From szilagyi@miat0.vein.hu Tue Jan 11 05:49:19 1994 Received: from sztaki.hu for szilagyi@miat0.vein.hu by www.ccl.net (8.6.4/930601.1506) id EAA21194; Tue, 11 Jan 1994 04:56:58 -0500 From: Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id ki11992; Tue, 11 Jan 1994 10:55:02 +0100 Received: by miat0.vein.hu with SMTP (5.61++/Vein-1.0) id AA17813; Tue, 11 Jan 94 10:56:11 +0100 Message-Id: <9401110956.AA17813@miat0.vein.hu> To: cmao771@charon.chpc.utexas.edu (Bersuker) Cc: chemistry@ccl.net, szilagyi@miat0.vein.hu Subject: Re: MM for Transition Metal Cpds In-Reply-To: Your message of "Mon, 10 Jan 94 14:16:11 CST." <9401102016.AA28428@charon.chpc.utexas.edu> Date: Tue, 11 Jan 94 10:56:10 +0100 X-Mts: smtp X-Charset: US X-Char-Esc: 0 Dear Dr. Isaac B. Bersuker, I aggree with you, really indeed. Yes, you are right about the electronic effect! BUT ! Let's see what is a molecular mechanics. It is only a model without serious chemical background (only with some physical, Hooke law ...) I do not want to modell electronic interaction, but molecular structure. I would like to get as fast as I can a correct molecular structure of these TM complexes (especially, tunsgten carbene complexes). With the help of this force field I can model the steric interactions in particular reactions. I prepared lot's of ab initio calculation using GAMESS SBK ECP on our complexes. A bigger molecule (NAT>30) takes 1 mounth to compute the geometry. We parametrized the MM method so we can use it. This same size or bigger mol. takes only 1 or less minutes to compute the geometry. (I think you know the differences, advantages and disadvantages, too). By the way, if someone needs the electronic structure of the TM complex, he/she must use the ab initio theory, of course. If you combined these two theory (MM and ab initio) you can increase your speed, because you have an approximately good structure after the MM minimisation. (I tested!) Sometimes, you know the electronic structure (approximately, but enough deeply) only need the mol. structure. Use the METMOD1 force field and your result will be close to the experimental (RMS error must be less, than 0.1). Concerning last part of your message, if you can give some seminar in our school probably we can grant some of your expences. Something is not clear, just write me!! I am waiting your answer! Rob From pbays@saintmarys.edu Tue Jan 11 07:49:07 1994 Received: from jade.saintmarys.edu for pbays@saintmarys.edu by www.ccl.net (8.6.4/930601.1506) id HAA22565; Tue, 11 Jan 1994 07:19:56 -0500 Received: by jade.saintmarys.edu (1.37.109.8/16.2) id AA08332; Tue, 11 Jan 1994 07:23:29 -0500 Date: Tue, 11 Jan 1994 07:22:05 -0500 (EST) From: Phil Bays Subject: Extended Huckel To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of a quick and dirty, downloadable program that does simple extended Huckel calculations?? Phil Bays Saint Marys College Notre Dame IN 46556 pbays@saintmarys.edu From EDWARDSP@vax.edinboro.edu Tue Jan 11 08:49:08 1994 Received: from tetra.vax.edinboro.edu for EDWARDSP@vax.edinboro.edu by www.ccl.net (8.6.4/930601.1506) id IAA23024; Tue, 11 Jan 1994 08:40:06 -0500 Received: from vax.edinboro.edu by vax.edinboro.edu (PMDF V4.2-11 #2652) id <01H7JTEBFNU0984XH6@vax.edinboro.edu>; Tue, 11 Jan 1994 08:39:44 EDT Date: Tue, 11 Jan 1994 08:39:44 -0400 (EDT) From: "Dr. Paul Edwards" Subject: Re: Extended Huckel To: pbays@saintmarys.edu Cc: chemistry@ccl.net Message-id: <01H7JTEBFNU2984XH6@vax.edinboro.edu> X-VMS-To: IN%"pbays@saintmarys.edu" X-VMS-Cc: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT CACAO might be useful for your purposes. I think it is available from www.ccl.net. It comes with reasonable documentation included references. Paul Edwards Edinboro