From cosgrove@zeneca-ph.co.uk Mon Feb 6 04:37:15 1995 Received: from eros.britain.eu.net for cosgrove@zeneca-ph.co.uk by www.ccl.net (8.6.9/930601.1506) id EAA20461; Mon, 6 Feb 1995 04:26:26 -0500 Received: from zeneca-ph.co.uk by eros.britain.eu.net with UUCP id ; Mon, 6 Feb 1995 09:25:59 +0000 From: Dave Cosgrove Date: Mon, 6 Feb 95 10:25:08 GMT Message-Id: <4768.9502061025@iciukph.zeneca-ph.co.uk> Received: from zeneca by iciukph.zeneca-ph.co.uk; Mon, 6 Feb 95 10:25:08 GMT To: mikes@biochemistry.oxford.ac.uk Cc: CHEMISTRY@ccl.net In-Reply-To: <199502010943.JAA15383@nmrpcd.ocms.ocms.ox.ac.uk> (message from mikes on Wed, 1 Feb 1995 09:43:25 GMT) Subject: Re: CCL:Public Domain Cluster Analysis Programs Mike, There is a library called STATLIB on the Hensa archive that contains a whole load of stuff on clustering. *** --- __o __o __o *** *** ------ \<, \<, \<, *** *** ----- ( )/ ( ) ( )/ ( ) ( )/ ( ) *** +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dave Cosgrove Zeneca Pharmaceuticals ---------------------------------- 8AF13, Mereside | Tel (0)625 515521 | Alderley Park | Fax (0)625 586900 | Macclesfield | | Cheshire | email cosgrove@zeneca-ph.co.uk | SK10 4TG ---------------------------------- Great Britain +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From jsavast@junix.ju.edu Mon Feb 6 05:37:25 1995 Received: from junix.ju.edu for jsavast@junix.ju.edu by www.ccl.net (8.6.9/930601.1506) id FAA20765; Mon, 6 Feb 1995 05:10:26 -0500 Received: by junix.ju.edu (5.61/1.39) id AA09176; Mon, 6 Feb 95 05:09:48 -0500 From: jsavast@junix.ju.edu (Joseph Savastano) Message-Id: <9502061009.AA09176@junix.ju.edu> Subject: DNA Benchmarks To: chemistry@ccl.net Date: Mon, 6 Feb 1995 05:09:47 -0500 (EST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 801 Greetings all, I am looking for Benchmarks , preferably in the pbd format, of B- DNA dodecamers. ANd also possibly NaDNA complexs. I have looked at several sites, namely the archives at osc. CAn some one point me in the right directi on for finding this in the net. Thank you. *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* JOSEPH A. SAVASTANO | * SPS ZONE 6 ASSOCIATE * Email | COUNCILOR Dept. of Physics | sps@junix.ju.edu * and * jsavast@junix.ju.edu | NEWTON MIALING LIST Chemistry | savastan@pinet.aip.org * MAINTAINER *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* From CHEM8@vax.york.ac.uk Mon Feb 6 05:38:31 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id FAA20858; Mon, 6 Feb 1995 05:27:19 -0500 Via: uk.ac.york.vax; Sat, 4 Feb 1995 12:54:44 +0000 Date: Sat, 4 Feb 95 12:54 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Conf. proceedings help required about publishing Message-ID: <"leeman.yor.225:04.01.95.12.54.45"@york.ac.uk> Hi Netters, I would like some help/information concerning the publication of conference proceedings. I have looked unsuccessfully through CCL's archives, so will summarize any responses I receive. Firstly I presume there are two main ways of doing this - either using a Journal or a Publishing House. Other? What are the (dis)advantages of these choices? Refereeing? Cost? etc. I believe there are also two ways of producing such proceedings - Photographically (on pre-defined forms) or electronically. Other? Again, what are the (dis)advantages of these choices? Cost? etc. Concerning Journals, the topic of the conference in question is super-computing. So which Journals are suitable? I would like their title, preferebly e-mail address or phone, else FAX or postal address + the name of a person to contact. Similarly for Publishing Houses - I know Elsevier, North-Holland, D.Reidel, Plenum and Kluwer do this sort of thing. Other? And the above contact proceedure(s). I would be grateful if any/some of these firms contacted me. My postal and e-mail addresses + direct phone are in the header of this message. Any other tips, suggestions, things to beware of, 'musts' or general info. will be appreciated, Thanking you all, John Waite From lrbu00@xd88.kodak.com Mon Feb 6 08:37:23 1995 Received: from Kodak.COM for lrbu00@xd88.kodak.com by www.ccl.net (8.6.9/930601.1506) id IAA22289; Mon, 6 Feb 1995 08:20:45 -0500 From: Received: from euler.