 for ; Tue, 27 Feb 2001 11:03:44 -0500 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id RAA08374 for <@firewall.syntem-sa.fr:chemistry@ccl.net>; Tue, 27 Feb 2001 17:00:51 +0100 (MET) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma107700; Tue, 27 Feb 01 17:00:02 +0100 Received: from victoria.syntem-sa.fr (victoria.syntem-sa.fr [10.0.0.44]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA61357 for <@laetitia.syntem-sa.fr:chemistry@ccl.net>; Tue, 27 Feb 2001 16:57:29 +0100 (MET) Received: from syntem-sa.fr (localhost [127.0.0.1]) by victoria.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA24680 for ; Tue, 27 Feb 2001 17:03:12 +0100 (MET) Sender: dturner@syntem-sa.fr Message-ID: <3A9BCFBF.67693093@syntem-sa.fr> Date: Tue, 27 Feb 2001 17:03:11 +0100 From: David Turner Reply-To: dturner@syntem.com Organization: Computational Drug Design, Syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Protease Inhibitors Entropy/Enthalpy 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 f1RG3jw00632 Thanks to all who replied - I now have plenty to be getting on with ... attached all replies received up to 27/2 David Original request: > > Can anybody point me to an article or articles discussing the > relative contributions of entropic and enthalpic terms to the > free energy of binding of substrates and/or inhibitors of HIV > protease or perhaps in more general terms for aspartic and the > various other classes of proteases? > |================================================================================| 1) From: Mark Forster Check out these recent references: a) Wang, W., Kollman, P.A., 2000. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. Journal of Molecular Biology 303 567-82. b) McCarrick, M.A., Kollman, P.A., 1999. Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. Journal of Computer Aided Molecular Design. 13 109-21 c) Molecular mechanisms of resistance: free energy calculations of mutation effects on inhibitor binding to HIV-1 protease. Rick SW, Topol IA, Erickson JW, Burt SK Protein Sci. 1998 Aug;7(8):1750-6. |================================================================================| 2) From: heberger@chemres.hu Although I am not familiar with proteases and alike the formulation of the question gave me the impression that you may face with the notorius compensation effect. If this is so, I have explanations and literature sources abundantly. bye Charles ******************************************************* Dr. Karoly Heberger Institute of Chemistry, Chemical Research Center, Hungarian Academy of Sciences H-1025 Budapest II., Pusztaszeri út 59-67. H-1525 Budapest, P. O. Box. 17, Hungary Fax: (36 1) 325 75 54; Phone: (36 1) 325 79 00; Email: heberger@cric.chemres.hu ******************************************************* |================================================================================| 3) From: Carol Parish The following paper provides binding thermodynamics for acetyl pepsin and a 9-mer peptide. Lugue, Todd, Gomez, Semo and Freire Biochemistry, 1998, 37, 5791-5797. If you recieve any other references would you be so kind as to summarize to the list or to me directly? Thanks, Carol Parish |================================================================================| 4) From: Salvatore Guccione ***I am not sure but I think some studies on have been performed by HINT. Look at the: www. eslc. vabiotevch. com or contact Glen Kellogg . "Glen E. Kellogg" Best Regards, Salvatore |================================================================================| 5) From: Bruce Allan Palfey Look at Gomez & Friere (1995) J. Mol. Biol., 252, 337-350 for an interesting analysis of endothiapepsin. I think Friere has also worked on the HIV protease, but I don't know the reference. ciao, Bruce Bruce Palfey, Department of Biological Chemistry, University of Michigan Ann Arbor, MI 48109-0606 |================================================================================| 6) From: Tudor.Oprea@astrazeneca.com My guess is that Vertex has loads of such data. They have played with HIV1PR for the past decade, and running microcalorimetric titration since. No idea if they published, but I suggest you start digging there. Another guess would be the Peter Rose & crew from Agouron, same stuff. Tudor |================================================================================| 7) From: Jordi Villa Check, Proteins: Structure, Function, and Genetics Volume 39, Issue 4, 2000. Pages: 393-407 Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease Yuk Yin Sham, Zhen Tao Chu, Holly Tao, Arieh Warshel * You can get it from the web at: http://www3.interscience.wiley.com/cgi-bin/abstract/72501371/START |================================================================================| 8) From: Shahar Keinan Try This: Bardi, J. S.; Luque, I.; Freire, E. Biochemistry 1997, 36, 6588-6596. Shahar |================================================================================| 9) From: Jan Torleif Pedersen Well - you are asking a perfectly valid question, but it has not been answered fully by anybody. I know of only one review which attempts to look at the drug binding energetics from a theoretical perspective and that is Michael Gilson. Please have a look at his very nice review : Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997 Mar;72(3):1047-69. Best Regards -- Jan |================================================================================| 10) From: Malcolm Gillies I don't know of a review, but this is a recent one with thermodynamic analysis of KNI-272/HIV-1 PR binding by microcalorimetry, and which also mentions previous data on acetylpepstatin, indinavir, saquinavir and nelfinavir. Hope that's some help. @article{velazquez00a, author = {A. Velazquez-Campoy and I Luque and M. J. Todd and M. Milutinovich and Y. Kiso and E. Freire}, number = {9}, year = {2000}, pages = {1801-1809}, journal = {Protein Sci.}, title = {Thermodynamic dissection of the binding energetics of {KNI-272}, a potent {HIV-1} protease inhibitor}, volume = {9} } cheers, Malcolm -- Malcolm Gillies PhD student, computational medicinal chemistry Dept Medicinal Chemistry, Faculty of Pharmacy, Utrecht University, The Netherlands |================================================================================| -- ________________________________________________________________ David Turner Synt:em Senior Modeling Scientist Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dturner@syntem.com France Tel: Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Direct Line: +33 (0)4 66 04 22 85 ________________________________________________________________ Discover New Drugs, Discover Synt:em http://www.syntem.com ________________________________________________________________ From chemistry-request@server.ccl.net Tue Feb 27 12:52:46 2001 Received: from marie.chem.purdue.edu (wthr419aa1.chem.purdue.edu [128.210.142.219]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RHqjw01412 for ; Tue, 27 Feb 2001 12:52:45 -0500 Received: from localhost (lev@localhost) by marie.chem.purdue.edu (SGI-SGI-8.9.3/8.9.3) with ESMTP id MAA01392 for ; Tue, 27 Feb 2001 12:52:51 -0500 (EST) X-Authentication-Warning: marie.chem.purdue.edu: lev owned process doing -bs Date: Tue, 27 Feb 2001 12:52:51 -0500 From: Lev Gorenstein X-X-Sender: cc: Subject: Re: CCL:Mott insulators and DFT & viruses In-Reply-To: <000701c0a0bc$f206c680$3b8506c1@chem.klte.hu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 27 Feb 2001, Tamas E. Gunda wrote: TEG> If it is a text (txt) or image (.jpg, .gif etc) file, you TEG> can open it without problem. Html format is also quite TEG> safe. HTML is not too safe... For example, the widespread Netscape Mail client has a "wonderful" option. The option is called "Enable JavaScript in news and mail" and, as I said, is on by default... And thus an HTML attachment (or a letter in HTML format, for that matter) with a malicious JavaScipt code could wreak nice little havoc on your machine... And of course there's that neat ICQ-style infection, when the attached file is actually an .exe program with the name "nice_picture.jpg .exe" (with enough spaces in the name to hide ".exe" beyond the message box field. TEG> If it is a doc file, save it and do not open immediately TEG> from the mailing program. When opening this separate doc TEG> file with the Word, press the shift button TEG> simultaneously. In this case Word does not start TEG> automatically macros or scripts. Well, you forgot to mention one more thing. ALWAYS check ANY outside file for viruses before opening it! Sounds so-o-o-o simple - yet so many people forget this... Of course, one should keep a fresh version of antivirus software with a constantly updated fresh .dat files... And switch to Linux ;-)) Lev -- Love thy neighbor but don't get caught. From chemistry-request@server.ccl.net Tue Feb 27 12:53:39 2001 Received: from drew.berry.edu (drew.berry.edu [66.20.28.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RHrdw01426 for ; Tue, 27 Feb 2001 12:53:39 -0500 Received: from fsgw.berry.edu (fsgw [10.0.1.15]) by drew.berry.edu (8.9.3/8.9.3) with SMTP id MAA21651 for ; Tue, 27 Feb 2001 12:53:37 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by fsgw.berry.edu; Tue, 27 Feb 2001 12:56:59 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Tue, 27 Feb 2001 12:52:05 -0500 Subject: Re: CCL:Question concerning Spartan molecular modeling software From: Gary Breton To: Message-ID: In-Reply-To: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Thanks to all that responded to my question concerning the molecular mechanics FF in PC SpartanPro. I received many responses that corroborated my finding that when utilizing MMFF94 (as contained within Spartan), the chlorine in chlorocyclohexane is found to be more stable in the axial