Univ. of PA From sauer@organik.uni-erlangen.de Tue Jan 11 11:00:16 1994 Received: from faui45.informatik.uni-erlangen.de for sauer@organik.uni-erlangen.de by www.ccl.net (8.6.4/930601.1506) id KAA23990; Tue, 11 Jan 1994 10:22:18 -0500 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA02935 (5.65c-6/7.3v-FAU); Tue, 11 Jan 1994 16:21:56 +0100 Received: by organik.uni-erlangen.de; id AA25692 (5.64/7.3n-FAU); Tue, 11 Jan 94 16:02:53 +0100 From: Wolfgang Sauer Message-Id: <9401111502.AA25692@derioc1.organik.uni-erlangen.de> Subject: Re: "Lock & Key" (Zuerich) To: CHEMISTRY@ccl.net (CompChem MailExploder) Date: Tue, 11 Jan 94 16:02:52 MET X-Mailer: ELM [version 2.3 PL11] > > I just noticed in Yate-Ching Yuan's summary posting the mentioning of > "Zuerich Lock & Key 15.-16.4.[1994(?)]". > Does anyone know anything more specific (scope, speakers, price, application > address etc.) about this conference? > Hi everybody, sorry for the delay. You probably got this several times by now, but since I am the original poster, I thought I should reply, no matter how late :-) That one is a meeting at ETH (Zuerich) commemorating the 100th anniversary of Emil Fischer postulating the "Lock & Key" concept. It is intended as a follow-up to the receptor research conference at Verbier (CH) (10.-14.4.), so there will be invited talks only. Lectures include: T.L.Blundell, F.Cramer, R.Huber, G.Jung, J.-M.Lehn, R.Hoffmann (at the banquet), M.F.Perutz, R.Poljak, G.Burnstock, H.Moehler, E.Mutschler and H.Kubinyi. Contact: LOCK + KEY c/o Bureco AG Postfach CH-4310 Rheinfelden Switzerland Charges: SFr 250.- (before 28.Feb.) 300.- (after 28.Feb.) Best regards and all the best, Wolfgang Sauer -- +======================================+=====================================+ | Wolfgang Sauer | | Institut fuer Organische Chemie I | Computational Chemistry Centre | | Henkestr. 42 | Naegelsbacher Str. 25 | | D-91054 Erlangen, FRG | D-91052 Erlangen, FRG | | sauer@organik.uni-erlangen.de | | Tel.: 49/0 - 9131 - 85 - 2952 | Tel.: 49/0 - 9131 - 85 - 6582 | | Fax: - 9132 | | +======================================+=====================================+ | "You have to be three standard deviations away from a normal personality | | to like UNIX." Morris Jones (C&T) | +======================================+=====================================+ From liang@chvymw.chem.ncsu.edu Tue Jan 11 11:49:46 1994 Received: from chvymw for liang@chvymw.chem.ncsu.edu by www.ccl.net (8.6.4/930601.1506) id KAA24313; Tue, 11 Jan 1994 10:54:15 -0500 From: Message-Id: <199401111554.KAA24313@www.ccl.net> Date: Tue, 11 Jan 1994 10:51:08 -0500 To: chemistry@ccl.net Subject: search for papers reviewing parameterization of force fields X-VMS-To: SMTP%"chemistry@ccl.net" Dear netters, I'm searching recent literature for REVIEW papers of parameterization of force field in molecular modeling without much success. In some lucky cases I found papers reviewing a particular type of force field, i.e., MM3, DREDING, UFF, etc, but most of the time I just got papers dealing with a small series of molecules, even a single molecule. Does anybody have a good lead to those papers which review (or invent) particular types of force fields, even the whole field of parameterization of force field in molecular modeling? I would appreciate it if you give me a clue, and if there are significant emails, I'll summarize them and post them to the list. Thanks. Weigen Liang From dqujfm0@PS.UIB.ES Tue Jan 11 11:50:36 1994 Received: from sc.uib.es for dqujfm0@PS.UIB.ES by www.ccl.net (8.6.4/930601.1506) id LAA24790; Tue, 11 Jan 1994 11:23:11 -0500 Received: from EAN_GATE by SC.UIB.ES (PMDF #12442) id <01H7KBGH0BKW000C9V@SC.UIB.ES>; Tue, 11 Jan 1994 17:15 1 Date: Tue, 11 Jan 1994 17:15:55 