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA10292; Mon, 6 Feb 95 08:21:02 -0500 Reply-To: lrbu00@xd88.kodak.com Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.Kodak.COM:fox@fenris.ucsf.EDU id AA17851; Mon, 6 Feb 95 08:17:32 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA16360; Mon, 6 Feb 1995 08:03:50 -0500 Date: Mon, 6 Feb 1995 08:03:50 -0500 Message-Id: <9502060803.ZM17126@xd88.kodak.com> In-Reply-To: fox@fenris.ucsf.EDU (Thomas Fox) "CCL:Summary: DFT and H" (Feb 4, 7:00pm) References: <9502050300.AA17641@fenris.ucsf.EDU> X-Mailer: Z-Mail (3.0.0 15dec93) To: fox@fenris.ucsf.EDU (Thomas Fox) Subject: Re: CCL:Summary: DFT and H Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 I do not argue with the numbers that any arbitrary program produces, but how can they be meaningful when there is no exchange for a 1-electron system ? The only functional I know of that does this CORRECTLY is that of Colle & Salvetti who get exactly 0 for exchange and correlation, because they use a 2-particle density matrix. There may be others. I don't understand how anything else could be "correct". I will accept rebuttals gracefully. Regards John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From SUTJIANTO@cmt.anl.gov Mon Feb 6 09:37:35 1995 Received: from anlcmt.cmt.anl.gov for SUTJIANTO@cmt.anl.gov by www.ccl.net (8.6.9/930601.1506) id IAA22761; Mon, 6 Feb 1995 08:54:42 -0500 Date: Mon, 6 Feb 1995 7:54:33 -0600 (CST) From: Amin Sutjianto To: CHEMISTRY@ccl.net Message-Id: <950206075433.20226ace@cmt.anl.gov> Subject: Madelung constant for Li2O Hi Netters, Could you tell me the Madelung constant for the crystalline Li2O ? Please give me references if there are. Thank you very much. Amin From OSELLA@ch.unito.it Mon Feb 6 09:39:16 1995 Received: from SILVER.CH.UNITO.IT for OSELLA@ch.unito.it by www.ccl.net (8.6.9/930601.1506) id IAA22401; Mon, 6 Feb 1995 08:38:17 -0500 Date: Mon, 6 Feb 1995 14:41:15 +0100 (WET) From: OSELLA@ch.unito.it (The Mad Al-Chemists Group) Message-Id: <950206144115.1239@ch.unito.it> Subject: Impact Factor To: chemistry@ccl.net X-Vmsmail-To: SMTP%"chemistry@ccl.net" Dear netters, we are searching information on any up to date Impact Factor and Citation Index data. Is there any internet site? Many Thanks, Domenico Osella From gl@ccl.net Mon Feb 6 09:40:46 1995 Received: from coil for gl@ccl.net by www.ccl.net (8.6.9/930601.1506) id IAA22769; Mon, 6 Feb 1995 08:55:16 -0500 Received: by coil (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA15247; Mon, 6 Feb 95 14:53:36 +0100 From: "Gerald Loeffler" Message-Id: <9502061453.ZM15245@coil.mdy.univie.ac.at> Date: Mon, 6 Feb 1995 14:53:31 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: books on DFT-MD sought Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear Net-chemists, after doing "classical" Molecular Dynamics of solvated proteins I'm thinking about treating small parts of my proteins with Density Functional Calculations, while retaining the old MD force field for the rest of the system. Since my background is mostly in classical MD, I'm in desparate need of GOOD literature! So if you have any must-reads in mind, please share your knowledge with me! I'm thinking of books, but very thorough reviews would certainly be welcome, too! Thanx in