From Poehlmann@rus.uni-stuttgart.de Fri May 5 05:48:33 1995 Received: from noc.BelWue.DE for Poehlmann@rus.uni-stuttgart.de by www.ccl.net (8.6.10/930601.1506) id FAA18219; Fri, 5 May 1995 05:37:02 -0400 Received: from awshp.rus.uni-stuttgart.de by noc.BelWue.DE with SMTP id AA01723 (5.65c8/IDA-1.4.4 for ); Fri, 5 May 1995 11:36:43 +0200 Received: by awshp.rus.uni-stuttgart.de (931110.SGI/BelWue-1.0SG(subsidiary)) (for poehlmann@rus.uni-stuttgart.de) id AA19493; Fri, 5 May 95 11:36:41 +0200 Message-Id: <9505050936.AA19493@awshp.rus.uni-stuttgart.de> Subject: powder diffraction cell data To: CHEMISTRY@ccl.net Date: Fri, 5 May 95 11:36:41 DST From: "Dr. Heinz Poehlmann" X-Mailer: ELM [version 2.3 PL11] Hi there, we are looking for a little program generating possible cell constants using reciprocal lattice vectors, out of measured powder diffraction data. Any help/hint appreciated. Heinz .-------------------------------------------------------------------------. | Dr. Heinz W. Poehlmann Regionales Rechenzentrum | | Manager Applications Department der Universitaet Stuttgart | | Computational Chemistry Support (University Computer Center) | | phone: (49)-711-685-5992 Allmandring 30 | | fax: (49)-711-6787626 D-70550 Stuttgart | | e-mail: poehlmann@rus.uni-stuttgart.de Germany | '-------------------------------------------------------------------------' From qftramos@usc.es Fri May 5 06:48:36 1995 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.6.10/930601.1506) id GAA18694; Fri, 5 May 1995 06:33:32 -0400 Received: by uscmail.usc.es (5.67b/1.34) id AA21185; Fri, 5 May 1995 12:37:14 +0200 Date: Fri, 5 May 1995 12:37:14 +0200 From: qftramos@usc.es (Antonio Fernandez Ramos) Message-Id: <199505051037.AA21185@uscmail.usc.es> To: chemistry@ccl.net Subject: Free Fortran77?? Dear netters: Is available a free Fortran77 or 90 for MS-DOS? Thanks Antonio Fernandez-Ramos E-mail : qftramos@usc.es From kmay@trans.net Fri May 5 08:03:33 1995 Received: from ns.trans.net for kmay@trans.net by www.ccl.net (8.6.10/930601.1506) id IAA19718; Fri, 5 May 1995 08:02:50 -0400 Received: from by ns.trans.net (4.1/SMI-4.1) id AB12884; Fri, 5 May 95 14:03:09 BST X-Sender: kmay@mailhost Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 May 1995 14:03:10 +0200 To: CHEMISTRY@ccl.net From: kmay@trans.net (Klaus J.W.May) Subject: Chemistry Software over Internet Hi Netters: more and more companies go netsurfing.Mostly they have a www homepage and present themselves. Some (very few) do now distribution of SW via Internet. And here's my question: I am currently compiling a list of chemistry related Software, available over Internet. Do you have any suggestions, experiences, discovered or conceived problems ? I'll post the compilation to the chemistry list, if wanted. What I know, so far, is that some time ago a Company called "Megalon" tried, But I have no idea, how this ended up. Interactive Simulations offers SCULPT via URL: http://www.intsim.com/~isigen. I recommed strongly to hack in there for everybody working with biomolecules! Neat program, free demoversion. Does realtime minimizations for 600 bucks. It's the one, which's development Dave and Jane Richardson guided. PLEASE RESPOND DIRECTLY TO ME (if it's not of common interest): kmay@trans.net Cheers Klaus %-) Klaus J.W. May e-mail: kmay@trans.net May & Partner SciTech Consult Phone/Fax: xx49-(89) 333 569 Mandlstr. 15 Mobile national: 0172-620 38 38 international: xx49-172-620 30 38 D - 80802 Munich GERMANY From lebail@naimn2.cnrs-imn.fr Fri May 5 08:18:33 1995 Received: from naimn1.cnrs-imn.fr for lebail@naimn2.cnrs-imn.fr by www.ccl.net (8.6.10/930601.1506) id IAA19817; Fri, 5 May 1995 08:11:56 -0400 From: Received: from naimn2 by naimn1.cnrs-imn.fr with SMTP; Fri, 5 May 1995 14:15:27 +0200 (WET-DST) Date: Fri, 5 May 1995 14:14:33 GMT Message-Id: <95050514143341@naimn2.cnrs-imn.fr> To: CHEMISTRY@ccl.net Subject: Re: CCL: powder diffraction cell data X-VMS-To: SMTP%"CHEMISTRY@ccl.net" From: "Dr. Heinz Poehlmann" : >we are looking for a little program generating possible cell constants >using reciprocal lattice vectors, out of measured powder diffraction data. >Any help/hint appreciated. The CCP14 suite contains executables (TREOR90, ITO, DICVOL91, among many other useful softwares for powder diffraction) for various operating systems. They are not little programs... ftp gserv1.dl.ac.uk (148.79.80.10) sub-directory ccp14 get first manual.ps (or manual.tex) , table1.ps, fig1.ps in sub-directory doc Armel Le Bail - Laboratoire des Fluorures, CNRS-URA-449, Universite du Maine, 72017 Le Mans Cedex, FRANCE - armel@ONE.univ-lemans.fr or lebail@naimn2.cnrs-imn.fr From rachelle@picard.niehs.nih.gov Fri May 5 09:33:34 1995 Received: from kamakazi.niehs.nih.gov for rachelle@picard.niehs.nih.gov by www.ccl.net (8.6.10/930601.1506) id JAA21586; Fri, 5 May 1995 09:20:45 -0400 Received: from picard.niehs.nih.gov by kamakazi.niehs.nih.gov via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@kamakazi.niehs.nih.gov:CHEMISTRY@ccl.net> id JAA09760; Fri, 5 May 1995 09:17:50 -0400 Received: by picard.niehs.nih.gov (931110.SGI/930416.SGI.AUTO) for @kamakazi.niehs.nih.gov:CHEMISTRY@ccl.net id AA26106; Fri, 5 May 95 09:21:54 -0400 Date: Fri, 5 May 95 09:21:54 -0400 From: rachelle@picard.niehs.nih.gov (Rachelle J. Bienstock) Message-Id: <9505051321.AA26106@picard.niehs.nih.gov> To: CHEMISTRY@ccl.net Subject: TCL Comp. Chem tools.. Dimitris K. Agrafiotis, PhD mentioned that "Tcl/Tk is rapidly becoming a de-facto standard for cross-platform GUI development". I'd like to mention that the new version of the Biosym MD program, Discover 94.0 uses TCL with extenstions (they call it BCL) input files.... Rachelle ##### (o o) +------------------------oooO---(__)---Oooo----------------------------+ | | | Dr. Rachelle Bienstock INTERNET :rachelle@picard.niehs.nih.gov | | National Institute of | | Environmental Health Sciences | | P.O. Box 12233 Mail Drop 10-03 Telephone : 919-541-3397 | | Research Triangle Park, NC 27709 Fax : 919-541-1578 | +----------------------------------------------------------------------+ || || (__) (__) From jkg1000@cus.cam.ac.uk Fri May 5 10:03:37 1995 Received: from bootes.cus.cam.ac.uk for jkg1000@cus.cam.ac.uk by www.ccl.net (8.6.10/930601.1506) id KAA22712; Fri, 5 May 1995 10:01:10 -0400 Received: from apus.cus.cam.ac.uk [131.111.8.2] (ident = root) by bootes.cus.cam.ac.uk with smtp (Smail-3.1.29.0 #36) id m0s7Nw2-000BzuC; Fri, 5 May 95 15:00 BST Received: by apus.cus.cam.ac.uk (Smail-3.1.29.0 #36) id m0s7Nw1-00034FC; Fri, 5 May 95 15:00 BST Date: Fri, 5 May 1995 15:00:47 +0100 (BST) From: "J.K. Gregory" To: CHEMISTRY@ccl.net Subject: ab initio programs In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to know if there is an ab initio program that will allow me to apply a static electric field to a molecule and still be able to calculate derivatives. I want to calculate a reaction path in the presence of a field and so I still need the derivatives. Cadpac can apply a field but cannot do derivatives in this field. Many thanks in advance. ---------------------------------------------------------------- | Jon Gregory Phone : +44 01223 336350 (direct) | | Department of Chemistry, Fax : +44 01223 336362 | | University of Cambridge. Email : jkg1000@cus.cam.ac.uk | ---------------------------------------------------------------- From haegele2@rz.uni-duesseldorf.de Fri May 5 11:33:35 1995 Received: from isis.rz.uni-duesseldorf.de for haegele2@rz.uni-duesseldorf.de by www.ccl.net (8.6.10/930601.1506) id LAA24843; Fri, 5 May 1995 11:30:27 -0400 Received: from pc.ac1.uni-duesseldorf.de by isis.rz.uni-duesseldorf.de with SMTP (PP) id <00243-0@isis.rz.uni-duesseldorf.de>; Fri, 5 May 1995 14:13:54 +0000 From: Gerhard Haegele Date: Fri, 5 May 95 15:23:16 +0100 Message-Id: <1773.haegele2@mail.rz.uni-duesseldorf.de_POPMail/PC_3.2.2> Reply-To: haegele X-POPmail-Charset: English To: chemistry@ccl.net Subject: probe interaction Hello netters! I have a question concerning the definition of a term in computational chemistry. How exactly is defined "probe interaction" and what is the physical meaning of it? We calculated probe interactions