From UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Wed Jun 16 04:14:36 1993 Date: Wed, 16 Jun 1993 08:14:36 -0400 (EDT) From: UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Subject: Info Soft delivery outside USA To: chemistry@ccl.net Message-Id: <01GZFJDUWRCY9GVEM5@phem3.acs.ohio-state.edu> E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-41-17 (lab);44-27-38-66(University) e-mail UDIM018 at FRORS31.BITNET I am making a general inquiry to those supplying software either free or purchased. Please reply privately. 1. CLASS: FREE This is supplied either by individuals by request or through ftp. The latter is uncontrolled in the sense that with the nets running internationally it can be received by anyone. Most people will copywrite free soft to prevent subsequent commerical exploitation without their benefiting. Question: Are you aware of any restrictions to that exportation with regard to specific countries? 2. CLASS: PAID This class is under copywrite and purchasers can not redistribute. More expensive softs which have a licensing agreement. A. Off the shelf Soft from Computer Stores, Mail order etc. This is copywrited and generally available outside the USA. If there is a restriction to exportation to still another country it is difficult to control. But what are the Department of Commerce's restrictions? B. Licensed Soft I know that exportation of licensed soft is restricted. I do not have a list of the nations under this restriction, but Cuba is one of them. There is an embargo against that country but the information sofar supplied me by the US Department of Commerce does not refer to a specific law and is vague in its own bureaucratic way as to what exceptions exists but clearly written in a manner to instill maximum prudence and encourgage software manufacturers to stay clear. If you have any information on dos and don'ts with regard to specific countries I would appreciate you contacting me privately. Note that American based scientific journals and computer magazines are legally being delivered to Cuba, but at what stage the NO occurs is not clear. Cubans visiting European Countries use US based soft they can not obtain in Cuba. I am not sure that is even legal under US law or what restrictions are imposed in licensing agreements, some of which are of dubious legality outside the USA unless specifically written to satisfy the legal requirements of the countries in which they are sold. Access to CRAYs and other advance machines is restricted. In such cases, many of us adhere to a sort of international honor code in not using pirated software nor aiding or abeting this practice. My inquiry here is in that sense with the idea that there should not be any restriction to the distribution of generally available software to the international community which is cited in scientific reviews. The general principle behind any scientific publication is that there is a sufficient description such that another person can repeat and verify the work. My inquiry has as a goal to determine what possible conflict occurs between the control practices of the US Government and expectations of the international scientific community with regard to the availability of software. From CLETNER@DESIRE.WRIGHT.EDU Sun Jun 16 04:22:29 1993 Date: 16 Jun 1993 08:22:29 -0400 (EDT) From: CLETNER@DESIRE.WRIGHT.EDU Subject: Full time course kinetics To: chemistry@ccl.net Message-Id: <01GZFTTLSE5E000RXJ@DESIRE.WRIGHT.EDU> Hi all, I'm not sure if this is exactly appropriate for this board but I'll give it a try. Is anybody out there doing full time course kinetics? I am starting to get programs to do the data analysis/collection and am interested any any information I can get. Thanks Chuck Charles Letner Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu For those in the MAC/PC debate: It's not the machine, it's the user. From roberto@demilo.boston.sgi.com Wed Jun 16 04:14:10 1993 Message-Id: <9306161214.AA01701@demilo.boston.sgi.com> To: Bingze Wang Subject: Re: MOPAC.6 migration on SGI INDIGO Date: Wed, 16 Jun 93 08:14:10 EDT