advance, Gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry Email: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 Mail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria #include "fancy_ASCII_picture" #include "funny_statement" #include "standard_disclaimer" From WANG@IRBM.IT Mon Feb 6 10:38:52 1995 Received: from V1.IRBM.IT for WANG@IRBM.IT by www.ccl.net (8.6.9/930601.1506) id JAA23741; Mon, 6 Feb 1995 09:49:50 -0500 From: Date: Mon, 6 Feb 1995 15:50:59 +0100 (WET) To: chemistry@ccl.net CC: WANG@IRBM.IT Message-Id: <950206155059.12ed@IRBM.IT> Subject: Code for Isosurfaces Dear all, Could someone tell me where I may find the source code for converting numbers at 3-D grids into isosurfaces ? We do have a commercial package which can nicely do part of the job but not all. Thank you for your information. Bingze Wang e-mail: wang@irbm.it From mmccar@postman.essex.ac.uk Mon Feb 6 11:54:01 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.9/930601.1506) id LAA25210; Mon, 6 Feb 1995 11:02:23 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <06748-0@postman.essex.ac.uk>; Mon, 6 Feb 1995 12:01:39 +0000 From: Mccarron M Date: Mon, 6 Feb 95 11:30:52 GMT Message-Id: <18759.9502061130@solb1.essex.ac.uk> To: chemistry Subject: CHARRM mutation Does anybody know what the easiest way to mutate one amino acid residue into another. Is construction of a hybrid necessary or is there some way to tell CHARMM that one amino acid exists in the reactant and the other exists in the product similar to what you would do for indivdual atoms in a hybrid. Thanks Matthew McCarron e-mail mmccar@essex From SATYAM@vms.cis.pitt.edu Mon Feb 6 14:37:36 1995 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.9/930601.1506) id NAA28774; Mon, 6 Feb 1995 13:52:25 -0500 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #6609) id <01HMQC9BT174DK77S9@vms.cis.pitt.edu>; Mon, 06 Feb 1995 13:52:11 -0400 (EDT) Date: Mon, 06 Feb 1995 13:52:11 -0400 (EDT) Subject: Are there any drug-design Software Available ?? To: chemistry@ccl.net Message-id: <01HMQC9BUWPUDK77S9@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, We are interested in knowing the ftp'able or otherwise available softwares for Drug-Design ? I will summarize the responses..if I get any.. Satyam From jdurant@mephisto.ca.sandia.gov Mon Feb 6 14:41:49 1995 Received: from mephisto.ca.sandia.gov for jdurant@mephisto.ca.sandia.gov by www.ccl.net (8.6.9/930601.1506) id NAA28896; Mon, 6 Feb 1995 13:56:50 -0500 Received: by mephisto.ca.sandia.gov (931110.SGI/890607.SGI) (for chemistry@ccl.net) id AA04345; Mon, 6 Feb 95 10:56:48 -0800 From: jdurant@mephisto.ca.sandia.gov (Joe Durant) Message-Id: <9502061856.AA04345@mephisto.ca.sandia.gov> Subject: attractive/repulsive interactions To: chemistry@ccl.net Date: Mon, 6 Feb 1995 10:56:48 -0800 (PST) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 843 Hello! I am interested in analyzing attractive and repulsive interactions in H-atom transfer reactions, A-H-B, where A and B are doublets. I have looked at Perturbational MO Analysis, but it seems to be limited to closed shell systems, and pi-bonds. What I would like to do is to break the interaction down in analogy to the way BEBO does it, into the attractive A-H and H-B interactions, and a repulsive A-B interaction. Any pointers? I will summarize responses if there is interest. Joe -- ###################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9055 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 # ###################################################################### From jkshin@neon.sait.samsung.co.kr Mon Feb 6 18:37:26 1995 Received: from han.hana.nm.kr for jkshin@neon.sait.samsung.co.kr by www.ccl.net (8.6.9/930601.1506) id SAA03461; Mon, 6 Feb 1995 18:24:16 -0500 Received: from saitgw.Sait.Samsung.Co.KR by han.hana.nm.kr (4.1/KUM-0.1) id AA04098; Tue, 7 Feb 95 08:25:25 KST Received: from neon.sait.samsung.co.kr by saitgw.Sait.Samsung.Co.KR (4.1/SMI-4.1) id AA06099; Tue, 7 Feb 95 08:19:57 KST Received: by neon.sait.samsung.co.kr (931110.SGI/920502.SGI) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA19153; Tue, 7 Feb 95 08:21:02 +0900 Date: Tue, 7 Feb 95 08:21:02 +0900 From: jkshin@neon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9502062321.AA19153@neon.sait.samsung.co.kr> To: -v@neon.sait.samsung.co.kr, chemistry@ccl.net Subject: Polyatomic surface reactions Hi I am trying to model the chemical reactions of some polyatomic gases on the polysilicon surface. Firstly, I want to calculate the reaction constants of those reactions and I found that the QCPE program "Polyrate" would fit this purpose. Is there any other possibilities? And does anybody know the contact point(fax or e-mail) of Donald G. Truhlar who is one of authors of "Polyrate"? Any suggestions shall be greatly appreciated. Bye. Jai K. Shin Senior research scientist, Samsung Adv. Inst. of Tech. jkshin@radon.sait.samsung.co.kr From jkl@ccl.net Mon Feb 6 19:10:15 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id RAA03178; Mon, 6 Feb 1995 17:50:08 -0500 Date: Mon, 6 Feb 1995 17:50:08 -0500 From: Jan Labanowski Message-Id: <199502062250.RAA03178@www.ccl.net> To: chemistry@ccl.net Subject: support the CCL, once again Cc: jkl@ccl.net Dear Netters, Since I received many questions concerning the contents/form of the letters for support of the Comp. Chem. List, I need to clarify some things. 1. What it should contain? It is up to you... I believe you may just write why the list is useful, and why it should be continued and improved in the future. You can address it to me, or to "To whom it may concern", whichever form is more convenient to you (but send them to me by regular mail or FAX). 2. Who should send it? All of you who think that the list is worth supporting. I mean ALL, in whatever country, organization, or position you are. You see... It is also a reality check for me... If I do not have a broad support, then why bother? If you cannot find time to write the letter, and if I get only a handful of them, you exercised your right to vote. If for some reason, you need a lengthy process of intraorganizational approval for such a letter, just write it as a private person to cut the red tape. 3. When to send it? As soon as possible. Primo, if you do not write it now, you will not write it... Secundo, I need them soon. I assume that mail from overseas needs some time to get here, but I can wait weeks, not months. If some of you missed my original appeal, it can be retrieved by sending a message: select chemistry cd ccl-proposal ls message.txt quit to MAILSERV@ccl.net Thank you for you attention. As always, I am thankful for suggestions and comments which you sent me via e-mail. I understand that the proposal is getting more and more out of date every day (it was written a year ago). I would appreciate your comments on how to make it better. Some ideas in the proposal are not really mine, but came from the CCL subscribers at that time. The progress is so fast that it is difficult to have a written document current for more than a month. My general idea (as you guessed right from the proposal) is to accomodate the widest possible audience of CCL, since diversity of technical means and expectations is really very wide. But at the same time, I want to provide means for creating "personal profile" for each subscriber which can be changed as you wish at any time via some simple interface. But this is obviously quite a substantial software and managerial project (believe me, I know what is out, and