UTC+0200 From: Juan Frau Subject: Compilation Problem with Interchem To: chemistry@ccl.net Message-id: <90*dqujfm0@PS.UIB.ES> Content-identifier: 90 Conversion: Prohibited X400-content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=es/ADMD=/C=/;940111171555] X400-received: by /PRMD=es/ADMD=/C=/; Relayed; Tue, 11 Jan 1994 17:15:55 UTC+0200 X400-recipients: non-disclosure:; X400-Originator: dqujfm0@PS.UIB.ES Dear Netters, Recently I tried compile on a Silicon (Indigo 4.0.5.f) the Interchem Package Compilation instructions were: f77 -Nc40 -col120 -o inter\ And the system replied Warning absolute symbol: readfile has two different values previous (used) definition from '/usr/lib/libgl_s.a' new (ignored) definition from '/usr/lib/libfm_s.a' Warning _cassearchstart:multiply defined previous (used) definition from '/usr/lib/libX11_s.a' new (ignored) definition from '/usr/lib/libmpc.a' This second mistake is repeated another times, but -cassearchstart is susbstitued by: _ssetlock _lockcas1start _lockcas1end _lockcas2start _lockcas2end _scsetlock _clockcas1start _clockcas1end _sunsetlock _unlockcas1start _unlockcas1end _unlockcas2start _unlockcas2end _scas _scasstart _scasfail _scasend _hcas _hcasstart _hcasmayhave _hcashavelock _hcasfail _hcasend _cassearchend If you have the solution to the problem, please tell me it. Thanks in advance.Juan ************************************************** Juan Frau. Universitat Illes Balears. Dep Quimica Palma de Mallorca 07071. Baleares. Spain Email:dqujfm0@ps.uib.es fax: 34 71 17-34-26 ************************************************** From shenkin@still3.chem.columbia.edu Tue Jan 11 12:49:10 1994 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id MAA25638; Tue, 11 Jan 1994 12:12:17 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA19816 (5.65c+CU/IDA-1.4.4/HLK for chemistry@ccl.net); Tue, 11 Jan 1994 12:12:10 -0500 Received: by still3.chem.columbia.edu (930416.SGI/930416.SGI.AUTO) for @cunixf.cc.columbia.edu:chemistry@ccl.net id AA05272; Tue, 11 Jan 94 12:11:38 -0500 Date: Tue, 11 Jan 94 12:11:38 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9401111711.AA05272@still3.chem.columbia.edu> To: chemistry@ccl.net Subject: Rasmol I mentioned Rasmol, a protein visualization program, in a recent posting. A couple of days ago I received email asking how to get the program. Unfortunately, I accidentally deleted the email. So I'm replying as best I can to the list; hopefully more than one person will be interested. Going into our local archives and looking at the documentation, the most I can say is that the authorship is as follows: Copyright (C) 1993 by Roger Sayle (ros@dcs.ed.ac.uk) The program comes from the University of Edinburgh. I don't know if it's ftp-able from the above host; perhaps someone with more precise information can follow-up. Thanks (or Sorry, as the case may be :-) ), -P. ********** "Democracy: The theory that the common people know what ********* ******** they want, and deserve to get it good and hard." (Mencken) ******** Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 From noy@tci002.uibk.ac.at Tue Jan 11 12:52:41 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id MAA25588; Tue, 11 Jan 1994 12:07:17 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA27275 (5.65c/IDA-1.4.4 for ); Tue, 11 Jan 1994 18:07:02 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA33452; Tue, 11 Jan 1994 18:07:00 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9401111707.AA33452@tci002.uibk.ac.at> Subject: Re: diagonalize a matrix To: chemistry@ccl.net Date: Tue, 11 Jan 1994 18:07:00 +0100 (NFT) In-Reply-To: <9401102337.AA22665@host11.lctn.u-nancy.fr> from "jyk@host11.lctn.u-nancy.fr" at Jan 11, 94 00:37:31 am