with CHARMm and got numerical results. Which dimension have these probe interactions (energy or potential)? Are there any citations about this topic? Sincerely PLEASE NOTE: MY MAILING ADDRESS HAS CHANGED: MY NEW EMAIL NUMBER IS: haegele@uni-duesseldorf.de ================================================================== message from Gerhard Haegele, haegele@uni-duesseldorf.de postal adress: Prof. Dr. G. Haegele Institut fuer Anorganische Chemie und Strukturchemie I Heinrich-Heine-Universitaet Duesseldorf Universitaetsstrasse 1, D-40225 Duesseldorf, Germany Phone ++49-211-311-2288, Fax ++49-211-311-2287 Phone ++49-211-311-3140, Fax ++49-211-311-3085 From smb@smb.chem.niu.edu Fri May 5 11:48:36 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/930601.1506) id LAA25017; Fri, 5 May 1995 11:37:03 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA06054 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net>); Fri, 5 May 1995 10:37:06 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@ccl.net) id AA25521; Fri, 5 May 95 10:16:37 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@ccl.net) id AA07984; Fri, 5 May 95 10:16:37 -0500 Date: Fri, 5 May 95 10:16:37 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9505051516.AA07984@smb.chem.niu.edu> To: CHEMISTRY@ccl.net Subject: 2nd Electronic Computational Chemistry Conference Preliminary Announcement of the 2nd Electronic Computational Chemistry Conference (ECCC-2) Following on the overwhelming success of the First Electronic Computational Chemistry Conference, held in Novemeber 1994, which attracted 74 papers and over 325 participants, we are pleased to announce that the Second ECCC will be held November 6 - December 1, 1995. This will be an electronic conference devoted to any and all aspects of computational chemistry - from ab initio calculations to drug design to molecular dynamics, etc. As before, this conference will be held entirely on the Internet, this time exclusively through the World-Wide Web. We have designed a new interface to the conference, eliminating the need for email. Discussions of the papers will proceed using a form-based interface. This system allows each participant total control over what messages to read and eliminates the mass mailings that slowed down ECCC-1. We also plan on mirroring the conference in Europe to assist access for our European participants. Complete instructions on how to register, prepare an abstract and submit a paper will be announced in June. Those of you who would like to participate should make sure to obtain a recent WWW browser, such as Netscape 1.1b3 or Mosaic 2.6 in preparation of the conference. Complete instructions on how to configure these browsers for the ECCC will be forthcoming. We have not yet finalized plans on publishing the proceedings of ECCC-2 but we are committed to publishing them in some form. We are happy to recieve any suggestions or comments on this issue. For your information, publication of the Proceedings of the First ECCC on CDROM is expected in August 1995. Further information will be announced through the Computational Chemistry List, CHEMINF-L, and on the NIU WWW server (http://hackberry.chem.niu.edu:70/homepage.html) or feel free to contact me (Steven Bachrach) directly with your questions and comments at smb@smb.chem.niu.edu We look forward to another exciting conference in November! Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From dimitris@3dp.com Fri May 5 12:03:37 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id LAA25464; Fri, 5 May 1995 11:59:13 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA00672; Fri, 5 May 95 12:02:25 -0400 Received: by europa.3dp.com (931110.SGI) id AA01318; Fri, 5 May 95 12:01:06 -0400 From: "Dimitris Agrafiotis" Message-Id: <9505051201.ZM1316@europa.3dp.com> Date: Fri, 5 May 1995 12:01:05 -0400 In-Reply-To: rachelle@picard.niehs.nih.gov (Rachelle J. Bienstock) "CCL:TCL Comp. Chem tools.." (May 5, 9:21am) References: <9505051321.AA26106@picard.niehs.nih.gov> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: rachelle@picard.niehs.nih.gov (Rachelle J. Bienstock), chemistry@ccl.net Subject: Re: CCL:TCL Comp. Chem tools.. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On May 5, 9:21am, Rachelle J. Bienstock wrote: > Subject: CCL:TCL Comp. Chem tools.. > > Dimitris K. Agrafiotis, PhD mentioned that "Tcl/Tk is rapidly becoming > a de-facto standard for cross-platform GUI development". I'd like to > mention that the new version of the Biosym MD program, Discover 94.0 uses > TCL with extenstions (they call it BCL) input files.... > > Rachelle Hopefully, it bears no resemblance to the original BCL... Rachelle's point, however, is a very important one. While Tcl/Tk has been used mostly as a scripting language, it is also a powerfull command interpreter that can be embedded to any interactive application. More importantly, Tcl features the simplest syntax of all programming languages I know, and can be easily mastered by a non-specialist. The point I am trying to make is that Tcl should be used as a standard command interpreter in all interactive molecular modeling packages so that users don't have to struggle with the peculiarities, idiosynracies and bugs of interactive shells developed by software houses that don't specialize in language design. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From hcj@mazda.wavefun.com Fri May 5 12:33:49 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id MAA26338; Fri, 5 May 1995 12:33:22 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA23354; Fri, 5 May 95 09:33:23 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo via smap (V1.3) id sma023351; Fri May 5 09:33:05 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA08319; Fri, 5 May 95 09:32:54 -0700 Date: Fri, 5 May 95 09:32:54 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9505051632.AA08319@mazda.wavefun.com> To: qftramos@usc.es Cc: chemistry@ccl.net In-Reply-To: <199505051037.AA21185@uscmail.usc.es> (qftramos@usc.es) Subject: Re: CCL:Free Fortran77?? Reply-To: hcj@wavefun.com >>>>> "Antonio" == Antonio Fernandez Ramos writes: Antonio> Dear netters: Is available a free Fortran77 or 90 for Antonio> MS-DOS? The only free fortran compiler I am aware of is by the GNU people. It has recently been released in beta form and is available from ftp://prep.ai.mit.edu/pub/gnu. I do not know whether or not it is portable to MS-DOS. Hope this helps! -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From hinsenk@ERE.UMontreal.CA Fri May 5 13:18:37 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id NAA27066; Fri, 5 May 1995 13:06:35 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA07969 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 5 May 1995 13:06:08 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA27683; Fri, 5 May 95 13:06:06 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA06895; Fri, 5 May 95 13:06:05 -0400 Date: Fri, 5 May 95 13:06:05 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9505051706.AA06895@cyclone.ERE.UMontreal.CA> To: dimitris@3dp.com Cc: rachelle@picard.niehs.nih.gov, chemistry@ccl.net In-Reply-To: <9505051201.ZM1316@europa.3dp.com> (dimitris@3dp.com) Subject: Re: CCL:TCL Comp. Chem tools.. Hopefully, it bears no resemblance to the original BCL... Rachelle's point, however, is a very important one. While Tcl/Tk has been used mostly as a scripting language, it is also a powerfull command interpreter that can be embedded to any interactive application. More importantly, Tcl Before everyone becomes too enthusiastic about Tcl, I would like to point out that Tcl - like most "scripting" languages - is very limited, especially when it comes to data manipulation. If all you want is to automatize a short sequence of actions, that's fine - but don't expect more from it. Personally, I would prefer scientific tools to be integrated with a really powerful programming language. It should be sufficient to do e.g. all kinds of data analysis. And it should be integrated well enough to allow e.g. the definition of potentials in MD simulations as user-defined functions. Such a system would improve productivity tremendously for some applications. And it is perfectly possible with today's technology - all it takes is an institution or company big enough and willing to realize such a project. be easily mastered by a non-specialist. The point I am trying to make is that Tcl should be used as a standard command interpreter in all interactive molecular modeling packages so that users don't have to struggle with the peculiarities, idiosynracies and bugs of interactive shells developed by software houses that don't specialize in language design. Standardization is attractive, as you point out. But the history of computing also shows the dangers of premature standardization, leading to standards that are not good enough for their purpose. Fortran and DOS come to mind as obvious examples, but there are some less obvious ones - like the X Window system, which has failed to provide uniform and efficient user interfaces for the Unix world. