From owner-chemistry@ccl.net Thu Oct 12 01:54:57 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id BAA18452; Thu, 12 Oct 1995 01:50:30 -0400 Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by bedrock.ccl.net (8.6.10/950822.1) id BAA02956; Thu, 12 Oct 1995 01:50:20 -0400 Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.6.10/8.6.9) id HAA15744 for chemistry@ccl.net; Thu, 12 Oct 1995 07:49:52 +0200 From: Jussi Eloranta Message-Id: <199510120549.HAA15744@voimax.voima.jkl.fi> Subject: Re: CCL:PC as a file server? To: chemistry@ccl.net Date: Thu, 12 Oct 1995 07:49:51 +0200 (EET) In-Reply-To: from "Craig Taverner" at Oct 11, 95 06:26:16 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1380 >All networking between linux and other unix machines seems to work very >well (we use extensive nfs and remote X11). If your clients are only >unix machines, then unix should be your server of choice. If your >clients are LAN machines (eg. windows for workgroups). Linux can still >be used (as we have with Samba). > Actually Linux can be server for: 1) nfs (unix) 2) samba (m$ windows) 3) Macintosh network (CAP) 4) Recently someone wrote Netware fileserver application for Linux (called linuxware). We are experimenting with Linux fileserver with XFS (shareware NFS and printing client for MSDOS). The results this far are very good! NCSA telnet & ftp and trumpet winsock can be used with xfs too. It is amazing that single 486/80MHz/16mb can serve our whole laboratory and still drive our old Varian EPR spectrometer, act as our www server and serve 2 - 5 simultanous users (running X applications) at the same time! So why pay considerable amount of money to get these "fancy" systems that usually don't even work well ;-) Linux is free. If one wants to do X windows programming then the lack of Motif may be a problem. The commerical Motif for Linux is about $99 (there is a free port developing called lesstif or something like that). Jussi Eloranta ps. All this stuff is available via non. ftp from sunsite.unc.edu:/pub/Linux and ftp.funet.fi:/pub/Linux From trunec@elanor.sci.muni.cz Thu Oct 12 04:24:59 1995 Received: from aragorn.ics.muni.cz for trunec@elanor.sci.muni.cz by www.ccl.net (8.6.10/950822.1) id EAA20029; Thu, 12 Oct 1995 04:20:13 -0400 Received: from elanor.sci.muni.cz by aragorn.ics.muni.cz with SMTP id AA09356 (5.67a8/IDA-1.4.4 for ); Thu, 12 Oct 1995 09:19:45 +0100 Received: from [147.251.76.21] (brablec.sci.muni.cz [147.251.76.21]) by elanor.sci.muni.cz (8.7/8.7) with SMTP id JAA27529 for ; Thu, 12 Oct 1995 09:19:54 +0100 (MET) From: "David Trunec" Date: Thu, 12 Oct 95 09:24:41 CST Message-Id: <62.trunec@elanor.sci.muni.cz_POPMail/PC_3.2.2> X-Popmail-Charset: English To: chemistry@www.ccl.net Subject: potential between Ar^+ and He Hello, I would like to calculate the cross section for elastic collisions between Ar^+ ion and He neutral atom. I need for this to know the potential U(r) between Ar^+ and He. I tried to use the following job %Chk=ArHe # UMP2/6-31G(d) SCAN SCF=DIRECT NOSYM ArHe calculation 1 2 Ar1 He1 Ar1 arhe arhe 2.0 30 0.2 under Gaussian 92. The result is wrong, the potential does not agree with the potential derived from scattering experiment and from asymptotic relations. Could anybody tell me how to calculate this potential ? Thanks, David Dr. David Trunec Dep. of Physical Electronics Faculty of Science Masaryk University Kotlarska 2 611 37 Brno Czech Republic E-mail trunec@sci.muni.cz Fax: +42-5-41211214 Tel: +42-5-41129430 From gl@coil.mdy.univie.ac.at Thu Oct 12 05:55:06 1995 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.6.10/950822.1) id FAA21449; Thu, 12 Oct 1995 05:53:23 -0400 Received: by coil.mdy.univie.ac.at (940816.SGI.8.6.9/930416.SGI.AUTO) id KAA26605; Thu, 12 Oct 1995 10:52:15 +0100 From: "Gerald Loeffler" Message-Id: <9510121052.ZM26603@coil.mdy.univie.ac.at> Date: Thu, 12 Oct 1995 10:52:04 +0100 In-Reply-To: Albert PALOMER "CCL:VIJAIE '95 at Barcelona" (Oct 11, 5:42pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Albert PALOMER , chemistry@www.ccl.net Subject: Re: CCL:VIJAIE '95 at Barcelona Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii That's exactly what I thought, too! On Oct 11, 5:42pm, Albert PALOMER wrote: > Subject: CCL:VIJAIE '95 at Barcelona > Hola Alicia, ja he vist que habies enviat el mail a www.ccl.net. > Moltes gracies i fins d'aci a una estona. > Albert > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: guest04@montsia.cesca.es > -- Original Sender From: Address: guest04@montsia.cesca.es > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >-- End of excerpt from Albert PALOMER -- Gerald Loeffler PhD student in Theoretical Biochemistry EMail: gl@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 SMail: 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 owner-chemistry@ccl.net Thu Oct 12 09:40:08 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA24253; Thu, 12 Oct 1995 09:29:52 -0400 Received: from europa.chem.uga.edu for robert@europa.chem.uga.edu by bedrock.ccl.net (8.6.10/950822.1) id JAA07143; Thu, 12 Oct 1995 09:29:50 -0400 Received: (from robert@localhost) by europa.chem.uga.edu (8.6.12/8.6.9) id JAA00885; Thu, 12 Oct 1995 09:29:43 -0400 Date: Thu, 12 Oct 1995 09:29:43 -0400 (EDT) From: Jenn-Huei Lii To: Cheol Choi cc: chemistry@ccl.net Subject: Re: CCL:G:Transform to redundant internal Coord? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Cheol, In order to overcome your problem, you can use a technique called "Generalized Inverse". Please see the following references. 1. L. B. Thomas and L. O. Patrick in "Generlized Inverse Matrices,"; Wiley-Interscience; New York, N. Y. (1957) 2. R. Fletcher, Computer Journal, 10, 392 (1968) -Robert On Wed, 11 Oct 1995, Cheol Choi wrote: > Dear CCLers. > > I have a simple question. > > First of all, let me define some terms. > > X : cartesian displacement coordinate > R : internal displacement coordinate > If I have N atoms, then I would have 3N of cartesians. > Also if I define nun-redundant internal coordinate, I would have > 3N-6 or 5 internal coordnate. > > There is A matrix which transform R into X. > X=A*R > > In general, one could get the inverse (since A is not square matrix, > this is not exactly inverse matrix) of A like > (Let me use B for inverse of A) > > A=transpose(B)*inverse(B*transpose(B)) > (This formula can only be used for direction independent quantities, such as > energy and only hold for nun-redundant internal coordinate.) > > > Now, my problem is this. > If I have redundant internal coordinate,which means that there are (is) > singularities in B matrix, I could not inverse the B*transpose(B). > Therefore I couldn't get the A matrix form B matrix. > > Gaussian94 uses the redundant internal coordinate to optimize geometry. > It actually calculates the hessian matrix in redundant internal > coordinate and also gives us the cartesian hessian matrix. So there might > be a transformation matrix between these coordinates. > > Please, let me konw how to get such a transformation matrix. > > Thank you in advance. > > > Cheol Ho Choi > > Georgetown Univ. > From 94970459@vax1.dcu.ie Thu Oct 12 08:23:12 1995 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.6.10/950822.1) id IAA22921; Thu, 12 Oct 1995 08:21:31 -0400 Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01HWCRF7TO7K8X0BKB@vax1.dcu.ie>; Thu, 12 Oct 1995 13:20:48 GMT Date: Thu, 12 Oct 1995 13:20:48 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Gibbs Free Energy To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@www.ccl.net Message-id: <01HWCRF7UQSI8X0BKB@vax1.dcu.ie> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"hyperchem@hyper.com", IN%"support@hyper.com" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Status: RO Hi, I am a user of HyperChem and I am interested in calculating Gibb's free energy of formation of complexes formed between calixarenes and neutral guests such as toluene. In the past somebody mentioned that while HyperChem cannot do this directly, a macro in excel could be written. What exactly should I get the macro to do? Secondly, while I know that the energies obtained in a molecular mechanics calculation have no absolute meaning, would the difference in energies of two optimised conformations of the same complex have any meaning? If so, what kind of energy are we talking about? Thirdly, is it possible to determine the contribution to each of the above energies made by the different types of interaction (van der Waals, pi-pi) between the host and the guest? Kind Regards, Paddy. Paddy Kane Dublin City University 94970459@vax1.dcu.ie From fgonzale@lauca.usach.cl Thu Oct 12 12:40:06 1995 Received: from lauca.