position rather than the equatorial position (contrary to experimental findings, and the general rule that substituents prefer the equatorial position in order to eliminate 1,3-diaxial interactions present in the axial position). I also received a response from Wavefunction which some of you may be interested in. I have summarized the responses since a few who responded asked me to do so. I should note: I carried out the same type of calculation utilizing methylcyclohexane instead of chlorocyclohexane and DID obtain the expected result (apparently MMFF94 being parametized for this application). Also, when I performed an ab initio 3-21G* calculation on the MM minimized structures of the axial and equatorial chair conformers of chlorocyclohexane, I DID obtain the expected result. It would appear therefore (to this beginner) that the safest route would be to utilize MMFF94 to obtain starting geometries for ab initio (or maybe semi-empirical or DFT) energy calculations rather than to read too much into the "steric" energies provided by MMFF94. Again, thanks for your help and best regards! Gary Breton Berry College ************************************************************ Wavefunction's response: It appears like MMFF94 does not correctly predict the known energy difference. My guess is MMFF94 has the Cl-H 1-4 term repulsive (positive energy), in both conformations. In going from the axial two of the 1-4/Cl-H contacts are replaced by two 1-5 repulsive terms. And the weight of the 1-5 contact is smaller than expected. More likely the weight of the 1-4 term is too high, but in most 1-4 cases the is partly canceled by a 1-4 torsion term. In general the VdW parameters are the hardest to fit using mechanics method. (Usually MP2 level is considered good.) For one, the functional form 6-12, 7-14-buffered, exp-6 etc. are very crude approximations. And the parameterization depends highly on the parametizing method. In Halgren's MMFF94 he put priority on: 1) Geometry 2) intra-molecular torsion term's and conformation 3) the near part of the VdW term (thus his buffered 7-14 VdW term). To this effect MMFF has a very highly tuned torsional profile which does as good as I know for conformations on a broad range of molecules. (Until a recent flurry of papers describing the importance of polarization terms in getting good conformations which all the force fields you've mentioned have ignored.) This heavy tuning of torsional terms has led to some non-optimal non-bonded terms. Another example of this is hydrogen bonds. While Halgren has done extensive work to get geometries of a large set of systems correct using only charges and a buffered 7-14 term, as well as some energetics for these systems, cases where there are strained H-Bonds fail because there are just not enough terms to model the correct behavior at intermediate distances, (where polarization dominates). **************************************************** Responses from others: 1. To me this force field seems more oriented towards providing good geometries than energies. (we use MMFF geometries mostly to carry out single-point calculations in view of estimating formation enthalpies). 2. What is the experimental difference in energies? Most force fields can easily be in error by a kcal or two, and assuming that the experimental difference is in that range all this result tells you is that the developers probably didn't consider that specific compound when developing the force field. A useful article on what sorts of conformational errors to expect is JACS volume 119, pages 5908-5920 (1997). 3. in principle this is the drawback of any molecular mechanics method, you cannot make prediction with them, just reproduce the type of molecule they have been parametrised with... 4. I performed the calculation using SYBYL. Several force fields are installed on the version that I am presently using. 1) MMFF94 with MMFF94 charges equatorial conformer 1.408 kcal axial conformer 1.061 kcal This differs in detail from your result. The author of the MMFF94 has published a test set. That might be worth trying in order to discover if Spartan has a faithful implementation of MMFF94. 2) Tripos force field without charges equatorial conformer 0.749 kcal axial conformer 0.945 kcal 3) Tripos force field with Gasteiger charges equatorial conformer 0.787 kcal axial conformer 1.123 kcal 4)I haven't had time to explore an ab initio calculation. In all case the energy difference is rather small. Can you trust a modeling calculation in this case? I am an experimentalist and naturally have a bias towards data from microwave spectroscopy, NMR spectroscopy, and electron diffraction. In determining 3D structures from NMR data, I combine modeling calculations with experimental constraints that I obtain from nuclear Overhauser effect measurements. > From: Gary Breton > Date: Fri, 23 Feb 2001 12:37:53 -0500 > To: > Subject: CCL:Question