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From ejfried@herzberg.ca.sandia.gov Fri May 5 14:18:38 1995 Received: from herzberg.ca.sandia.gov for ejfried@herzberg.ca.sandia.gov by www.ccl.net (8.6.10/930601.1506) id OAA28866; Fri, 5 May 1995 14:15:10 -0400 Received: (from ejfried@localhost) by herzberg.ca.sandia.gov (8.6.11/8.6.10) id SAA21301 for CHEMISTRY@ccl.net; Fri, 5 May 1995 18:13:49 GMT From: "Ernest Friedman-Hill" Message-Id: <9505051113.ZM21299@herzberg> Date: Fri, 5 May 1995 11:13:49 -0700 In-Reply-To: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) "CCL:TCL Comp. Chem tools.." (May 5, 1:06pm) References: <9505051706.AA06895@cyclone.ERE.UMontreal.CA> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: Re: CCL:TCL Comp. Chem tools.. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On May 5, 1:06pm, Hinsen Konrad (hinsenk@ERE.UMontreal.CA) wrote: > Before everyone becomes too enthusiastic about Tcl, I would like > to point out that Tcl - like most "scripting" languages - is > very limited, especially when it comes to data manipulation. > If all you want is to automatize a short sequence of actions, > that's fine - but don't expect more from it. Actually, you really are selling Tcl short. Some very nice applications can be and have been written using Tcl and the various extensions that are available. It *is* a complete programming language. The portability, extensibility, and lisp-like ability to treat code as data and vice-versa make it ideal for developing large heterogeneous distributed systems. > > Personally, I would prefer scientific tools to be integrated with a > really powerful programming language. It should be sufficient to do > e.g. all kinds of data analysis..... > The point of buying scientific tools is that they themselves are supposed to do "all kinds of scientific analysis." If you need to write complex components in the tool's extension language, you haven't bought all the tools you need! On the other hand, one of the nice things about Tcl is the very clean methodology for integrating extensions and external commands. If you need a Tcl FFT command, and you have an FFT routine in Fortran or C, it's an easy matter to turn it into a Tcl command that you can call from within Tcl scripts. I would therefore tell vendors of tools which use Tcl as an extension language to make sure to supply their code as libraries, so that the user can add new Tcl commands to suit their own application. > Standardization is attractive, as you point out. But the history > of computing also shows the dangers of premature standardization, > leading to standards that are not good enough for their purpose. > Fortran and DOS come to mind as obvious examples, but there are > some less obvious ones - like the X Window system, which has > failed to provide uniform and efficient user interfaces for the > Unix world. I would posit that no one ever chose FORTRAN, DOS *or* X/Windows as a standard - they were simply what was available at the time that they were needed. I (sort of) agreee with your cautions about standards, but people should not interpret this as an exhortation to wait for the ultimate tool before they begin work on anything! Things need to get done in the interim. -- --------------------------------------------------------- Ernest Friedman-Hill Senior Member of Technical Staff Scientific Computing Department Sandia National Laboratories Org. 8117, MS 9214 PO Box 969 Livermore, CA 94550 From given@tiber.nist.gov Fri May 5 15:03:41 1995 Received: from tiber.nist.gov for given@tiber.nist.gov by www.ccl.net (8.6.10/930601.1506) id OAA29578; Fri, 5 May 1995 14:50:54 -0400 Received: from localhost by tiber.nist.gov (8.6.4/10.1) id OAA18174; Fri, 5 May 1995 14:50:54 -0400 Date: Fri, 5 May 1995 14:50:54 -0400 From: given@tiber.nist.gov (James A Given) Message-Id: <199505051850.OAA18174@tiber.nist.gov> To: chemistry@ccl.net Subject: RMS Fits and Symmetries Cc: gilson@indigo14.ccl.net RMS Fits For Structures That Have Symmetries Dear CCL Participants: I have what I hope is a common problem. We are generating ligand conformations for use in drug design. The ligands we use can contain groups with various symmetries, e.g., benzene rings. Does anyone know how to take such symmetries into account when calculating RMS fit? As a simple example of the problem that arises, imagine a molecule with a plane of symmetry through its center. If the molecule is flipped over and then superposed with the original, the RMS calculation of the difference between the two should be zero. But a naive calculation of the RMS will not give zero, because the pairing of atoms induced by the superposition is not the identity pairing, i.e., the atom marked '1' in the original will not be coincident with the atom marked '1' in the copy. Perhaps the simplest case of this problem occurs when comparing different conformations of a ring molecule. Is there provision in standard software packages for handling this problem? Is there a stand-alone program that will accept as input a list of symmetries (where each symmetry is given as a list of atom pairs to be switched) and calculate the lowest value of the RMS that can be obtained by first applying these symmetries? Jim Given Center for Advanced Research in Biotechnology Rockville, MD given@tiber.nist.gov From dimitris@3dp.com Fri May 5 15:08:51 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id OAA29590; Fri, 5 May 1995 14:51:26 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA01879; Fri, 5 May 95 14:54:38 -0400 Received: by europa.3dp.com (931110.SGI) id AA02145; Fri, 5 May 95 14:53:20 -0400 From: "Dimitris Agrafiotis" Message-Id: <9505051453.ZM2143@europa.3dp.com> Date: Fri, 5 May 1995 14:53:19 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Re: TCL Comp. Chem tools.. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On May 5, 1:06pm, Hinsen Konrad wrote: > Subject: CCL:TCL Comp. Chem tools.. > > Before everyone becomes too enthusiastic about Tcl, I would like > to point out that Tcl - like most "scripting" languages - is > very limited, especially when it comes to data manipulation. > If all you want is to automatize a short sequence of actions, > that's fine - but don't expect more from it. > > ... > > Standardization is attractive, as you point out. But the history > of computing also shows the dangers of premature standardization, > leading to standards that are not good enough for their purpose. > Fortran and DOS come to mind as obvious examples, but there are > some less obvious ones - like the X Window system, which has > failed to provide uniform and efficient user interfaces for the > Unix world. You realize, of course, that Tcl can be used from inside C or C++ if you need access to sophisticated data handling capabilities. In fact, we use this functionality extensively at 3D Pharmaceuticals with very impressive results. I do agree that there is need for a unified language, but that's not going to happen for a long, long time. As for standardization, my feeling is that having a premature standard is far better than having no standard at all. Still, your comments are valid and very well taken. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From dimitris@3dp.com Fri May 5 15:13:38 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id OAA29559; Fri, 5 May 1995 14:50:00 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA01868; Fri, 5 May 95 14:53:11 -0400 Received: by europa.3dp.com (931110.SGI) id AA01963; Fri, 5 May 95 14:51:52 -0400 From: "Dimitris Agrafiotis" Message-Id: <9505051451.ZM1961@europa.3dp.com> Date: Fri, 5 May 1995 14:51:51 -0400 In-Reply-To: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) "CCL:TCL Comp. Chem tools.." (May 5, 1:06pm) References: <9505051706.AA06895@cyclone.ERE.UMontreal.CA> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: hinsenk@ERE.UMontreal.CA (Hinsen Konrad), chemistry@ccl.net Subject: Re: TCL Comp. Chem tools.. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On May 5, 1:06pm, Hinsen Konrad wrote: > Subject: CCL:TCL Comp. Chem tools.. > > Before everyone becomes too enthusiastic about Tcl, I would like > to point out that Tcl - like most "scripting" languages - is > very limited, especially when it comes to data manipulation. > If all you want is to automatize a short sequence of actions, > that's fine - but don't expect more from it. > > ... > > Standardization is attractive, as you point out. But the history > of computing also shows the dangers of premature standardization, > leading to standards that are not good enough for their purpose. > Fortran and DOS come to mind as obvious examples, but there are > some less obvious ones - like the X Window system, which has > failed to provide uniform and efficient user interfaces for the > Unix world. You realize, of course, that Tcl can be used from inside C or C++ if you need access to sophisticated data handling capabilities. In fact, we use this functionality extensively at 3D Pharmaceuticals with very impressive results. I do agree that there is need for a unified language, but that's not going to happen for a long, long time. As for standardization, my feeling is that having a premature standard is far better than having no standard at all. Still, your comments are valid and very well taken. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From hinsenk@ERE.UMontreal.CA Fri May 5 15:18:44 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id PAA29991; Fri, 5 May 1995 15:13:39 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA10693 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Fri, 5 May 1995 15:13:05 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA25771; Fri, 5 May 95 15:13:03 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA09470; Fri, 5 May 95 15:13:01 -0400 Date: Fri, 5 May 95 15:13:01 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9505051913.AA09470@cyclone.ERE.UMontreal.CA> To: ejfried@herzberg.ca.sandia.gov Cc: CHEMISTRY@ccl.net In-Reply-To: <9505051113.ZM21299@herzberg> (ejfried@herzberg.ca.sandia.gov) Subject: Re: CCL:TCL Comp. Chem tools.. Actually, you really are selling Tcl short. Some very nice applications can be and have been written using Tcl and the various extensions that are available. It *is* a complete programming language. The portability, I know. So theoretically you can any program in TCL that can be written at all - but that doesn't mean it's going to be easy or pleasant. Tcl suffers from a serious lack in support of data structures, which are as important as control structures when writing non-trivial code. extensibility, and lisp-like ability to treat code as data and vice-versa make it ideal for developing large heterogeneous distributed systems. I have some doubts about its suitability for *large* systems of any kind. The point of buying scientific tools is that they themselves are supposed to do "all kinds of scientific analysis." If you need to write complex components in the tool's extension language, you haven't bought all the tools you need! Normally I need some tools that I can't buy anywhere, e.g. because they are very specialized. So I need the ability to extend whatever tools I use. Currently I use C-Shell scripts or Emacs macros, but that is only a workaround. And some programs (Gaussian 90 frustrated me a few days ago) do their best to make this difficult. from within Tcl scripts. I would therefore tell vendors of tools which use Tcl as an extension language to make sure to supply their code as libraries, so that the user can add new Tcl commands to suit their own application. That's a good starting point, but doesn't always work. Some tools simply cannot be provided as classic libraries. Component libraries based on SOM or similar technologies are much more flexible - but there you are already beyond the limits of Tcl. I would posit that no one ever chose FORTRAN, DOS *or* X/Windows as a standard - they were simply what was available at the time that they were Of course by standardization I meant the creation of de-facto standards. needed. I (sort of) agreee with your cautions about standards, but people should not interpret this as an exhortation to wait for the ultimate tool before they begin work on anything! Things need to get done in the interim. Obviously. But when people perceive the need for uniform tools, they should use one designed for the purpose at hand (and if necessary design a new one), rather than use the first one that looks good enough at first sight. Until the needs are clear, we would be better off if different vendors would try different strategies to see how they work in practice. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From hinsenk@ERE.UMontreal.CA Fri May 5 15:33:39 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id PAA00538; Fri, 5 May 1995 15:25:10 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA10892 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 5 May 1995 15:23:10 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA28167; Fri, 5 May 95 15:23:09 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA09647; Fri, 5 May 95 15:23:08 -0400 Date: Fri, 5 May 95 15:23:08 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9505051923.AA09647@cyclone.ERE.UMontreal.CA> To: dimitris@3dp.com Cc: chemistry@ccl.net In-Reply-To: <9505051451.ZM1961@europa.3dp.com> (dimitris@3dp.com) Subject: Re: TCL Comp. Chem tools.. You realize, of course, that Tcl can be used from inside C or C++ if you need access to sophisticated data handling capabilities. In fact, If you have the source code of the tool that uses Tcl. As a user, you normally don't. As for standardization, my feeling is that having a premature standard is far better than having no standard at all. Still, your comments That's exactly where I disagree. The computer industry is full of premature standards, and they are very difficult to get rid of. Very soon compatibility with the standard becomes the major criterion in designing new products, just as it happens now in the PC world. I don't know whether anyone has ever estimated the economic cost of IBM-compatibility, but I am sure it is an impressive number. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From thomas_w@btm2x2.mat.uni-bayreuth.de Fri May 5 16:33:44 1995 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.6.10/930601.1506) id QAA01572; Fri, 5 May 1995 16:26:01 -0400 Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA11556; Fri, 5 May 95 13:41:26 +0200 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA10001; Fri, 5 May 95 13:40:50 +0200 Date: Fri, 5 May 95 13:40:50 +0200 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9505051140.AA10001@btm2x2.mat.uni-bayreuth.de> To: chemistry@ccl.net Subject: [Summary] Methods for converting internal to external coordinates Dear Netters, last week I posted a question about methods for converting internal to external coordinates. I want to thank all peole who replied and the OSC for providing thisg reat and really useful list. Below is a summary of the messages I got. Some replies are in German; if translations are needed, please refer to me or the original senders. So long, Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| Lehrstuhl II f. Mathematik |\ \ | || Universitaet Bayreuth | \ \ | || | \ \ | || 95440 Bayreuth | \ \\ || Germany | \ \\ || Tel. +49 (921) 553386 | \ \\ || Fax +49 (921) 553385 | \-------|| +---------------+ Original question: -------------------- A colleague of mine is looking for conversion methods from internal to external 3D-coordinates. Given a set of points, their distances, angles and dihedral angles, he wants to compute Cartesian coordinates in space. We know that this routine is implemented in many packages and to avoid reinventing the wheel we wondered if somebody out there could point us to a description of the method (no code or complete program since it shall be adapted to our own data structure). What we already know is MOPAC on the one hand, which, however, has a slightly different approach, and BABEL on the other hand, which also tells nothing about the underlying methods. From joerg@ibm530.chemie.th-merseburg.de ----------------------------------------------- ich habe die Konvertierung von Z-Matrix (innere Koordinaten) zu kartesischen Koordinaten so geloest, das ich das Molekuel nach und nach aufbaue. 