X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 5002 : : Dear Netters : : Has somebody a program, which allows to diagonalize a 3*3 : matrix as easily as possible : : thank you : : Kempf Jean-Yves Dear Dr. Kempf, I have enclosed a routine for matrix diagonalisation using JACOBI method ( The code is free, but copyrighted by CCP5 group, Daresbury, UK ). I would like to add an important note about the algorithm. The Jacobi method, as one knows, modifies only the lower triangle of the matrix. Once you use the code, you have to map the lower triangle which is already modified to the upper which is left unchanged, for example In the main program: call jacobi(mat1,mat2,3,1.0E-8) mat2(1,2) = mat2(2,1) mat2(1,3) = mat2(3,1) mat2(2,3) = mat2(3,2) Apart from the code, you may obtain other matrix numerical codes from netlib@ornl.gov by anonymously ftping to netlib2.cs.utk.edu or by e-mail. Mail to netlib@ornl.gov having the content as follows, send index from eispack When you get the index of the code, if you want, i.e., diagonal you can send command typically, send diagonal from eispack. ( Note that the package name "diagonal" may not exist. it's just my example ). I believe you will enjoy other diagonalisation scheme beside "jacobi". with best wishes, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci.uibk.ac.at, noy@tci2.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Tel : (43)(512) 5073232 (office) , (43)(512) 2215201 (home) FAX : (43)(512) 5073225 Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- ************************************************************************ * U.3 JACOBI Diagonalisation of symmetric matrices by jacobi method * ************************************************************************ subroutine jacobi(a,v,n,eps) dimension a(n,n),v(n,n) logical any C ---------------------------- Note --------------------------------- C *** a = starting matrix C *** b = diagonalized matrix C *** n = dimension of matrix C *** eps = criteria for convergence C *** probably you can try 1.0E-6, 1.0E-8 C *** The less the value is, the more accurate the outcome and C *** the more time spent. C *** Noted by: Teerakiat C *** C *** This part of the program is cited to CCP5, Daresbury C *** Collobarative Group, UK. C ---------------------------------------------------------------------- * * set v equal to identity * do 10 j=1,n do 10 i=1,n v(i,j)=0.0 if(i.eq.j) v(i,j)=1.0 10 continue * * scale matrix a * scl=0.0 do 1 i=1,n scl=scl+a(i,i)**2 1 continue scl=sqrt(scl)/3.0 do 2 j=1,n do 2 i=1,n a(i,j)=a(i,j)/scl 2 continue * * calculate quantity tes * tes=0.0 do 3 i=2,n do 3 j=1,i-1 tes=tes+2.0*a(i,j)**2 3 continue tes=sqrt(tes) * * loop while tes .gt. eps * icnt=0 100 continue icnt=icnt+1 * * loop while array elements are changing * jcnt=0 110 continue jcnt=jcnt+1 any=.false. * * loop over array elements * do 120 i=2,n do 120 j=1,i-1 if(abs(a(i,j)).le.tes) go to 120 any=.true. * v1=a(j,j) v2=a(i,j) v3=a(i,i) u=0.5*(v1-v3) if(abs(u).lt.eps) then omg=-1.0 else omg=-v2/sqrt(v2**2+u**2) if(u.lt.0.0) omg=-omg endif s=omg/sqrt(2.0*(1.0+sqrt(1.0-omg**2))) c=sqrt(1.0-s**2) * do 130 k=1,n if(k.ge.i) then temp=a(k,j)*c-a(k,i)*s a(k,i)=a(k,j)*s+a(k,i)*c a(k,j)=temp else if(k.lt.j) then temp=a(j,k)*c-a(i,k)*s a(i,k)=a(j,k)*s+a(i,k)*c a(j,k)=temp else temp=a(k,j)*c-a(i,k)*s a(i,k)=a(k,j)*s+a(i,k)*c a(k,j)=temp endif endif * temp=v(k,j)*c-v(k,i)*s v(k,i)=v(k,j)*s+v(k,i)*c v(k,j)=temp 130 continue * a(j,j)=v1*c**2+v3*s**2-2.0*v2*s*c a(i,i)=v1*s**2+v3*c**2+2.0*v2*s*c a(i,j)=(v1-v3)*s*c+v2*(c**2-s**2) 120 continue * if(any) then if(jcnt.lt.50) then go to 110 else print 101 endif endif * tes=tes/float(n) if(tes.gt.eps) then if(icnt.lt.50) then go to 100 else print 101 endif endif * * rescale matrix a * do 4 j=1,n do 4 