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.6.10/950822.1) id MAA29975; Thu, 12 Oct 1995 12:25:17 -0400 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.9/8.6.12) id MAA22871 for chemistry@www.ccl.net; Thu, 12 Oct 1995 12:26:33 -0300 From: Fdo Danilo Gonzalez Nilo Message-Id: <199510121526.MAA22871@lauca.usach.cl> Subject: polyelectrolyte? To: chemistry@www.ccl.net Date: Thu, 12 Oct 95 12:26:32 ADT Hi all! Has anyone some references about molecular simulation of sintetic polyelectrolyte????? Im waiting your response!! thanks!! Danilo/// -- ************************************************************************* Fernando Danilo Gonzalez N. |\/| /-\ | /_ /` | | | /`\ |`)* Facultad de Quimica y Biologia | | \-/ |_ |_, |_, \_/ |_ | | | \* dpto. de Ciencias Quimicas |\/| /-\ |\ /_ | | |\ | /` * universidad de Santiago de Chile | | \-/ |/ |_, |_ | | \| |_)* casilla 307, Santiago-2, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 *************************************************************************x From owner-chemistry@ccl.net Thu Oct 12 16:25:08 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id QAA06290; Thu, 12 Oct 1995 16:14:33 -0400 Received: from lynx.csn.net for craig@SoftShell.com by bedrock.ccl.net (8.6.10/950822.1) id QAA08623; Thu, 12 Oct 1995 16:14:31 -0400 Received: from zazu.softshell.com ([204.132.165.27]) by lynx.csn.net (8.6.12/8.6.9) with SMTP id OAA12278 for ; Thu, 12 Oct 1995 14:14:29 -0600 Message-ID: Date: 12 Oct 1995 14:12:27 -0700 From: "Craig Shelley" Subject: 3D Structure Files To: chemistry@ccl.net X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time: 2:10 PM OFFICE MEMO 3D Structure Files Date: 10/12/95 Many months ago I recall someone posting to this list about a database of chemical structures with 3D coordinates. I cannot find that reference. I would like to know any sources (ftp sites, etc.) with free (public domain) chemical structures with 3D coordinates - inorganic or organic. Send e-mail to me, Craig Shelley (craigs@softshell.com) and I will summarize to the list. Thanks. From dan@sage.syntex.com Thu Oct 12 16:37:19 1995 Received: from sage.syntex.com for dan@sage.syntex.com by www.ccl.net (8.6.10/950822.1) id QAA06281; Thu, 12 Oct 1995 16:14:29 -0400 Received: by sage.syntex.com (950215.SGI.8.6.10/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id NAA15389; Thu, 12 Oct 1995 13:13:40 -0700 From: dan@sage.syntex.com (Dr. Daniel L. Severance) Message-Id: <9510121312.ZM15387@sage.syntex.com> Date: Thu, 12 Oct 1995 13:12:23 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: QSAR software for combinatorial chemistry Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We are looking for software to fulfill the following requirements. Any help is appreciated! Combinatorial Libraries <-> QSAR Analysis. Interfacing the tracking, robotic screening and data collection of combinatorial libraries with QSAR software is a difficult task. In many established companies, the robotic equipment is already in place and generates screening data in the form of Oracle or Excel tables or the like. The structural information may be available in a 2D format such as a MACCS.sd file. We are not aware of any efficient and elegant solutions to generating QSAR data, which would be applicable to large combinatorial libraries and would not require significant changes to the existing equipment or statistical analysis software. Such a solution would allow for the painless clustering of compounds and the analysis of pharmacophore features within the clusters in an automated way. We would be interested in hearing about approaches and solutions (partial or complete) to this problem. Thanks! -- Dr. Daniel L. Severance dan@sage.syntex.com Staff Researcher Work phone: (415) 354-7509 Roche Bioscience (formerly Syntex) Home phone: (415) 969-5818 R6W-002 Fax (Work): (415) 354-7363 3401 Hillview Ave Palo Alto, CA 94303 From owner-chemistry@ccl.net Thu Oct 12 18:55:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA09396; Thu, 12 Oct 1995 18:42:43 -0400 Received: from gusun.acc.georgetown.edu for SUNDIUS@phcu.helsinki.fi by bedrock.ccl.net (8.6.10/950822.1) id SAA09922; Thu, 12 Oct 1995 18:42:38 -0400 Received: from LUMO.helsinki.fi by gusun.acc.georgetown.edu; (5.x/1.1.8.2/6Jan9518:19pm) id AA27208; Thu, 12 Oct 1995 18:38:05 -0400 Received: from phcu.helsinki.fi by phcu.helsinki.fi (PMDF V4.3-13 #1) id <01HWDD1OJ4MOM9MS0Z@phcu.helsinki.fi>; Fri, 13 Oct 1995 00:42:27 +0200 (EET) Date: Thu, 