1.Atom (0,0,0); 2.Atom (d,0,0); 3.Atom (x2+d*cos(180-w), d*sin(180-w), 0); alle naechsten Atome lege ich mit dem Abstand zum vorhergenden Atom parallel zur X-Achse (x-Koordinate die selbe wie Nachbar). Da jetzt der Bindungswinkel und der Torisonswinkel wilkuerlich sind, aendere ich dann den Winkel und den Torionswinkel so, das der in der Z-Matrix definierte Wert erhalten wird. der Code ist in C in meinem Programm implementiert und benoetigt Routinen zum Berechnen und Aendern von Bindungslaengen, Winkeln und Torsionswinkeln. Wenn Du willst, stelle ich Dir die Routinen zusammen. Es ist allerdings keine mathematisch analytische Loesung des Problemes im Sinne von nur einer Formel P(x,y,z) = f(d,w,t) der Algorithmus laeuft aber seit laengerem stabil in meinem Programm. folgendes Beispiel: Methan H3 / H1--C2 \ \ H4 H5 alle distancen 1 alle winkel 109x Torsion 4-2-1-3 120x 5-2-1-3 240x H1 0 0 0 C2 1 0 0 H3 1+cos(71) sin(71) 0 jetzt: H4 zunaechst y wie Nachbar(C2) = 0 x = x(2)+d = 2 z wie Nachbar(C2) = 0 daraus ergeben sich ein Winkel(4-2-1) von 180x der wird nun korrigiert zu 109x der Torsionwinkel ist nun zufllig und mua zu 120x korrigiert werden usw. From Karl.F.Moschner@urlus.sprint.com --------------------------------------- Try QCPE. It's a nice place to "shop". There are a series of programs for calculation of atomic coordinates. The most likely candidate is COORD QCPE#419, but there may also be a newer version. QCPE Creative Arts Building 181 Indiana University Bloomington, IN 47405 USA Phone: (812) 855-4784 FAX: (812) 855-5539 E-mail: qcpe@ucs.indiana.edu For information and catalogues: login: anonymous@qcpe6.chem.indiana.edu password: guest Karl F. Moschner, Ph. D. Unilever Research U. S. From fredvc@esvax.dnet.dupont.com ------------------------------------- Despite your reluctance to deal with existing code, the easiest way to get something working is to adapt an existing program to read/write the data files/structures that you prefer... which is what I did some time ago. Also, the methodology is quite transparent in a well-documented program. Appended is my current version of COORD, adapted from something that QCPE distributes. I have, infact, modified it on two separate occasions because of changes in the form of the output file that were desired. Feel free to do whatever you need to do to make it work in your environment. FREDERIC A. VAN-CATLEDGE The DuPont Company ------------------------------ CUT HERE ------------------------------------- PROGRAM COORD_XYZ C************************************************************************** C C C COORD CALCULATES THE COORDINATES IN 3-DIMENSIONAL MOLECULES,GIVEN C THE BOND LENGTHS,BOND ANGLES AND DIHEDRAL ANGLES C C THE CARD OUTPUT FROM COORD CAN BE USED DIRECTLY AS INPUT TO MINDO3 C OR REINER SUSTMANN'S NDDO PROGRAMS C C C ******* INPUT DATA FOR EACH MOLECULE ***** C FIRST CARD HAS MOLECULE CHARGE IN COLS.1-2,AND HAS THE MOLECULE C NAME IN COLS.3-63 C SECOND CARD. NOAT I2 C IZAT(1) I2 C IZAT(2) I2 C IZAT(3) I2 C KWIK I1 C R12 F7.4 C R23 F7.4 C THETA F14.7 C EACH SUCCESSIVE CARD. NA I2 C NB I2 C NC I2 C ND I2 C IZAT(ND) I2 C ILAZY I1 C RCD F7.4 C THBCD F14.7 C PHABCD F14.7 C C A CARD WITH 99 IN COLS.1-2 MUST BE ADDED AT THE END OF C THE ENTIRE DECK OF MOLECULES TO TERMINATE THE PROGRAM C C CARDS FOR ATOMS WITH IZAT>99 ARE NOT PUNCHED C C************************************************************************** C IMPLICIT REAL*8 (A-H,O-Z) DIMENSION IAT(100), NAT(100,10),COVRAD(99),ATWT(99) DIMENSION X(100),Y(100),Z(100),RIJ(100,100),IZAT(100),NAME(15) LOGICAL QDONE(100),QFILE CHARACTER*2 EL(99) CHARACTER*4 SCREXT,CEXT,OUTEXT,INEXT CHARACTER*20 OFIL CHARACTER*24 NEWFIL C COMMON/COVRAD/COVRAD,ATWT,EL C COMMON /WORK/ X, Y, Z, DEGRAD C DATA DEGRAD/1.74532925199432D-02/ DATA SCREXT/'.SCR'/,CEXT/'.XYZ'/,OUTEXT/'.OUT'/,INEXT/'.Q'/ C SQRT2 = DSQRT ( 2.0D0 ) SQRT3 = DSQRT ( 3.0D0 ) THTET = DACOS(-1.D0/3.D0)/DEGRAD THTRI = 120. C D OPEN(UNIT=46,FILE='COORD.TRK',TYPE='NEW') C 100 CONTINUE WRITE ( 6, 9000 ) READ ( 5, 9010, END=250 ) OFIL NCH = INDEX(OFIL, ' ') -1 C NEWFIL = OFIL(1:NCH) // SCREXT WRITE ( 6, 9020 ) NEWFIL OPEN(UNIT=23,NAME=NEWFIL,TYPE='NEW',CARRIAGECONTROL='LIST') C NEWFIL = OFIL(1:NCH) // CEXT WRITE ( 6, 9030 ) NEWFIL OPEN(UNIT=21,NAME=NEWFIL,TYPE='NEW',CARRIAGECONTROL='LIST') C NEWFIL = OFIL(1:NCH) // OUTEXT OPEN(UNIT=16,NAME=NEWFIL,TYPE='NEW',CARRIAGECONTROL='FORTRAN') WRITE ( 6, 9040 ) NEWFIL C NEWFIL = OFIL(1:NCH) // INEXT INQUIRE(FILE=NEWFIL,EXIST=QFILE) IF (QFILE) THEN WRITE ( 6, 9045 ) NEWFIL IGET = 15 IPRMPT = 36 OPEN(UNIT=IGET,TYPE='OLD',NAME=NEWFIL,READONLY) OPEN(UNIT=IPRMPT,NAME='NLA0:',TYPE='NEW') ELSE IGET = 5 IPRMPT = 6 END IF C C************************************************************************ C WRITE ( IPRMPT, 9050 ) READ ( IGET, 9060 ) ICHG, ( NAME(I), I = 1, 15 ) IF (ICHG .EQ. 99) GO TO 240 C OPEN(UNIT=22,TYPE='SCRATCH',FORM='UNFORMATTED') C WRITE ( 23, 9070 ) ICHG, ( NAME(I), I = 1, 15 ) C C>>>>>NOAT IS THE NUMBER OF ATOMS. IZAT(I) IS THE ATOMIC NUMBER OF ATOM C NUMBER I. KWIK ALLOWS AUTOMATIC CALCULATION OF COORDINATES OF C ATOMS 1, 2, 3 IN SIMPLE CASES, KWIK = 0, TETRAHEDRAL, KWIK = 1, C ANGLE 120 DEGREES, KWIK = 2, ANGLE SUPPLIED AS DATAUM. C R12, R23 ARE BOND LENGTHS. THETA IS THE 123 BOND ANGLE. C WRITE ( IPRMPT, 9080 ) READ(IGET,9090)NOAT,(IZAT(I),I=1,3),KWIK,R12,R23,THETA IF (KWIK .EQ. 0) THEN THETA = THTET ELSE IF (KWIK .EQ. 1) THEN THETA = THTRI ENDIF C C>>>>>WRITE INPUT TO VARIOUS FILES WRITE(23,9100)NOAT,(IZAT(K),K=1,3),KWIK,R12,R23,THETA WRITE ( 16, 9240 ) ( NAME(I), I = 1, 15 ) , ICHG WRITE ( 16, 9250 ) NOAT, ( IZAT(I), I = 1, 3 ) , KWIK IF (KWIK .LT. 2) THEN WRITE ( 16, 9260 ) R12, R23, THETA ELSE WRITE ( 16, 9265 ) R12, R23, THETA END IF WRITE ( 16, 9270 ) C C>>>>>CALC TRIG FCNS OF BOND ANGLE THETAK = THETA * DEGRAD CCOS = DCOS ( THETAK ) SSIN = DSIN ( THETAK ) C C>>>>>CALC XYZ FOR ATOMS 1, 2, & 3 DO 110 I = 1, 3 X(I) = 0.0 Y(I) = 0.0 Z(I) = 0.0 QDONE(I) = .TRUE. 110 CONTINUE C X(2) = R12 X(3) = R12 - R23 * CCOS Y(3) = R23 * SSIN C C>>>>>SET COORDINATE FLAG FOR REMAINING ATOMS DO 120 I = 4, NOAT QDONE(I) = .FALSE. 120 CONTINUE C C>>>>>LOOP TO CALC REMAINING XYZ COORDINATES DO 160 I = 4, NOAT C C>>>>>>>ATOMS NA, NB, NC, HAVE KNOWN COORDINATES AND ARE NOT COLLINEAR. C IZAT(ND) IS THE ATOMIC NUMBER OF ATOM ND. THBCD IS THE BCD BOND C ANGLEIN DEGREES AND PHABCD THE DIHEDRAL ANGLE OF CD RELATIVE TO C AB, MEASURED CLOCKWISE ALONG THE DIRECTION B TO C. ILAZY ALLOWS C AUTOMATIC CALCULATION OF ANGLES IN NORMAL TETRAHEDRAL AND PLANAR C SYSTEMS. ILAZY = 0, 1, 2, 3, 4, 5 TETRAHEDRAL WITH DIHEDRAL C ANGLES OF RESPECTIVELY 0, 60, 120, 180, 240, 310 DEGREES. C ILAZY = 6, 7 PLANAR CIS, TRANS RESPECTIVELY. ILAZY = 8, ATOMS C B, C, D COLLINEAR. ILAZY = 9, ANGLES FROM DATA C WRITE ( IPRMPT, 9110 ) READ(IGET,9120)NA,NB,NC,ND,IZAT(ND),ILAZY,RCD,THBCD,PHABCD IF (ILAZY .LT. 6) THEN THBCD = THTET PHABCD = ILAZY * 60. ELSE IF (ILAZY .LT. 8) THEN THBCD = THTRI PHABCD = (ILAZY - 6) * 180. ELSE IF (ILAZY .EQ. 8) THEN THBCD = 180. PHABCD = 0. ELSE IF (DABS(THBCD - 180.) .LT. 0.01) THEN THBCD = 180. PHABCD = 0. END IF ENDIF C C>>>>>>>WRITE INPUT TO .SCR FILE WRITE(23,9130)NA,NB,NC,ND,IZAT(ND),ILAZY,RCD,THBCD,PHABCD C C>>>>>>>CHECK THAT COORDINATES OF ATOMS NA, NB, NC HAVE BEEN CALCULATED 130 CONTINUE IF(.NOT.