concerning Spartan molecular modeling software > > Hello folks, > > I hope at least some of you have some experience with PC Spartan Pro. I > recently purchased several copies of the software and began testing it with > some routine molecular mechanics (MMFF94) calculations. Amazingly, when I > computed the energy of chlorocyclohexane with the Chlorine in the equatorial > position ( 1.4 kcal/mol) it was of HIGHER energy than when the Cl was axial > (1.1 kcal/mol). This is contrary to experiment. I ran the same calculation > utilizing CambridgeSoft's Chem3D, with Hyperchem (MM+), and MOLGEN (MM2) and > received the proper result (i.e., Cl prefers to be equatorial in the chair > conformation) and the calculated energy differences were consistent with the > experimental values. > > Has anyone else observed this? is it a result of the force field? Am I doing > something wrong in Spartan that I am NOT doing in the other packages? If it > is the force field, can I replace the parameters contained within Spartan? > > Thanks for your help! > > Gary W. Breton > Department of Chemistry > Berry College > PO Box 495016 > Mount Berry, GA 30149 > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Feb 27 12:59:55 2001 Received: from server3.safepages.com ([216.127.146.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RHxsw01458 for ; Tue, 27 Feb 2001 12:59:54 -0500 Received: from Hppav (06-029.008.popsite.net [209.69.76.29]) by server3.safepages.com (Postfix) with SMTP id 35424230DA for ; Tue, 27 Feb 2001 17:59:45 +0000 (GMT) Message-ID: <001c01c0a0e7$110e1900$0100a8c0@webrise.net> From: "Jim Kress" To: References: <157A51F55AAAD3119CD70008C7B1629DDAACDB@lvlxch01.unitedcatalysts.com> <000701c0a0bc$f206c680$3b8506c1@chem.klte.hu> Subject: Re: CCL:Mott insulators and DFT & viruses Date: Tue, 27 Feb 2001 12:59:43 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 HTML is not a safe format to open. It can contain malicious embedded JavaScript, VBscript, or java applets. Jim ----- Original Message ----- From: "Tamas E. Gunda" To: Sent: Tuesday, February 27, 2001 7:58 AM Subject: CCL:Mott insulators and DFT & viruses > > I'm afraid to open attachments I didn't expect, with all the viruses > > floating around. Please use plain text whenever possible. (Artem, I'm > > sorry about cc'ing this to the list, but you're not the only "offender" > > here). > > > > --David Shobe > > It is understandable. However, some advices: > > If it is a text (txt) or image (.jpg, .gif etc) file, you can open it without problem. Html format is also quite safe. > > If it is a doc file, save it and do not open immediately from the mailing program. When opening this separate doc file with the Word, press the shift button simultaneously. In this case Word does not start automatically macros or scripts. > > Or open it with WordPad, which is a stupid simple program and it has no built-in scripting features. Resave it in > Word format, if want to keep the letter. > > This may feel a bit complicated, but that is the price for more security. > > > > > Dr Tamas E. Gunda > Research Group for Antibiotics of the Hungarian Acad. Sci. > University of Debrecen, POBox 36 > H-4010 Debrecen, Hungary > tel.: (+36-52) 512 900/2472 > fax: (+36-52) 512 914 > e-mail: tamasgunda@tigris.klte.hu > home-page: www.klte.hu/~gundat/gunda.htm > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Tue Feb 27 13:27:29 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RIRTw01621 for ; Tue, 27 Feb 2001 13:27:29 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA00170; Tue, 27 Feb 2001 13:27:30 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 27 Feb 2001 13:26:02 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G9F000MNHRAG7@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 27 Feb 2001 13:23:34 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 27 Feb 2001 13:26:32 -0500 Content-return: allowed Date: Tue, 27 Feb 2001 13:26:31 -0500 From: "Shobe, Dave" Subject: RE: Mott insulators and DFT & viruses To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAACEE@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-2 I have heard, however, that a file can appear as funnyjoke.txt in your mail program, but really be funnyjoke.txt.vbs -- the multiple extensions confuse the mail program, and what you think is just a text file is actually an executable. I have also heard that HTML files can be dangerous, and in fact even more dangerous than most extensions, since they can be programmed to execute from the preview pane. I do have anti-virus software here but I don't want to rely on it as my only defense. --David Shobe -----Original Message----- From: Tamas E. Gunda [mailto:tamasgunda@tigris.klte.hu] Sent: Tuesday, February 27, 2001 7:58 AM To: chemistry@ccl.net Subject: CCL:Mott insulators and DFT & viruses > I'm afraid to open attachments I didn't expect, with all the viruses > floating around. Please use