12 Oct 1995 23:40:12 +0200 (EET) From: Tom Sundius U of Helsinki +358 0 1918339 Subject: Re: CCL:G:Transform to redundant internal Coord? In-Reply-To: Your message dated "Wed, 11 Oct 1995 18:19:03 -0400 (EDT)" To: Chemistry@ccl.net, choic@gusun.acc.georgetown.edu Message-Id: <01HWDFAGIGTYM9MS0Z@phcu.helsinki.fi> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Cheol Choi had a matrix problem: > There is A matrix which transform R into X. > X=A*R > In general, one could get the inverse (since A is not square matrix, > this is not exactly inverse matrix) of A like > (Let me use B for inverse of A) > A=transpose(B)*inverse(B*transpose(B)) > (This formula can only be used for direction independent quantities, such as > energy and only hold for nun-redundant internal coordinate.) This problem occurs in chemistry for instance when one tries to invert the transformation between cartesian and internal displacement coordinates: R = BX. If B is rectangular, this can be done by multiplying both sides of the equation on the left by the transpose of B. If the inverse of B*transpose(B) exists, one gets the above expression for A. Since A satifies the equation BA = I, it is actually a right inverse of B (also called a pseudo-inverse or general inverse). This pseudo-inverse can, for instance, be used when transforming force constant matrices expressed in cartesian coordinates into internal coordinates. This was shown, for instance, in a paper by Collier (W.B. Collier, J. Chem. Phys. 88, 7295 (1988)). Generalized inverses have also been used in several papers by Peter Pulay (see, for instance, P.Pulay and G. Fogarasi, J. Chem. Phys. 96, 2856 (1992)). Many text-books have chapters on generalized inverses, as for instance Stephen Barnett: Matrices, Methods and Applications (Oxford Applied Mathematics and Computing Science Series) Oxford 1990. > Now, my problem is this. > If I have redundant internal coordinate,which means that there are (is) > singularities in B matrix, I could not inverse the B*transpose(B). > Therefore I couldn't get the A matrix form B matrix. This is a well-known problem. In a chapter in "Generalized Inverses and Applications" ed. by M. Zuhair Nashed, Academic Press (1976), B. Noble discusses several methods for computing the generalized inverse. He gives as an example the rectangular matrix 1 1 1 A = 1 1+e 1-e where e is a small number. If the generalized inverse is calculated according to the above formula, it is easy to get A*transpose(A) calculated as 3 3 3 3 because of roundoff, and then it cannot be inverted. As Noble points out, this problem can be solved, for instance, by LU decomposition of the A matrix. Another method to compute the pseudo-inverse if the matrix is almost singular is to use singular value decomposition (SVD), which is much discussed in the book: W.H. Press, B.P. Flannery, S.A. Teukolsky and W.T. Vetterling, Numerical Recipes (Cambridge University Press, 1986). > Gaussian94 uses the redundant internal coordinate to optimize geometry. > It actually calculates the hessian matrix in redundant internal > coordinate and also gives us the cartesian hessian matrix. So there might > be a transformation matrix between these coordinates. Yes, see the paper by Collier, and also papers by Pulay. -T. Sundius- sundius@phcu.helsinki.fi From owner-chemistry@ccl.net Thu Oct 12 10:43:04 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA26994; Thu, 12 Oct 1995 10:43:03 -0400 Received: from nessie.mcc.ac.uk for darryl@om3.ch.umist.ac.uk by bedrock.ccl.net (8.6.10/950822.1) id KAA22282; Thu, 12 Oct 1995 10:43:01 -0400 Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Thu, 12 Oct 1995 15:42:35 +0100 Received: by om3.ch.umist.ac.uk (940406.SGI/) for chemistry%ccl.net@nessie.mcc.ac.uk id AA14197; Thu, 12 Oct 95 15:59:24 +0100 Date: Thu, 12 Oct 1995 15:59:24 +0100 (BST) From: Darryl Ellson Subject: MELDF Program To: chemistry@ccl.net Message-Id: I would be interested in hearing from users of the MELDF program. Particularly it's applicability for the calculation of anisotropic coupling constants, also it's ease of use and system requirements etc. Many Thanks. Darryl A. Ellson. |_o_| []=(_)=[] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD Molecular Simulation & Design Laboratory Tel: 061-236-3311 x4476 Fax: 061-236-7677 E-mail: darryl@trigger.ch.umist.ac.uk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~