From: Roberto Gomperts Your message dated: Tue, 15 Jun 93 20:24:23 EST |> |> Dear netters: |> |> We're trying to port MOPAC 6 from a SUN 4/490 to an SGI Indigo. The |> program runs but the energies for molecules with more than one heavy |> atoms are screwed up. |> |> Anybody seen this before? |> |> Bingze Wang |> |> --- Dear Dr Wang, You can order the Mopac 6.0 version for SGI from QCPE. The supplied Makefiles support most of the current SGI platforms including the Indigo line. Best regards, -- Roberto Roberto Gomperts roberto@sgi.com phone: (508) 562 4800 Fax: (508) 562 4755 "Gracias a la vida, que me ha dado tanto ..." Violeta Parra From noy@tci002.uibk.ac.at Wed Jun 16 19:14:43 1993 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9306161614.AA37511@tci002.uibk.ac.at> Subject: Reacfield and Ewald To: chemistry@ccl.net Date: Wed, 16 Jun 1993 18:14:43 +0100 (DFT) Dear Netters, I have some questions concerning the long range interaction calculation in computer simulations ( MC and MD ). Can anybody tell me the advantage and disadvantage of the use of Ewald summations and Reaction-field method ? How to select which one suitable for a particular system ? Thanks in advance, Teerakiat ---------------------------------------------------------------------------- NAME : Teerakiat Kerdcharoen (NOY) ADDRESS : Theoretische Chemie Innrain 52 a, A-6020, Austria E-MAIL : noy@tci.uibk.ac.at,noy@tci2.uibk.ac.at,c72454@cx.uibk.ac.at c72454@u1.uibk.ac.at, c70854@tci3.uibk.ac.at noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Thailand ) RESEARCH : Computer Aided Molecular & Material Designs / CAMD ----------------------------------------------------------------------------- When you want to forget, you will always remember. When you want to remember, you will always forget. From wolpert@neon.chem.utk.edu Wed Jun 16 10:52:19 1993 Date: Wed, 16 Jun 93 14:52:19 EDT From: wolpert@neon.chem.utk.edu (Edward Wolpert) Message-Id: <9306161852.AA01835@neon.chem.utk.edu> To: CHEMISTRY@ccl.net Subject: Enzyme structures wanted... I have a basic question for people who have access to the cambridge database. I run Sybyl 6.0 at UTK, and several of the users here would like to know if there exists any enzymes related to cell signaling. If there are any people with access to enzyme structures of this type, please email me back. Mainly, I'm looking for sybyl mol2 files that are in the public domain. Thanks, Edward Wolpert wolpert@neon.chem.utk.edu From wolpert@neon.chem.utk.edu Wed Jun 16 10:52:27 1993 Date: Wed, 16 Jun 93 14:52:27 EDT From: wolpert@neon.chem.utk.edu (Edward Wolpert) Message-Id: <9306161852.AA01838@neon.chem.utk.edu> To: CHEMISTRY@ccl.net Subject: Enzyme structures wanted... I have a basic question for people who have access to the cambridge database. I run Sybyl 6.0 at UTK, and several of the users here would like to know if there exists any enzymes related to cell signaling. If there are any people with access to enzyme structures of this type, please email me back. Mainly, I'm looking for sybyl mol2 files that are in the public domain. Thanks, Edward Wolpert wolpert@neon.chem.utk.edu From d3f012@pellucidar.pnl.gov Wed Jun 16 04:45:16 1993 Date: Wed, 16 Jun 93 11:45:16 -0700 From: d3f012@pellucidar.pnl.gov Subject: Followup on Argus 1.2 To: chemistry@ccl.net Message-Id: <9306161845.AA10417@pellucidar.pnl.gov> The new version contains executables for Sun4, IBM RS/6000, HP, and SGI. I no longer export a DECstation version since I don't have access to this platform anymore. Also, I no longer have access to a Cray YMP. Therefore, I'm sorry to report that I could not include a YMP version in the 1.2 release. Any kind benefactors want to give me a YMP account? Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. 