i=1,n 4 a(i,j)=scl*a(i,j) return 101 format(4x,'WARNING Convergence problem in jacobi') end From memura@theory.chemistry.cambridge.ac.uk Tue Jan 11 13:50:26 1994 Received: from ib.rl.ac.uk for memura@theory.chemistry.cambridge.ac.uk by www.ccl.net (8.6.4/930601.1506) id NAA26580; Tue, 11 Jan 1994 13:42:57 -0500 Received: from letterbox.rl.ac.uk by ib.rl.ac.uk (IBM VM SMTP V2R1) with TCP; Tue, 11 Jan 94 18:42:43 GMT Via: uk.ac.cam.ch.theor; Tue, 11 Jan 1994 18:43:23 +0000 From: username Date: Tue, 11 Jan 94 18:41:15 GMT Message-Id: <23691.9401111841@theory.chemistry.cambridge.ac.uk> To: chemistry Subject: Hay-Wadt ECPs request Cc: memura@theory.chemistry.cambridge.ac.uk Hello all, I would be very grateful if anyone could furnish me with an ascii file containing the Hay Wadt effective core potentials as described in JCP vol 82 1985 (2 articles pp270 and 284) or else a site from which these may be obtained. Could you please send any information to this address, memura@theor.ch.cam.ac.uk Many thanks Mike Mura Cambridge From CHENS@MSUVX1.MEMST.EDU Tue Jan 11 13:54:22 1994 Received: from msuvx1.memst.edu for CHENS@MSUVX1.MEMST.EDU by www.ccl.net (8.6.4/930601.1506) id NAA26324; Tue, 11 Jan 1994 13:13:39 -0500 Received: from MSUVX1.MEMST.EDU by MSUVX1.MEMST.EDU (PMDF V4.2-14 #3869) id <01H7K07H72688WZPUN@MSUVX1.MEMST.EDU>; Tue, 11 Jan 1994 12:08:08 CST Date: Tue, 11 Jan 1994 12:08:08 -0600 (CST) From: CHENS@MSUVX1.MEMST.EDU Subject: Optimizing Linear Structure in GAMESS To: chemistry@ccl.net Message-id: <01H7K07H84R68WZPUN@MSUVX1.MEMST.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I've been trying to optimize the geometry of two C2H2 molecules situated along a straight line with a certain fixed distance separating the two molecules (ie. H-C-C-H H-C-C-H) using GAMESS program. The intent is to hold the four carbon atoms in a straight line with a fixed distance between the two central carbon atoms and allow all the other parameters to be fully optimized. I tried using linear bends in the ZMAT group but the job terminated with a message "roundoff error in bends". Does anyone have any idea what the problem could be? Any comments will be appreciated. S. Chen From jlozano@imim.es Tue Jan 11 13:56:57 1994 Received: from relay.rediris.es for jlozano@imim.es by www.ccl.net (8.6.4/930601.1506) id NAA26564; Tue, 11 Jan 1994 13:42:41 -0500 Received: from rediris.es by relay.rediris.es (PMDF V4.2-11 #4193) id <01H7KFH76NI88WW11C@relay.rediris.es>; Tue, 11 Jan 1994 19:10:45 GMT+1 X400-Received: by mta iris-dcp in /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Tue, 11 Jan 1994 19:10:17 UTC+0100 X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Tue, 11 Jan 1994 19:05:33 UTC+0100 Date: Tue, 11 Jan 1994 19:05:33 UTC+0100 From: juanjo Subject: MEPSIM To: chemistry@ccl.net Message-id: <35*/S=jlozano/O=imim/PRMD=iris/ADMD=mensatex/C=es/@MHS> Content-identifier: 35 Content-type: TEXT/PLAIN; CHARSET=ISO-8859-1 Content-transfer-encoding: 8BIT Conversion: Prohibited X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;940111190533] X400-Originator: jlozano@imim.es X400-Recipients: chemistry@ccl.net Announcemment of MEPSIM 2.1 package MEPSIM is a computational system developped by the Department of Medical Informatics of the Institut Municipal d'Investigacio Medica of Barcelona. It permits an integrated computation and analysis of the Molecular Electrostatic Potential (MEP). It includes the following main modules: MEPMIN: A program which allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima their values and all the geometrical relationships between them (distances, angles and dihedral angles). This program uses the exact definition of MEP. MEPCOMP: This program computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes this electrostatic similarity. MEPCONF: Performs the same process than MEPCOMP, but considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. MEPPLA: A program that supplies the MEP values for the points of a grid defined on a plane which is defined by any set of three points. The results of this program can be easily converted into isopotential lines using third parties graphical software. UTILITIES: Programs for use outputs of computational methods: Mopac, Gaussian9x, Gamess US and UK. There are a program useful for visualize graphically the MEP using INSIGHT package. (Biosym Tech; San Diego;CA) It is assumed that the user has a general knowledge about molecular modeling and quantum chemistry. We recommend the reading of the following papers to become familiarized with the methods that lie under these programs. Automatic determination of mep patterns of molecules and its aplication to caffeine metabolism inhibitors. F.Sanz, F.Manaut, J.Jose, J.Segura, M.Carbo, R. de la Torre. Journal of Molecular Structure (Theochem) 170(1988),171-180. Automatic search for maximum similarity between molecular electrostatic potential distributions. F.Manaut, F.Sanz, J.Jose, M.Milesi. Journal of Computed-Aided Molecular Design ,5(1991),371-380. Automatic Determination of maximum electrostatic alignment between methotrexate and dihidrofolic acid. F.Manaut, E.Lozoya, F.Sanz. In Qsar:Rational approaches to the design of bioactive compounds. C.Silipo and A.Vittoria(editors) 1991.Elsevier .p339-342. Maximum electrostatic similarity between biomolecules optimizing both relative biomolecules optimizing both relative positions and conformations. F.Sanz, F.Manaut , J.A.Sanchez and E.Lozoya. Journal of Molecular Structure (Theochem) 230(1991) 437-446. MEPSIM:A computational package for analysis and comparison of molecular electrostatic potentials. F.Sanz, F.Manaut, J.Rodriguez, E.Lozoya, E.Lopez de Briņas. Journal of Computer-Aided Molecular Design 7,(1993)337-347. *MEPSIM runs on VAX/VMS and SGI computers . There is a limited version for 386's and 486's with DOS or MS-Windows. *Prices: MEPSIM is not expensive. Very low prices for academic institutions. If you have interested in MEPSIM . Please send a mail to Juanjo Lozano. JLOZANO@IMIM.ES Ferran Sanz. FERRAN@IMIM.ES Francesc Manaut. SISTEMA@IMIM.ES From BIENSTOCK@NIEHS.NIH.GOV Tue Jan 11 14:49:12 1994 Received: from NIEHS.NIH.GOV for BIENSTOCK@NIEHS.NIH.GOV by www.ccl.net (8.6.4/930601.1506) id OAA27159; Tue, 11 Jan 1994 14:05:46 -0500 Received: from NIEHS.NIH.GOV by NIEHS.NIH.GOV (PMDF V4.2-13 #3461) id <01H7K3OLAF8W95OR4B@NIEHS.NIH.GOV>; Tue, 11 Jan 1994 13:37:56 EST Date: Tue, 11 Jan 1994 13:37:56 -0500 (EST) From: Rachelle Bienstock Subject: Rasmol To: chemistry@ccl.net Message-id: <01H7K3OLC14I95OR4B@NIEHS.NIH.GOV> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT For all those interested: The complete source code and user documentation for both the UNIX/X11 version and the IBM PC/MS Windows 3.1 version of Rasmol may be obtained by anonymous ftp from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. The UNIX/X11 source code is contained in the file RasMol2.tar.Z and the MS Windows source code and executable in the file raswin.zip. both of these files include a Postscript user reference manual. I hope this helps all those interested in Rasmol. Rachelle Bienstock National Institute of Environmental Health Sciences From stoutepf@chemsci1.es.dupont.com Tue Jan 11 14:58:24 1994 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.4/930601.1506) id OAA27472; Tue, 11 Jan 1994 14:26:00 -0500 Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991); id AA22005; Tue, 11 Jan 94 14:25:07 -0500 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com (4.1/SMI-4.1) id AA17597; Tue, 11 Jan 94 14:23:25 EST Message-Id: <9401111923.AA17597@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Tue, 11 Jan 1994 14:24:06 -0500 To: CHEMISTRY@ccl.net, shenkin@still3.chem.columbia.edu (Peter Shenkin) From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: Rasmol >I mentioned Rasmol, a protein visualization program, in a recent >posting. > [...] >I don't >know if it's ftp-able from the above host; perhaps someone with >more precise information can follow-up. > It's ftp-able from ftp.dcs.ed.ac.uk in /pub/rasmol From the README file: + RasMol2 is a X Windows tool intended for the visulisation of proteins + and nucleic acids. RasMol requires to be either an 8 bit pseudo colour + or a 24 bit true colour display. The program reads in a specifed + Brookhaven protein databank file and determines the connectivity from + the residue information provided. This is then rendered on the screen + in a variety of formats. Currently available options include depth-cued + line drawings, sticks, space filling `union of spheres', `ball and + stick' and protein ribbons representations. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- ARA/Fax: +1 (302) 695 4324 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From noy@tci002.uibk.ac.at Tue Jan 11 15:07:15 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id OAA27553; Tue, 11 Jan 1994 14:33:18 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA28127 (5.65c/IDA-1.4.4 for ); Tue, 11 Jan 1994 20:32:41 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA27897; Tue, 11 Jan 1994 20:32:39 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9401111932.AA27897@tci002.uibk.ac.at> Subject: Re: Rasmol To: chemistry@ccl.net Date: Tue, 11 Jan 1994 20:32:38 +0100 (NFT) In-Reply-To: <9401111711.AA05272@still3.chem.columbia.edu> from "Peter Shenkin" at Jan 11, 94 12:11:38 pm X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 3591 Dear Netters, This may help for one who wants the information about RasMol. Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci.uibk.ac.at, noy@tci2.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- +++++++++++++++++++++++++++ informations here ++++++++++++++++++++++++++ RasMol 2.1 Molecular Graphics Visualisation tool. Roger Sayle Biocomputing Research Unit University of Edinburgh June 1993 This posting is to announce the public release of the RasMol 2.1, molecular graphics visualisation program. The package has been developed in the BRU over the last few years, and following the recent collapse of commercialisation negotiations is now being offered FREE!! It was claimed in a recent conference to be the fastest available uniprocessor program for drawing shadowed spacefilled molecules. On a SparcStation it can shadow a 10,000 atom protein in less than 10 seconds. RasMol is an X Window System tool intended for the visualisation of proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) files and interactively renders them in a variety of formats on either an 8bit or 24bit colour display. The complete source code and user documentation for both the UNIX/X11 version and the IBM PC/MS Windows 3.1 version may be obtained by anonymous ftp as RasMol2.tar.Z from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. A compressed version of the PostScript user reference is also available in the same directory as rasmol.ps.Z. The program is intended for teaching and generating publication quality images. The program has both a menu system and a full featured command line interface. Different parts and representations of the molecule may be coloured or displayed in a number of formats independently. Currently supported formats include wireframe, ball and stick, backbone and