plain text whenever possible. (Artem, I'm > sorry about cc'ing this to the list, but you're not the only "offender" > here). > > --David Shobe It is understandable. However, some advices: If it is a text (txt) or image (.jpg, .gif etc) file, you can open it without problem. Html format is also quite safe. If it is a doc file, save it and do not open immediately from the mailing program. When opening this separate doc file with the Word, press the shift button simultaneously. In this case Word does not start automatically macros or scripts. Or open it with WordPad, which is a stupid simple program and it has no built-in scripting features. Resave it in Word format, if want to keep the letter. This may feel a bit complicated, but that is the price for more security. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Feb 27 14:35:52 2001 Received: from mr.usu.edu (mr.usu.edu [129.123.1.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RJZnw02390 for ; Tue, 27 Feb 2001 14:35:49 -0500 Received: from tapaskar (tapaskar.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id CD8B01D2D3 for ; Tue, 27 Feb 2001 12:35:56 -0700 (MST) Message-ID: <007301c0a0f4$597aac50$25037b81@tapaskar> From: "Tapas Kar" To: "CCL" Subject: CCSD(T) convergence problem Date: Tue, 27 Feb 2001 12:34:49 -0700 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Is there any option or keyword in Gaussian98 to solve the convergence problem with CCSD(T)? ------------------------------------------------------------------ "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ------------------------------------------------------------------ Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu From chemistry-request@server.ccl.net Tue Feb 27 14:35:25 2001 Received: from ccl.net (ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RJZOw02384 for ; Tue, 27 Feb 2001 14:35:24 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA18347; Tue, 27 Feb 2001 14:35:25 -0500 (EST) Date: Tue, 27 Feb 2001 14:35:24 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Your coordinator on viruses and CCL in general Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL world community... I will try to be brief... It does not come easy for me {:-)}... 1) Please... DO NOT SEND MIME encoded mail to CCL if you can. In fact, each and every message which has a mime type application/something is stopped by the CCL distribution software for me to check. It is a pain. It cannot be given to studends, since it requires expertise... While there are packages which scan mail for viruses, they tend to be overprotective, and I will still need to review the stuff... Also, they cost money, and need to be maintained... PLEASE USE PLAIN TEXT MAIL!!! 99.99% of CCL messages do not require anything more than ASCII text. I can see that many people are using this M$ mail beautification and also send their mail as HTML encoded in the Netscape... If you think your mail is better when it is HTML encoded listen to this: I (Jan Labanowski) usually read my mail from my main OSC server via xterm on my Linux machine at home using pine. When the mail is HTML (or whatever) encoded, I could only see it by spawning a viewer, but since I am remotely logged in, I DO NOT DO IT!!! It is too slow to display Netscape browser by using Xwindow remote $DISPLAY setting. (it is more than 10 Megabytes of pixels to transfer -- even my cable modem is not too fast for this). If this is a message from someone I know, I am saving an attachment or a message to a file, and then examine it with the text editor, and only when it is worth viewing with a browser, I copy the file to my local machine and view it with the local browser. Whoever sends me an HTML encoded mail is WASTING a lot of my time... Thank you for the bold, italic, and underline and red, but I do not need it!!! If I do not know the person, I automatically hit delete... Sorry, most of my HTML encoded mail ends up deleted without reading... 2) People, YOU HAVE TO HELP ME IN KEEPING CCL RUNNING!!! The list of positions offered at: http://www.ccl.net/chemistry/announcements/jobs/ is quite successful and people are praising me for the results. People tell me that it is more successful than premiere and traditional ways of advertizing positions. It is probably true, since you are advertizing to a select group of people whom you want to hire. I do not have to remind you that advertizing a position in the press or the commercial web site costs thousands of dollars. You know this, you were paying these fees many times. I also maintain the list of conferences. http://www.ccl.net/chemistry/announcements/conferences/ However, frankly, it is a lot of work to maintain these services. You see, I do not keep this stuff there to advertize my own company, since I do not have any, and you are not my prospective customers. I hoped that people who benefited from these services will support CCL with donations. Only