what is not there yet...). The summer survey of the list provided me with a lot of insight. Thank you again for responding. The results of the survey will be made available soon. I really read all your comments and think about them, even if I cannot answer right away (or do not answer them at all -- in case when it is just a comment, not a question). Jan 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 From vazquez@iqm.unicamp.br Mon Feb 6 20:37:31 1995 Received: from kalypso.iqm.unicamp.br for vazquez@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id TAA04669; Mon, 6 Feb 1995 19:58:40 -0500 Received: (from vazquez@localhost) by kalypso.iqm.unicamp.br (8.6.9/8.6.9) id WAA01070 for CHEMISTRY@ccl.net; Mon, 6 Feb 1995 22:54:42 -0200 From: Pedro A M Vazquez Message-Id: <199502070054.WAA01070@kalypso.iqm.unicamp.br> Subject: Re: CCL:Code for Isosurfaces To: CHEMISTRY@ccl.net Date: Mon, 6 Feb 1995 22:54:39 -0200 (EDT) In-Reply-To: <950206155059.12ed@IRBM.IT> from "WANG@IRBM.IT" at Feb 6, 95 09:09:09 pm Organization: Instituto de Quimica Unicamp X-Mailer: ELM [version 2.4 PL24] Content-Type: text Content-Length: 389 Hello Look for Isovis and XDataSlice in ftp.ncsa.uiuc.edu:/Unix Pedro WANG@IRBM.IT said: > > Dear all, > > Could someone tell me where I may find the source code for converting > numbers at 3-D grids into isosurfaces ? We do have a commercial > package which can nicely do part of the job but not all. Thank you > for your information. > > Bingze Wang > e-mail: wang@irbm.it > From rvgloss@criba.edu.ar Mon Feb 6 22:37:27 1995 Received: from sic4.cnea.edu.ar for rvgloss@criba.edu.ar by www.ccl.net (8.6.9/930601.1506) id VAA05466; Mon, 6 Feb 1995 21:39:02 -0500 Received: from criba.edu.ar by sic4.cnea.edu.ar with smtp (Smail3.1.28.1 #1) id m0rbfok-00040OC; Mon, 6 Feb 95 23:38 GMT-3:00 Received: by criba.edu.ar (4.1/SMI-4.1) id AA29168; Mon, 6 Feb 95 23:37:24 WDT Date: Mon, 6 Feb 95 23:37:24 WDT From: rvgloss@criba.edu.ar (Daniel Glossman) Message-Id: <9502070237.AA29168@criba.edu.ar> To: chemistry@ccl.net Subject: Kohn-Sham programa Dear netters, does anybody know about a FTPable LDA Kohn-Sham atomic program? Thn\anks in advance Dr. Daniel Glossman rvgloss@arcriba.edu.ar From helden@gaucho.ucsb.edu Mon Feb 6 22:40:07 1995 Received: from hub.ucsb.edu for helden@gaucho.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id VAA05528; Mon, 6 Feb 1995 21:46:47 -0500 Received: from gaucho.ucsb.edu by hub.ucsb.edu; id AA10405 sendmail 4.1/UCSB-2.1-sun Mon, 6 Feb 95 18:46:41 PST for CHEMISTRY@ccl.net Received: by gaucho.ucsb.edu (AIX 3.2/UCB 5.64/4.03) id AA39685; Mon, 6 Feb 1995 18:39:20 -0800 From: helden@gaucho.ucsb.edu (Gert von Helden) Message-Id: <9502070239.AA39685@gaucho.ucsb.edu> Subject: Semiempirical vs. empirical force fields? To: CHEMISTRY@ccl.net Date: Mon, 6 Feb 1995 18:39:18 +22305458 (PST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1161 Hi there, I have a question regarding the quality of semiempirical vs. empirical methods. We have been annealing small polyptides (9 amino acids, 150 atoms) using the amber force field by repeatedly running MD at high temp., cooling it down and finally minimizing it. The standard amber ff has been used with a constant dielectric of 1. We then take the lowest energy conformations and reoptimize them with PM3. The conformational changes are quite large with the PM3 geometries being somewhat more open. Also, the relative energies change a lot. In some situations conformation A is lower then B by 7 kcal/mol using amber but B is lower that A by 5 kcal/mol using PM3. We would like to compare the calculations to gas phase experiments. So which method is better and more reliable? Thanks, Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++