From gmercier@mail.med.upenn.edu Fri Jan 10 08:15:22 1997 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.3/950822.1) id HAA14160; Fri, 10 Jan 1997 07:58:51 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.8.4/8.8.4) id HAA22292 for CHEMISTRY@www.ccl.net; Fri, 10 Jan 1997 07:58:52 -0500 (EST) From: "Gustavo A. Mercier Jr" Message-Id: <199701101258.HAA22292@mail.med.upenn.edu> Subject: quaternions from direction cosine matrix? To: CHEMISTRY@www.ccl.net Date: Fri, 10 Jan 1997 07:58:52 -0500 (EST) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! I need assistance with the following problem that arises in rigid body dynamics. Molecular rotations can be described using quaternions rather than Euler angles with the advantage that the equations are well behaved. To specify the initial configuration I need the center of mass and the quaternions describing the orientation of the molecules. I can get the direction cosine matrix from a diagonalization of the Moment of Inertia Matrix. After I specify a given convention for the Euler angles (eg. x convention in the Allen and Tidsley book), I get a relationship between this matrix and the matrix specified in terms of quaternions. (See Allen and Tidsley.) Problem: In solving for the quaternions (qo,q1,q2,q3), I get equations for the square of the quaternions (qo**2, q1**2, q2**2, q3**2). Obviously, this leaves the sign undefined. That is the problem! Question: How do you define the sign of the quaternion knowing the values of the direction cosine matrix and not the actual Euler angles? Any assistance would be appreciated. The goal here is to filter Amber output in to the program Moldy. If anybody is interested in this filter I will gladly make it public once it is coded and tested. Thanks for the assistance! -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 From fampl@usc.es Fri Jan 10 10:15:23 1997 Received: from uscmail.usc.es for fampl@usc.es by www.ccl.net (8.8.3/950822.1) id KAA14764; Fri, 10 Jan 1997 10:02:30 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA21540; Fri, 10 Jan 1997 16:02:28 +0100 Date: Fri, 10 Jan 1997 16:02:27 +0100 (MET) From: Manuel Pereiro Lopez To: chemistry@www.ccl.net Subject: About angular moment. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE =09Hello, my friends: =09I=ABd like to know the value of the angular moment of the Fe=20 (Iron). If somebody can help me and find out this value, I=ABd like to know= =20 it. Results will be appreciated. =09=09=09=09=09=09Manuel Pereiro.=20 From maerker@ccc.uni-erlangen.de Fri Jan 10 12:17:12 1997 Received: from faui45.informatik.uni-erlangen.de for maerker@ccc.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id LAA15701; Fri, 10 Jan 1997 11:16:50 -0500 (EST) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id RAA19856 (8.7.6/7.5c-FAU); for ; Fri, 10 Jan 1997 17:16:29 +0100 (MET) Received: from [131.188.128.55] (lc2.organik.uni-erlangen.de [131.188.128.55]) by organik.uni-erlangen.de with SMTP id RAA08974 (8.6.12/7.4f-FAU); for ; Fri, 10 Jan 1997 17:16:20 +0100 Date: Fri, 10 Jan 1997 17:16:20 +0100 X-Sender: maerker@derioc1.organik.uni-erlangen.de Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: maerker@ccc.uni-erlangen.de (Christoph Maerker) Subject: HMO bond-bond polarizability matrix Dear CCL readers, I am looking for a free HMO program for Macintosh computers which also calculates and diagonalizes the atom-atom, atom-bond, and bond-bond polarizability matrices. A graphical input interface and editable parameter sets are highly desirable. Any hints to relevant URL's, ftp sites or other notes will be appreciated. Sincerely yours, Christoph PS Happy New Year to everybody ! +=======================+=======================+ | Mr. Christoph Maerker| | Institut fuer Organische Chemie I | | Universitaet Erlangen-Nuernberg | email: maerker@ccc.uni-erlangen.de | Henkestrasse 42 | FAX: 09131-85-9132 | D-91054 Erlangen, Germany | phone: 09131-85-6580 +=======================+=======================+ From critchlr@pleiades.chiron.com Fri Jan 10 14:15:25 1997 Received: from mail2.pilot.net for critchlr@pleiades.chiron.com by www.ccl.net (8.8.3/950822.1) id NAA17046; Fri, 10 Jan 1997 13:52:58 -0500 (EST) Received: from artemis.chiron.com (unknown-46-3.chiron.com [206.189.46.3]) by mail2.pilot.net with ESMTP id KAA15972; Fri, 10 Jan 1997 10:52:33 -0800 (PST) Received: (from mailmand@localhost) by artemis.chiron.com id JAA21069; Fri, 10 Jan 1997 09:38:54 -0800 (PST) Received: from mercury.chiron.com(165.140.29.1) by artemis.chiron.com via smap (V1.3) id sma021065; Fri Jan 10 09:38:53 1997 Received: from pleiades.chiron.com (pleiades.chiron.com [165.140.41.131]) by mercury.chiron.com (v8_jeh/v8_jeh) with ESMTP id KAA03338; Fri, 10 Jan 1997 10:58:04 -0800 (PST) Received: (from critchlr@localhost) by pleiades.chiron.com (8.7/8.7) id KAA01981; Fri, 10 Jan 1997 10:52:33 -0800 (PST) Date: Fri, 10 Jan 1997 10:52:33 -0800 (PST) From: Roger Critchlow Message-Id: <199701101852.KAA01981@pleiades.chiron.com> To: "Gustavo A. Mercier Jr" Cc: CHEMISTRY@www.ccl.net Subject: CCL:quaternions from direction cosine matrix? In-Reply-To: <199701101258.HAA22292@mail.med.upenn.edu> References: <199701101258.HAA22292@mail.med.upenn.edu> Gustavo A. Mercier, Jr. writes: > > Question: How do you define the sign of the quaternion knowing the values > of the direction cosine matrix and not the actual Euler angles? > Possibly my favorite formula: given two unit vectors, u and v, the quaternion, q, formed from: scalar_part(q) = vector_dot_product(u,v) vector_part(q) = vector_cross_product(u,v) is a unitary quaternion which rotates the vector u in the plane defined by u and v by twice the signed angle from u to v. So to construct a quaternion which rotates a unit vector u into a unit vector w, one need only construct a unit vector v which bisects the angle between u and w. -- rec -- From lawson@argus.cem.msu.edu Fri Jan 10 14:26:54 1997 Received: from argus.cem.msu.edu for lawson@argus.cem.msu.edu by www.ccl.net (8.8.3/950822.1) id NAA16966; Fri, 10 Jan 1997 13:42:12 -0500 (EST) From: Received: from bohr.cem.msu.edu by argus.cem.msu.edu via ESMTP (950413.SGI.8.6.12/951211.SGI) for id NAA08091; Fri, 10 Jan 1997 13:42:18 -0500 Received: by bohr.cem.msu.edu (950413.SGI.8.6.12/) for chemistry@www.ccl.net id NAA15447; Fri, 10 Jan 1997 13:42:36 -0500 Date: Fri, 10 Jan 1997 13:42:36 -0500 Message-Id: <199701101842.NAA15447@bohr.cem.msu.edu> To: chemistry@www.ccl.net Subject: viewmol question????? I am having trouble running the viewmol binary: >Viewmol was developed under Linux, but is currently known to >run also on IBM's AIX, SGI's IRIX, Digital's OSF1, and HP's HP-UX. >It requires OpenGL or its freeware clone Mesa. 'ldd viewmol' gives 'libXm.so.2 => not found' It seems the binary file also requires $Motif :( since the libs are dynamically linked. The author left no email address in the documentation so if anyone has contact or he is a reciever of CCL; would it be possible to privide the binaries with static libs? If I am wrong about the Motif, then what is libXm.so.2 and where can I get a copy? Dan Lawson Michigan State University lawson@argus.cem.msu.edu ___________ ############ # # Dynamic linking is great for creating small binary files, but it is # not so great when the user must download and compile 20 Mb of # library support files. # J. Handy ############ From ahocquet@tamarugo.cec.uchile.cl Fri Jan 10 15:15:25 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id OAA17286; Fri, 10 Jan 1997 14:28:18 -0500 (EST) Received: from [146.83.10.50] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA21676; Fri, 10 Jan 1997 16:28:12 +0400 Date: Fri, 10 Jan 1997 16:28:12 +0400 Message-Id: <9701101928.AA21676@tamarugo.cec.uchile.cl> To: chemistry@www.ccl.net From: ahocquet@tamarugo.cec.uchile.cl (Alexandre Hocquet) Subject: looking for bipyrimidine... Estimados CCLeros, Given the cost of a bibliographic search, i am once again taking shamelessly advantage of the resources of the CCL community. I am currently looking for any structural (either experimental or computational) data about 2,2'-bipyrimidine, that is to say (if i remember well...i lost my iupac-english dictionary) a biphenyle with the four carbons vicinal to the bridge replaced by nitrogens. I would be interested too in any nitrogen containing, biphenyle like, heteroaromatic... I, of course, will provide a summary if there are sufficient answers. Thanks for your worldwide cooperation. Alexandre Hocquet ahocquet@cec.uchile.cl Laboratorio de Cristalografia Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago CHILE fax : 56 2 696 73 59 From mn1@helix.nih.gov Fri Jan 10 15:19:48 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id PAA17485; Fri, 10 Jan 1997 15:00:20 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.3/8.8.3) id PAA10427; Fri, 10 Jan 1997 15:00:20 -0500 (EST) Date: Fri, 10 Jan 1997 15:00:20 -0500 (EST) From: "M. Nicklaus" Message-Id: <199701102000.PAA10427@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Need exact reference Cc: mn1@helix.nih.gov CCL'er, Could someone please help me out with the exact bibliographic reference, i.e. the page numbers, for I. Pettersson and T. Liljefors, Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields, published in Vol. 9 of Reviews in Computational Chemistry, Lipkowitz, Boyd (Eds.). Thanks in advance, Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From markus@dali.isdn.uni-koeln.de Fri Jan 10 22:15:28 1997 Received: from dali.isdn.uni-koeln.de for markus@dali.isdn.uni-koeln.de by www.ccl.net (8.8.3/950822.1) id VAA22730; Fri, 10 Jan 1997 21:44:49 -0500 (EST) Received: (from markus@localhost) by franck.pc.uni-koeln.de (8.8.4/8.7.3) id DAA15334; Sat, 11 Jan 1997 03:44:59 +0100 Sender: markus@franck.pc.uni-koeln.de To: chemistry@www.ccl.net Subject: Re: CCL:viewmol question????? References: <199701101842.NAA15447@bohr.cem.msu.edu> Mime-Version: 1.0 (generated by tm-edit 7.96) Content-Type: text/plain; charset=US-ASCII From: Markus Dickebohm Date: 11 Jan 1997 03:44:56 +0100 In-Reply-To: lawson@argus.cem.msu.edu's message of Fri, 10 Jan 1997 13:42:36 -0500 Message-ID: Lines: 23 X-Mailer: Gnus v5.2.40/XEmacs 19.14 X-URL: http://www.uni-koeln.de/~acp66 X-PGP-Key: finger m.dickebohm@uni-koeln.de X-PGP-Fingerprint: A0 FE 17 0C A6 B7 7A 0F F0 A0 04 45 F4 91 54 A7 X-Face: (EiYvvA${"nyp)>kY)*s@0|x+.`PH2*GP}HF}/U6e>vR>0R#V9IF'@a>ce?{OudAu}2Om|K S6R{JT$|\ZF(IHHey5B(*+8.N_Z.c]O2KVJSxAT-y6RNmspR{:=^^0-fq,>z'a+4'JQyxPMWnZ5#h< (Rq{]7T;:kg^k0-P64revjBT+P)^^':u9>]f2UEFssRXw2a}A63'eq2mhgY].cTp8LvDz0Jf$:CLW= Dl|Y73lr >> "lawson" == lawson wrote on Fri, 10 Jan 1997 13:42:36 -0500: lawson> It seems the binary file also requires $Motif :( since the lawson> libs are dynamically linked. The author left no email address lawson> in the documentation so if anyone has contact or he is a lawson> reciever of CCL; would it be possible to privide the binaries lawson> with static libs? Unfortunately I have some problems compiling viewmol from source. I already contacted the author and received a reply, but unfortunately not all of the problems are solved so far. If this is the case maybe I can provide a statically linked version of viewmol. In any case I can say that "viewmol" is really impressive. lawson> If I am wrong about the Motif, then what is libXm.so.2 and lawson> where can I get a copy? No, you are perfectly right: "viewmol" _is_ dependent on Motif. Maybe you can give LessTif a try to compile viewmol -- many applications run happily with Lesstif (a free Motif clone) dynamically linked. Hope this helps, Markus