few do. THANK YOU A LOT FOR YOUR SUPPORT. But I need more supporters... So, if you got a job, or if you hired someone because of these services, please consider supporting CCL http://www.ccl.net/chemistry/aboutccl/supporting/ Just send me a check made to CCL Development Fund (OSC) to the address below. People who organize conferences also benefit from the attendence which is brought by advertizing conferences on CCL. And software vendors get a tremendous exposure from the discussions on CCL. So, please consider supporting CCL if you experienced some benefits from it. Your support is needed, or I will have to trim down the maintainance and upkeep of this resource. CCL needs to show that it is substantially supported by its subscribers/users to be considered useful for my parent organization. If you do not think it is worth supporting than you will see its decline. It is that simple... "Money makes the world go'round". Please help and understand... Jan Your infrequent moderator, but mostly just maintainer... Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Tue Feb 27 15:29:33 2001 Received: from emb22.resnet.cornell.edu (emb22.resnet.cornell.edu [128.253.200.106]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RKTXw02897 for ; Tue, 27 Feb 2001 15:29:33 -0500 Received: from pobox.com (128.253.86.74) by emb22.resnet.cornell.edu with ESMTP (Eudora Internet Mail Server 1.3.1); Tue, 27 Feb 2001 15:31:58 -0500 Message-ID: <3A9C0E32.7F70CECC@pobox.com> Date: Tue, 27 Feb 2001 15:29:38 -0500 From: Eric Bennett X-Mailer: Mozilla 4.75 [en] (X11; U; OSF1 V4.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Question concerning Spartan molecular modeling software References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Gary Breton wrote: > It would appear > therefore (to this beginner) that the safest route would be to utilize > MMFF94 to obtain starting geometries for ab initio (or maybe semi-empirical > or DFT) energy calculations rather than to read too much into the "steric" > energies provided by MMFF94. That is not necessarily valid as a general principle. A force field that is well-parameterized for the specific system you are studying can give better results than semi-empirical methods. See for example the Journal of Computational Chemistry, vol 12 number 2, pages 200-208 (1991) for some examples where MM2 predicts conformational energy differences better than AM1 and PM3. (And in most of the force field reviews I have seen MMFF is usually as good as MM2, or better.) -- Eric Bennett ( ericb@pobox.com ; http://www.pobox.com/~ericb ) From chemistry-request@server.ccl.net Tue Feb 27 16:13:14 2001 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1RLDDw03203 for ; Tue, 27 Feb 2001 16:13:13 -0500 Received: from localhost (qoajnv@localhost) by uscmail.usc.es (8.9.1/8.9.1) with ESMTP id WAA26287 for ; Tue, 27 Feb 2001 22:13:20 +0100 (MET) Date: Tue, 27 Feb 2001 22:13:20 +0100 (MET) From: Armando Juan Navarro Vazquez To: chemistry@ccl.net Subject: planewawe methods Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All Can anyone point me to reviews on Car-Parrinello and in general planewawe methods. I did a search on CA but wihtout too much success TIA Armando Navarro Departamento de quimica organica Facultade de quimica Santiago de Comnpostela Spain From chemistry-request@server.ccl.net Tue Feb 27 22:32:43 2001 Received: from simak.acpub.duke.edu (simak.acpub.duke.edu [152.3.232.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S3Whw05715 for ; Tue, 27 Feb 2001 22:32:43 -0500 Received: from godzilla3.acpub.duke.edu (zl2@godzilla3.acpub.duke.edu [152.3.233.44]) by simak.acpub.duke.edu (8.9.3/8.9.3/Duke-5.0.0) with SMTP id WAA21455; Tue, 27 Feb 2001 22:32:50 -0500 (EST) Date: Tue, 27 Feb 2001 22:32:48 -0500 (EST) From: Zhenyu Lu X-Sender: zl2@godzilla3.acpub.duke.edu To: chemistry@ccl.net Subject: help on electrostatic-potential derived charges Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: I tried calculating the electrostatic-potential derived charges for a system of 115 atoms, with a backgroud charge distribution. (9800 atoms ). I am using Gaussian 98. The calculation can finish SCF and generate the electrostatic potential, but it stopped when fitting point charges to eletrostatic potential and gave a core file. no error message is given at the end of the output file. My input ROUTE is: %Mem=10MW %nproc=4 %chk=pde #T HF/Gen Pseudo=Read charge=angstroms Population=MK NoSymm The end of the output file is : ................. Atomic Center 113 is at 11.457587108.961226 36.510564 Atomic Center 114 is at 12.070104118.785778 37.360621 Atomic Center 115 is at 18.604609113.064751 37.285621 3897 points will be used for fitting atomic charges Fitting point charges to eletrostatic potential I have calculated the ESP charges for a system of 85 atoms, and it works well. Does anyone know what's problem ? Thanks in advance! best, Zhenyu