(QDONE(NA).AND.QDONE(NB).AND.QDONE(NC)))GO TO 230 C 140 CONTINUE WRITE ( 22 ) NA, NB, NC, ND, IZAT(ND), ILAZY, RCD, THBCD, PHABCD C THETA = THBCD PHI = PHABCD R = RCD CALL GETXYZ(NA, NB, NC, ND, R, THETA, PHI) QDONE(ND) = .TRUE. 160 CONTINUE C REWIND 22 DO 180 I = 4, NOAT 170 CONTINUE READ ( 22 ) NA, NB, NC, ND, IZ, ILAZY, RCD, THBCD, PHABCD IF (ILAZY .LT. 9) THEN WRITE(16,9140)NA,NB,NC,ND,IZ,ILAZY,RCD,THBCD,PHABCD ELSE WRITE(16,9145)NA,NB,NC,ND,IZ,ILAZY,RCD,THBCD,PHABCD END IF 180 CONTINUE CLOSE ( UNIT=22 ) C WRITE ( 16, 9150 ) C NCON = NOAT DO 200 I = 1, NOAT IF (IZAT(I) .GT. 99) NCON = NCON - 1 DO 190 J = 1, NOAT RIJ(I,J)=DSQRT((X(I)-X(J))**2+(Y(I)-Y(J))**2+(Z(I)-Z(J))**2) 190 CONTINUE 200 CONTINUE C C&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& C CODE FOR READING A .C FILE C&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& C READ ( 21, 9000 ) ID C READ ( 21, 9010 ) NATOMS, ICHG, IMULT, IANG C BOHR = IANG .EQ. 0 C NEL = -ICHG C DO 100 K = 1, NATOMS C READ ( 21, 9020 ) IZ, X(K), Y(K), Z(K) C 100 CONTINUE C9000 FORMAT(A80) C9010 FORMAT(4I) C9020 FORMAT(I,3F) C&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& WRITE ( 21, 9160 ) ( NAME(I), I = 1, 15 ) WRITE ( 21, 9170 ) NOAT, ICHG SX = 0. SY = 0. SZ = 0. SW = 0. DO 220 I = 1, NOAT IF (IZAT(I) .LE. 99) THEN IT = IZAT(I) W = ATWT(IT) SW = SW + W SX = SX + W*X(I) SY = SY + W*Y(I) SZ = SZ + W*Z(I) IF (COVRAD(IT) .EQ. 0.) THEN RAD1 = 1.65 ELSE RAD1 = 1.15 * COVRAD(IT) ENDIF IAT(I) = 0 DO 210 J = 1, NOAT IF (I .NE. J) THEN IF (IZAT(J) .LE. 99) THEN JT = IZAT(J) IF (COVRAD(JT) .EQ. 0.) THEN RAD2 = 1.65 ELSE RAD2 = 1.15 * COVRAD(JT) ENDIF IF (RIJ(I, J) .LE. RAD1+RAD2) THEN IAT(I) = IAT(I) + 1 NAT(I,IAT(I)) = J ENDIF ENDIF ENDIF 210 CONTINUE ENDIF 220 CONTINUE C C.....MOVE TO CENTER-OF-MASS COORDINATES XO = SX/SW YO = SY/SW ZO = SZ/SW DO 225 I = 1, NOAT X(I) = X(I) - XO Y(I) = Y(I) - YO Z(I) = Z(I) - ZO IF (IZAT(I) .LE. 99) THEN WRITE(21,9180)IZAT(I),X(I),Y(I),Z(I),I,IAT(I), & (NAT(I,K),K=1,IAT(I)) WRITE(16,9190)I,X(I),Y(I),Z(I),(NAT(I,L),L=1,IAT(I)) END IF 225 CONTINUE C WRITE ( 16, 9240 ) ( NAME(K), K = 1, 15 ) , ICHG WRITE ( 16, 9200 ) CALL NATPRT ( RIJ, NOAT, NOAT, 100, 10, 0 ) GO TO 100 C 230 CONTINUE WRITE ( 6, 9210 ) NA, NB, NC, ND WRITE ( 23, 9210 ) NA, NB, NB, ND IF (.NOT.QDONE(NA)) WRITE ( 23, 9220 ) NA IF (.NOT.QDONE(NB)) WRITE ( 23, 9220 ) NB IF (.NOT.QDONE(NC)) WRITE ( 23, 9220 ) NC 240 CONTINUE WRITE ( 23, 9230 ) ICHG 250 CONTINUE STOP 9000 FORMAT(//1H$,7X,'ENTER FILE ID (CTRL/Z TO END)... ') 9010 FORMAT(A) 9020 FORMAT('0 INPUT IS SAVED IN FILE ',A24) 9030 FORMAT('0 CONNECTIVITY FILE IS ',A24) 9040 FORMAT('0 SUMMARY IS IN FILE ',A24,', WHICH CAN BE PRINTED') 9045 FORMAT('0(INPUT IS TAKEN FROM FILE ',A24,')') 9050 FORMAT(1H0,'CHARGE, NAME = (I2,15A4)'/) 9060 FORMAT (I,15A4) 9070 FORMAT(I2,',',15A4) 9080 FORMAT(1H0,'# ATOMS, Z1, Z2, Z3, KWIK, R12, R23, THETA'/, 1 ' KWIK = 0,1,2 FOR TET, 120 OR THETA SUPPLIED'/) 9090 FORMAT(5I,3F) 9100 FORMAT(I4,4(',',I4),3(',',F12.5)) 9110 FORMAT(1H0,'NA, NB, NC, ND, Z(ND), LAZY, RCD,' 1 ' THBCD, PHABCD'/' LAZY=0,1,2,3,4,5 FOR TET WITH', 2 ' PHI=0,60,120,180,240,310: 6,7 FOR CIS,TRANS: ' 3 '8 COLINEAR: 9 SUPPLIED'/) 9120 FORMAT(6I,3F) 9130 FORMAT(I4,5(',',I4),3(',',F12.5)) 9140 FORMAT(1H ,4I5,2I8,F12.5,2F12.3,3X,'(STD. ANGLES)') 9145 FORMAT(1H ,4I5,2I8,F12.5,2F12.3) 9150 FORMAT(1H0,2X,'NO. OF ATOM',5X,'X-COORDINATE',5X, 1 'Y-COORDINATE',5X,'Z-COORDINATE'/) 9160 FORMAT(15A4,20X) 9170 FORMAT(I3,', ',I2,', 1, 1, <- (ANGSTROMS)') 9180 FORMAT(I3,', ',F15.10,', ',F15.10,', ',F15.10,', ', 1 I3,', ',I1,', ',9(I3,', ')) 9190 FORMAT(1H ,8X,I2,3X,3F17.6,10I5) 9200 FORMAT(1H0,21HINTERATOMIC DISTANCES,//) 9210 FORMAT(1H0,38HCOORDS.OF 1 REFERENCE ATOM UNAVAILABLE,4I5) 9220 FORMAT('0 ATOM',I4.' XYZ NOT CALC-D') 9230 FORMAT(I2) 9240 FORMAT(1H1,15A4,7HCHARGE=,I3) 9250 FORMAT (8H0NOAT = I2, 14H IZAT(1) = I2, 14H IZAT(2) = I2, 114H IZAT(3) = I2, 11H KWIK = I1) 9260 FORMAT (' R12 = ',F7.4,4X,'R23 = ',F7.4,4X,'THETA = ',F10.3,3X, & '(STD. ANGLE)') 9265 FORMAT (' R12 = ',F7.4,4X,'R23 = ',F7.4,4X,'THETA = ',F10.3) 9270 FORMAT(1H0,2X,'NA',3X,'NB',3X,'NC',3X,'ND',3X, 1 'IZAT(ND)',2X,'ILAZY',4X,'RCD',7X,'THBCD', 2 6X,'PHABCD'/) END SUBROUTINE NATPRT(A,N,M,MA,NC,II) IMPLICIT REAL*8 (A-H,O-Z) C...Translated by FPP 5.0 (3.03N9) 08/16/92 22:09:51 C...Switches: format=9000:10,indal=2 C************************************************************** C * C SUBROUTINES AND FUNCTIONS CALLED FROM THIS ROUTINE * C * C NO SUBROUTINES OR FUNCTIONS CALLED FROM THIS PROGRAM UNIT * C * C************************************************************** DIMENSION A(MA,MA) C MATPRT PRINTS MATRICES** FROM KLOPMANS PROGRAM SCF KK = 0 NCM1 = NC - 1 J = 0 L = 1 IF (II - 1 .GT. 0) THEN L = II - 10 II = 0 KK = 5 ENDIF DO 150 IZ = L, M, NC NIF = IZ + NCM1 NIF = MIN0 ( M,NIF ) J = J + N - II * (IZ - 1 ) IF (J - 52 .GE. 0) THEN I = 0 J = 0 ELSE I = 1 ENDIF IF (I + KK - 1 .LT. 0) GO TO 100 IF (I + KK - 1 .EQ. 0) GO TO 110 GO TO 120 100 CONTINUE WRITE ( 16, 9000 ) 110 CONTINUE WRITE ( 16, 9010 ) ( K, K = IZ, NIF ) 120 CONTINUE IJ = 2 * (NIF - IZ + 1 ) + 1 IF (II .GT. 0) THEN DO 130 IR = IZ, N JJ = IR JJ = MIN0 ( NIF,JJ ) WRITE ( 16, 9020 ) IR, ( A(IR,IC), IC = IZ, JJ ) 130 CONTINUE ELSE DO 140 IR = 1, N WRITE ( 16, 9020 ) IR, ( A(IR,IC), IC = IZ, NIF ) 140 CONTINUE ENDIF 150 CONTINUE RETURN 9000 FORMAT (1H1) 9010 FORMAT(1H0,/10I12) 9020 FORMAT(1H I2,10F12.5) END BLOCK DATA ATOMS IMPLICIT REAL*8 (A-H,O-Z) DIMENSION COVRAD(99),ATWT(99) CHARACTER*2 EL(99) C COMMON/COVRAD/COVRAD,ATWT,EL C DATA COVRAD/ 1 0.3200, 0.9300, 1.2300, 0.9000, 0.8200, 0.7700, 2 0.7500, 0.7300, 0.7200, 0.7100, 1.5400, 1.3600, 3 1.1800, 1.1100, 1.0600, 1.0200, 0.9900, 0.9800, 4 2.0300, 1.7400, 1.4400, 1.3200, 1.2200, 1.1800, 5 1.1700, 1.1700, 1.1600, 1.1500, 1.1700, 1.2500, 6 1.2600, 1.2200, 1.2000, 1.1600, 1.1400, 1.1200, 7 2.1600, 1.9100, 1.6200, 1.4500, 1.3400, 1.3000, 8 1.2700, 1.2500, 1.2500, 1.2800, 1.3400, 1.4800, 9 1.4400, 1.4100, 1.4000, 1.3600, 1.3300, 1.3100, 1 2.3500, 1.9800, 1.6900, 1.6500, 1.6500, 1.6400, 2 1.6300, 1.6200, 1.8500, 1.6100, 1.5900, 1.5900, 3 1.5800, 1.5700, 1.5600, 1.5600, 1.5600, 1.4400, 4 1.3400, 1.3000, 1.2800, 1.2600, 1.2700, 1.3000, 5 1.3400, 1.4900, 1.4800, 1.4700, 1.4600, 1.4600, 6 1.4500, 0.0000, 0.0000, 0.0000, 0.0000, 1.6500, 7 0.0000, 1.4200, 0.0000, 0.0000, 0.0000, 0.0000, 8 0.0000, 0.0000, 0.0000/ C DATA ATWT/ & 1.00797, 4.00260, 6.93900, 9.01220, 10.81100, & 12.01115, 14.00670, 15.99940, 18.99840, 20.18300, & 22.98980, 24.31200, 26.98150, 28.08600, 30.97380, & 32.06400, 35.45300, 39.94800, 39.10200, 40.08000, & 44.95600, 47.90000, 50.94200, 51.99600, 54.93800, & 55.84700, 58.93300, 58.71000, 63.54000, 65.37000, & 69.72000, 72.59000, 74.92200, 78.96000, 79.90900, & 83.80000, 85.47000, 87.62000, 88.90500, 91.22000, & 92.90600, 95.94000, 98.00000, 101.07000, 102.90500, & 106.40000, 107.87000, 112.40000, 114.82000, 118.69000, & 121.75000, 127.60000, 126.90400, 131.30000, 132.90500, & 137.34000, 138.91000, 140.12000, 140.90700, 144.24000, & 147.00000, 150.35000, 151.96000, 157.25000, 158.92400, & 162.50000, 164.93000, 167.26000, 168.93400, 173.04000, & 174.97000, 178.49000, 180.94800, 183.85000, 186.20000, & 190.20000, 192.20000, 195.09000, 196.96700, 200.59000, & 204.37000, 207.19000, 208.98000, 210.00000, 210.00000, & 222.00000, 13*250.0/ C DATA EL/' H','HE','LI','BE',' B',' C',' N',' O', 1 ' F','NE','NA','MG','AL','SI',' P',' S','CL', 2 'AR',' K','CA','SC','TI',' V','CR','MN','FE', 3 'CO','NI','CU','ZN','GA','GE','AS','SE','BR', 4 'KR','RB','SR',' Y','ZR','NB','MO','TC','RU','RH', 5 'PD','AG','CD','IN','SN','SB','TE',' I','XE', 6 'CS','BA','LA','CE','PR','ND','PM','SM','EU','GD', 7 'TB','DY','HO','ER','TM','YB','LU','HF','TA',' W', 8 'RE','OS','IR','PT','AU','HG','TL','PB','BI','PO', 9 'AT','RN','FR','RA','AC','TH','PA',' U','NP','PU','AM','CM', 1'BK','CF','ES'/ END SUBROUTINE GETXYZ(NA, NB, NC, ND, RIJ, THETA, PHI) C************************************************************************** C IMSL ROUTINES CALLED: DMRRRR - MATRIX MULTIPLY (REAL * REAL) C DCRGRG - MATRIX COPY (REAL TO REAL) C DLINRG - MATRIX INVERSION (REAL) C************************************************************************** IMPLICIT REAL*8 (A-H,O-Z) DIMENSION X(100),Y(100),Z(100) COMMON /WORK/ X, Y, Z, DEGRAD C DIMENSION Q(4,4), R(4,4), RTOT(4,4), TMP(4,4), E(4,4) C DATA EPS/1.0D-08/ C C-----LOAD Q ARRAY DO 5 J = 1, 4 DO 4 I = 1, 4 RTOT(I,J) = 0. Q(I,J) = 0. E(I,J) = 0. 