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. ************************************************************************** From d3f012@pellucidar.pnl.gov Wed Jun 16 04:40:57 1993 Date: Wed, 16 Jun 93 11:40:57 -0700 From: d3f012@pellucidar.pnl.gov Subject: Argus 1.2 released To: chemistry@ccl.net Message-Id: <9306161840.AA10379@pellucidar.pnl.gov> I've just placed a new minor release of Argus (version 1.2) in the anonymous ftp directory. Look at the "Changes" file found in the tarfile for details of the modifications. Instructions for obtaining Argus via anonymous ftp are included below. Argus is an electronic structure code; mainly for semi-empirical model Hamiltonians. Argus is available at no cost via anonymous ftp. The ftp site is pnlg.pnl.gov (130.20.64.11). Look in the argus directory. Make sure you download and read the README file first. Argus is Copyrighted and Licensed software. All you have to do is read the files License.doc and Copyright, and agree with the conditions contained in those documents. Feel free to contact me with problems/suggestions. Enjoy, Mark. ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 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. ************************************************************************** ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. 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. ************************************************************************** From yama@molbio.ethz.ch Wed Jun 16 23:20:27 1993 From: Bernhard Anton Pabsch Date: Wed, 16 Jun 93 21:20:27 +0200 Message-Id: <9306161920.AA17449@noldi> To: chemistry@ccl.net Subject: Scarecrow with Gromos Hello Netters, here is a question for the experienced Scarecraw user: ----------- you looked at wiggling molecules generated with Gromos if so what exactly did you feed Scarecraw to do that the binary trajectory coordinates (tape12) the binary trajectory velocities (tape13) or any formatted stuff? i have tried a few input possibilities what i get after reading in nicely the formatted structure file is either nothing in case of the formatted tape12 or a wild chaos of too big lines whirling over the screen in case of binary tape12 or tape13 surely i am doing something wrong but i have checked the obvious things so SOS OSO SOS Thanks for listening bap-man ----------------------------------------------------------------------------- Bernhard A. Pabsch yama@molbio.ethz.ch Laboratorium fuer organische Chemie MOM_10@CZHETH5A.bitnet ETH Hoenggerberg (HPM G32) Tel. ++41 1 377 34 89 CH-8093 Zuerich/Switzerland Fax ++41 1 372 00 53 ----------------------------------------------------------------------------- From jle@world.std.com Wed Jun 16 13:59:28 1993 Date: Wed, 16 Jun 1993 17:59:28 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199306162159.AA03745@world.std.com> To: chemistry@ccl.net Subject: MM3 missing params and question Folks... I've noticed that there are several parameters that have been published in MM3 articles that are not included in the set provided with the MM3 program. Specifically, several parameters in J. Am. Chem. Soc. 114,6120(1992): Torsional 58-75-56-58 (listed twice, with different values) Electronegativity correction 5-56 56-end 58 connected 5-56 56-end 75 connected Are these missing from the program's set, or improper entries/typos in the article? On another front, as computers get significantly faster, has anybody (particularly those in the author community) given any thought to including a non-bonded interaction cutoff mechanism in MM3 (or MM2)? Since 500+ atoms can now easily be run, the time-consumption of the non-bonded term is getting significant. Thanks in advance! Joe Leonard jle@world.std.com From PAULOFBG@VORTEX.UFRGS.BR Wed Jun 16 14:05:10 1993 Date: Wed, 16 Jun 1993 17:05:10 -0300 From: PAULOFBG@VORTEX.UFRGS.BR Subject: CCD e-mail To: chemistry@ccl.net Message-Id: <01GZGC4CYXQE0008SD@vortex.ufrgs.br> HI!! could anyone send me the CCD (Cambridge structural database) e-mail? Thanks in advance PAULO FERNANDO From PAULOFBG@VORTEX.UFRGS.BR Wed Jun 16 14:19:34 1993 Date: Wed, 16 Jun 1993 17:19:34 -0300 From: PAULOFBG@VORTEX.UFRGS.BR Subject: CCD and BMRB e-mail To: chemistry@ccl.net Message-Id: <01GZGCID1UOY0008SD@vortex.ufrgs.br> HI!! Can anybody tell me the FTP adress of : Cambridge Structural Database ( CCD ) BioMagResBank ( BMRB ) Thanks in advance PAULO FERNANDO