4 CONTINUE RTOT(J,J) = 1. E(J,J) = 1. Q(4,J) = 1. 5 CONTINUE Q(1,1) = X(NA) Q(2,1) = Y(NA) Q(3,1) = Z(NA) Q(1,2) = X(NB) Q(2,2) = Y(NB) Q(3,2) = Z(NB) Q(1,3) = X(NC) Q(2,3) = Y(NC) Q(3,3) = Z(NC) Q(4,4) = 0. C D WRITE(46,7999)NA, NB, NC, ND, RIJ, THETA, PHI D7999 FORMAT('1ENTERING *GETXYZ*; ATOM SEQUENCE, R/TH/PH = ',4I5, D & 3F12.5) D ASSIGN 9 TO IQW D GO TO 1000 9 CONTINUE C C-----TRANSLATE ORIGIN TO ATOM B 10 CONTINUE CALL DCRGRG(4, E, 4, R, 4) DO 15 I = 1, 3 R(I,4) = -Q(I,2) 15 CONTINUE C D WRITE(46,7998) D7998 FORMAT(////'0TRANSLATE ORIGIN TO ATOM B') D ASSIGN 16 TO IRQW D GO TO 2000 C 16 CONTINUE CALL DMRRRR(4, 4, R, 4, 4, 4, Q, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, Q, 4) CALL DMRRRR(4, 4, R, 4, 4, 4, RTOT, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, RTOT, 4) C D ASSIGN 19 TO IQW D GO TO 1000 C 19 CONTINUE C C-----Z-ROTATION: ATOM C INTO XZ-PLANE (YC->0) 20 CONTINUE CALL DCRGRG(4, E, 4, R, 4) DXY = DSQRT(Q(1,3)**2 + Q(2,3)**2) IF (DXY .LT. EPS) GO TO 29 R(1,1) = Q(1,3)/DXY R(2,2) = R(1,1) R(1,2) = Q(2,3)/DXY R(2,1) = -R(1,2) C D WRITE(46,7997) D7997 FORMAT(////'0Z-ROTATION: ATOM C INTO XZ-PLANE (YC->0)') D ASSIGN 26 TO IRQW D GO TO 2000 26 CONTINUE C CALL DMRRRR(4, 4, R, 4, 4, 4, Q, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, Q, 4) CALL DMRRRR(4, 4, R, 4, 4, 4, RTOT, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, RTOT, 4) C D ASSIGN 29 TO IQW D GO TO 1000 29 CONTINUE C C-----Y-ROTATION: ATOM C ONTO Z-AXIS (XC->0) 30 CONTINUE CALL DCRGRG(4, E, 4, R, 4) DXZ = DSQRT(Q(3,3)**2 + Q(1,3)**2) IF (DXZ .LT. EPS) GO TO 39 R(3,3) = Q(3,3)/DXZ R(1,1) = R(3,3) R(3,1) = Q(1,3)/DXZ R(1,3) = -R(3,1) C D WRITE(46,7996) D7996 FORMAT(////'0Y-ROTATION: ATOM C ONTO Z-AXIS (XC->0)') D ASSIGN 36 TO IRQW D GO TO 2000 C 36 CONTINUE CALL DMRRRR(4, 4, R, 4, 4, 4, Q, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, Q, 4) CALL DMRRRR(4, 4, R, 4, 4, 4, RTOT, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, RTOT, 4) C D ASSIGN 39 TO IQW D GO TO 1000 C 39 CONTINUE C C-----Z-ROTATION: ATOM A INTO XZ-PLANE (YA = 0) 40 CONTINUE CALL DCRGRG(4, E, 4, R, 4) DXY = DSQRT(Q(1,1)**2 + Q(2,1)**2) IF (DXY .LT. EPS) GO TO 49 R(1,1) = Q(1,1)/DXY R(2,2) = R(1,1) R(1,2) = Q(2,1)/DXY R(2,1) = -R(1,2) C D WRITE(46,7995) D7995 FORMAT(////'0Z-ROTATION: ATOM Z INTO XZ-PLANE (YA = 0)') D ASSIGN 46 TO IRQW D GO TO 2000 C 46 CONTINUE CALL DMRRRR(4, 4, R, 4, 4, 4, Q, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, Q, 4) CALL DMRRRR(4, 4, R, 4, 4, 4, RTOT, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, RTOT, 4) C D ASSIGN 49 TO IQW D GO TO 1000 C 49 CONTINUE C C-----ADD ATOM D IN LOCAL COORDINATES IF (THETA .EQ. 180.) THEN Q(3,4) = Q(3,3) + RIJ ELSE THBCD = THETA * DEGRAD PHABCD = PHI * DEGRAD DZ = RIJ * DCOS(THBCD) DXY = RIJ * DSIN(THBCD) Q(3,4) = Q(3,3) - DZ Q(1,4) = DXY * DCOS(PHABCD) Q(2,4) = DXY * DSIN(PHABCD) END IF Q(4,4) = 1. D WRITE(46,6995) D6995 FORMAT(////'0ADD ATOM D IN LOCAL COORDINATES') D ASSIGN 59 TO IQW D GO TO 1000 59 CONTINUE C C-----PUT INVERSE OF RTOT-MATRIX INTO R-MATRIX; APPLY INVERSE TRANSFORM CALL DLINRG(4, RTOT, 4, R, 4) WRITE(46,7994) 7994 FORMAT(////'0APPLY INVERSE TRANSFORM') D ASSIGN 96 TO IRQW D GO TO 2000 96 CONTINUE CALL DMRRRR(4, 4, R, 4, 4, 4, Q, 4, 4, 4, TMP, 4) CALL DCRGRG(4, TMP, 4, Q, 4) D ASSIGN 99 TO IQW D GO TO 1000 C 99 CONTINUE X(ND) = Q(1,4) Y(ND) = Q(2,4) Z(ND) = Q(3,4) C RETURN C============================================================================ 1000 CONTINUE D WRITE(46,9999) D9999 FORMAT('0 CURRENT (Q MATRIX)'/) D DO 1010 I = 1, 4 D WRITE(46,9998)(Q(I,J),J = 1, 4) D1010 CONTINUE D9998 FORMAT('|',4F15.9,'|') D GO TO IQW C============================================================================ 2000 CONTINUE D WRITE(46,8999) D8999 FORMAT('0TRANSFORMATION: (R-MATRIX) * (Q-MATRIX)'/) D DO 2010 I = 1, 4 D WRITE(46,8998)(R(I,J),J=1,4), (Q(I,K),K=1,4) D2010 CONTINUE D8998 FORMAT(' |',4F15.9,'|',6X,'|',4F15.9,'|') D GO TO IRQW C============================================================================ C END From: David Heisterberg ------------------ The following is some Fortran code to do the conversion, but it explains the method pretty well. -------- C C Z2C C Convert Z matrix to cartesian coordinates. C C The Z matrix coordinates are simply local polar coordinates in which C c0 - defines the local origin C c1 - defines the local z axis C c2 - defines the local +zx quadrant C SUBROUTINE z2c (n, nc, zc, cc, q, lerr) IMPLICIT CHARACTER (A-Z) C C n - number of centers C nc - neighbor (or connectivity) indices C zc - zmatrix (r, a, d) coordinates C cc - cartesian coordinates C q - quality of local coordinates (best if < 1) C lerr - lun on which to report fatal errors C fatal errors are C forward referenced neighbors C numerically degenerate local axes C INTEGER n INTEGER nc (3, *) DOUBLEPRECISION zc (3, *) DOUBLEPRECISION cc (3, *) DOUBLEPRECISION q (*) INTEGER lerr C DOUBLEPRECISION qeps PARAMETER (qeps = 0.001) C DOUBLEPRECISION c0 (3), c2 (3) DOUBLEPRECISION x (3), y (3), z (3) DOUBLEPRECISION xnorm, ynorm, znorm DOUBLEPRECISION sint, cost DOUBLEPRECISION xfac, yfac, zfac DOUBLEPRECISION r, a, d INTEGER i, i0, i1, i2 C C center 1 at the origin C IF (n .LT. 1) RETURN cc (1, 1) = 0.0D0 cc (2, 1) = 0.0D0 cc (3, 1) = 0.0D0 q (1) = 0.0D0 C C center 2 on z axis C IF (n .LT. 2) RETURN r = zc (1, 2) cc (1, 2) = 0.0D0 cc (2, 2) = 0.0D0 cc (3, 2) = r q (2) = 0.0D0 C C center 3 in zx plane C IF (n .LT. 3) RETURN r = zc (1, 3) a = zc (2, 3) i0 = nc (1, 3) i1 = nc (2, 3) C C check i0 and i1 C IF ((i0 .LE. 0) .OR. (i0 .GE. 3)) THEN WRITE (lerr, 1000) i0, i STOP ELSEIF ((i1 .LE. 0) .OR. (i1 .GE. 3)) THEN WRITE (lerr, 1001) i1, i STOP ENDIF C C find the local origin and +z axis C c0 (3) = cc (3, i0) z (3) = SIGN (1.0D0, cc (3, i1) - c0 (3)) C C target coordinates are in local +xz quadrant C cc (1, 3) = r * sin (a) * z (3) cc (2, 3) = 0.0D0 cc (3, 3) = r * cos (a) * z (3) + c0 (3) q (3) = 0.0D0 C C centers 4 to n C DO 10000 i = 4, n r = zc (1, i) a = zc (2, i) d = zc (3, i) i0 = nc (1, i) i1 = nc (2, i) i2 = nc (3, i) C C check i0, i1, i2 C IF ((i0 .LE. 0) .OR. (i0 .GE. i)) THEN WRITE (lerr, 1000) i0, i STOP ELSEIF ((i1 .LE. 0) .OR. (i1 .GE. i)) THEN WRITE (lerr, 1001) i1, i STOP ELSEIF ((i2 .LE. 0) .OR. (i2 .GE. i)) THEN WRITE (lerr, 1002) i2, i STOP ENDIF C C c0 is the local origin C c0 (1) = cc (1, i0) c0 (2) = cc (2, i0) c0 (3) = cc (3, i0) C C the local z axis C check for degeneracy C z (1) = cc (1, i1) - c0 (1) z (2) = cc (2, i1) - c0 (2) z (3) = cc (3, i1) - c0 (3) znorm = SQRT (z (1) * z (1) + z (2) * z (2) + z (3) * z (3)) IF (znorm .LE. 0.0D0) THEN WRITE (lerr, 1011) 'Z', i STOP ENDIF C C c2 defines the local +zx quadrant C c2 (1) = cc (1, i2) - c0 (1) c2 (2) = cc (2, i2) - c0 (2) c2 (3) = cc (3, i2) - c0 (3) C C the local y axis is z cross c2 C check for degeneracy C y (1) = z (2) * c2 (3) - z (3) * c2 (2) y (2) = z (3) * c2 (1) - z (1) * c2 (3) y (3) = z (1) * c2 (2) - z (2) * c2 (1) ynorm = SQRT (y (1) * y (1) + y (2) * y (2) + y (3) * y (3)) IF (ynorm .LE. 0.0D0) THEN WRITE (lerr, 1011) 'Y', i STOP ENDIF C C the local x axis is y cross z C check for degeneracy C x (1) = y (2) * z (3) - y (3) * z (2) x (2) = y (3) * z (1) - y (1) * z (3) x (3) = y (1) * z (2) - y (2) * z (1) xnorm = SQRT (x (1) * x (1) + x (2) * x (2) + x (3) * x (3)) IF (xnorm .LE. 0.0D0) THEN WRITE (lerr, 1011) 'X', i STOP ENDIF C C cost = ABS (z dot c2) C sint = ynorm C if sint is very small compared to cost, "floor" it at qeps * cost C cost = ABS (z (1) * c2 (1) + z (2) * c2 (2) + z (3) * c2 (3)) sint = ynorm IF (sint .LT. qeps * cost) sint = qeps * cost q (i) = cost / sint C C normalize the axes C (do this as late as possible to preserve accuracy, and do C it as a separate step because the magnitude of the norms C are only known to be commensurate with the axis components) C x (1) = x (1) / xnorm x (2) = x (2) / xnorm x (3) = x (3) / xnorm y (1) = y (1) / ynorm y (2) = y (2) / ynorm y (3) = y (3) / ynorm z (1) = z (1) / znorm z (2) = z (2) / znorm z (3) = z (3) / znorm C C fold r, a, d into the 'fac'tors C xfac = r * SIN (a) * COS (d) yfac = r * SIN (a) * SIN (d) zfac = r * COS (a) C C now the target coordinates are a simple affine transformation of C the local axes C cc (1, i) = xfac * x (1) + yfac * y (1) + zfac * z (1) + c0 (1) cc (2, i) = xfac * x (2) + yfac * y (2) + zfac * z (2) + c0 (2) cc (3, i) = xfac * x (3) + yfac * y (3) + zfac * z (3) + c0 (3) 10000 CONTINUE C RETURN C 1000 FORMAT ('z2c: invalid c0 (', I6, ') for center ', I6) 1001 FORMAT ('z2c: invalid c1 (', I6, ') for center ', I6) 1002 FORMAT ('z2c: invalid c2 (', I6, ') for center ', I6) 1011 FORMAT ('z2c: degenerate local axis (', A, ') for center ', I6) C END From: tj ODonnell ---------------------------------------- This is the way I do it. With n atoms, there are 3n Cartesian coordinates needed to descibe the molecule in space. However, there are only 3n-6 internal coordinates available. So we make the assumption that atom 1 (which has NO internal coordinates) is at (0,0,0). Atom 2 has 1 internal coord (a bond distance) and is assumed to be along the x axis. Atom 3 has 2 internals (a bond distance and angle) and is assumed to be in the xy plane. From this point on, it is simply a matter of geometry to find the location of atoms 4...n (having distance, bond angle and torsion (or plane) angle). Any atom d can be thought of as related to atoms c-b-a such that d-c-b-a forms two planes dcb and cba. The torsion angle is the angle between these planes. The bond angle is the dcb angle and the bond distance is the dc distance. IT IS IMPORTANT TO KNOW THE CONVENTION FOR THE SIGNS OF THE TORSION ANGLES OR YOU MAY GET THE WRONG ENANTIOMER OF THE MOLECULE. Unfortunately, people make different assumptions and if it is not known, there is nothing you can do but guess. The only two assumptions are that a positive torsion angle is either a clockwise or counter-clockwise rotation of plane dcb relative to plane cba. Hope this helps. Let me know if I can help any more. TJ O'Donnell http://www.eecs.uic.edu/~tj/ From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) -------------------------------------------------- Wenn die internen Koordinaten in Form einer Z-Matrix vorliegen, ist die Sache einfach: jede Zeile enthaelt die komplette Information fuer die Position eines Atoms relativ zu den vorherigen, deren Positionen bereits bekannt sind. Die drei Koordinaten jeder Zeile sind Kugelkoordinaten in einem Koordinatensystem, das durch die Positionen der drei Referenzatome definiert ist. Nur die drei ersten Atome erfordern eine Sonderbehandlung, da einige Koordinaten nicht festgelegt sind und damit beliebig gewaehlt werden koennen. Nicht vergessen: Wenn der Winkel 180 Grad betraegt, sollte der Diederwinkel ignoriert werden. Es hat keinen Sinn, lineare Winkel zu verbieten, wie es etwa Gaussian macht. Wenn die Eingabe etwas flexibler sein soll (was ich persoenlich bevorzuge), wird die Strategie etwas komplizierter. In jedem Schritt muss man zunaechst ein Atom suchen, fuer das drei interne Koordinaten relativ zu bereits fixierten Atomen vorhanden sind. Danach geht es weiter wie oben. Bei Interesse kann ich einen relativ lesbaren C++-Code anbieten, der natuerlich eine etwas praezisere Beschreibung darstellt. Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Universite de Montreal | Fax: +1-514-343-7586 From: edu@lasierra.lasierra.edu (lee wilson) --------------------------------------------- Dear Thomas; Not sure what you mean about MOPAC6 being different. If you have a set of internal coordinates: bond distances, bond angles and dihedral angles- it will give readily the xyz coordinates. That is given a Z-matrix of internal coordinates in a MOPAC input file (.MNI or .DAT) with XYZ and 0SCF (either one or both, think) would give a MOPAC output file which displays the cartesion coordinates. If you want to get the coordinates that will do it. However I gather that you are interested in incorporating a routine into software. Seems that you could adapt an appropriate MOPAC routine. lee wilson From ejfried@herzberg.ca.sandia.gov Fri May 5 17:18:41 1995 Received: from herzberg.ca.sandia.gov for ejfried@herzberg.ca.sandia.gov by www.ccl.net (8.6.10/930601.1506) id RAA02489; Fri, 5 May 1995 17:15:44 -0400 Received: (from ejfried@localhost) by herzberg.ca.sandia.gov (8.6.11/8.6.10) id VAA21465 for chemistry@ccl.net; Fri, 5 May 1995 21:14:24 GMT From: "Ernest Friedman-Hill" Message-Id: <9505051414.ZM21463@herzberg> Date: Fri, 5 May 1995 14:14:24 -0700 In-Reply-To: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) "CCL:TCL Comp. Chem tools.." (May 5, 3:23pm) References: <9505051923.AA09647@cyclone.ERE.UMontreal.CA> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Re: CCL:TCL Comp. Chem tools.. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hinsen Konrad (hinsenk@ERE.UMontreal.CA) has been railing against the use of Tcl for scripting chemistry tools, and against the premature establishment of standards. Don't get me wrong, folks, I am certainly aware of the problems that we all deal with that were caused by the 16-bit segmented PC architecture becoming a de facto standard. But what would you have us all do, Mr. Konrad? Folks with PCs used them to design today's better architectures. No one said, "everyone must use the PC-clone architecture." It just happened, and as a result, computers became cheap commodities and the world benefitted immeasurably. Structured programming would never have been invented if the power of high-level language programming hadn't been demonstrated by FORTRAN. Remember, early FORTRAN programmers were looked down on as coddled and wimpy because they weren't programming in the one true language, assembler (which, before that, was for wimps who couldn't hack direct-to-binary.) Good standards are those that allow a lot of people to get a lot of work done. Bad standards are those invented by folks whose idea of work is forming committees to design standards that no one asked for. If you have positive ideas to contribute, let's hear them. -- --------------------------------------------------------- Ernest Friedman-Hill Senior Member of Technical Staff Scientific Computing Department Sandia National Laboratories Org. 8117, MS 9214 PO Box 969 Livermore, CA 94550 From rsjuds@california.sandia.gov Fri May 5 18:18:43 1995 Received: from california.sandia.gov for rsjuds@california.sandia.gov by www.ccl.net (8.6.10/930601.1506) id SAA03553; Fri, 5 May 1995 18:02:17 -0400 Received: (from rsjuds@localhost) by california.sandia.gov (8.6.11/1.15) id PAA15440 for chemistry@ccl.net; Fri, 5 May 1995 15:02:06 -0700 From: rsjuds@california.sandia.gov (judson richard s) Message-Id: <199505052202.PAA15440@california.sandia.gov> Subject: Genetic algorithms in chemistry To: chemistry@ccl.net Date: Fri, 5 May 1995 15:02:05 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 576 I am putting together a review article on the uses of genetic algorithms in chemistry. I have read just about everything published through the end of 1994. I would appreciate getting reprints/preprints of relevant papers coming out since then. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering, MS 9214 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | (510)294-2234 (FAX) | | email: rsjuds@ca.sandia.gov | | | ----------------------------------------------- From gavin@vangogh.chem.uab.edu Fri May 5 23:48:45 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id XAA06558; Fri, 5 May 1995 23:38:25 -0400 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA08963; Fri, 5 May 1995 22:33:06 -0500 Date: Fri, 5 May 1995 22:33:06 -0500 Message-Id: <9505060333.AA08963@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: Scan=Opt in G94 Dear Sir, I run the relaxed PES scan in G94, but it does not work! This is my input file: $RunGauss %chk=test.chk #HF/STO-3G Scan=Opt xap86 0 1 H O 1 r1 H 2 r1 1 a1 r1 0.99 S 3 0.02 a1 100.0 S 3 1.00 The G94 only optimize the geometry, but not scan the PES! Someone has the experience on this jobs? Thanks! Gavin Tsai