space filling spheres. The space filling spheres may even be shadowed. The molecule may be manipulated using scroll bars, the command line or from a dials box if attached. The resulting image may be saved at any point in PostScript, GIF, PPM, Sun rasterfile or Microsoft BMP formats. For more details see the RasMol user reference. The current version of the program has been tested on sun3, sun4, hp9000, sequent and mips (dec,sgi and E&S) machines compiled under both gcc and the native compiler. The version for Microsoft Windows requires version 7 of the Microsoft Optimizing C Compiler and the SDK. Binaries for the IBM PC and compatibles will be made available if there is sufficient interest. The source code is public domain and available under the terms of the GNU public license agreement. Any comments, suggestions or questions about the package may be directed to "rasmol@dcs.ed.ac.uk". -- Roger Sayle JANET: ros@uk.ac.ed.dcs Department of Computer Science UUCP: ..!mcsun!uknet!dcs!ros University of Edinburgh ARPA: ros%dcs.ed.ac.uk@nsfnet-relay.ac.uk Edinburgh EH9 3JZ, UK. Tel: (+44) 031 650 5163 (direct line) From noy@tci002.uibk.ac.at Tue Jan 11 15:14:25 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id OAA27592; Tue, 11 Jan 1994 14:35:55 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA28182 (5.65c/IDA-1.4.4 for ); Tue, 11 Jan 1994 20:35:43 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA31262; Tue, 11 Jan 1994 20:35:42 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9401111935.AA31262@tci002.uibk.ac.at> Subject: Re: Rasmol To: chemistry@ccl.net Date: Tue, 11 Jan 1994 20:35:41 +0100 (NFT) In-Reply-To: <9401111711.AA05272@still3.chem.columbia.edu> from "Peter Shenkin" at Jan 11, 94 12:11:38 pm X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 3591 Dear Netters, This may helps for one who wants the information about RasMol. Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci.uibk.ac.at, noy@tci2.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- ++++++++++++++++++++++++++ information here ++++++++++++++++++++++++++++++ RasMol 2.1 Molecular Graphics Visualisation tool. Roger Sayle Biocomputing Research Unit University of Edinburgh June 1993 This posting is to announce the public release of the RasMol 2.1, molecular graphics visualisation program. The package has been developed in the BRU over the last few years, and following the recent collapse of commercialisation negotiations is now being offered FREE!! It was claimed in a recent conference to be the fastest available uniprocessor program for drawing shadowed spacefilled molecules. On a SparcStation it can shadow a 10,000 atom protein in less than 10 seconds. RasMol is an X Window System tool intended for the visualisation of proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) files and interactively renders them in a variety of formats on either an 8bit or 24bit colour display. The complete source code and user documentation for both the UNIX/X11 version and the IBM PC/MS Windows 3.1 version may be obtained by anonymous ftp as RasMol2.tar.Z from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. A compressed version of the PostScript user reference is also available in the same directory as rasmol.ps.Z. The program is intended for teaching and generating publication quality images. The program has both a menu system and a full featured command line interface. Different parts and representations of the molecule may be coloured or displayed in a number of formats independently. Currently supported formats include wireframe, ball and stick, backbone and space filling spheres. The space filling spheres may even be shadowed. The molecule may be manipulated using scroll bars, the command line or from a dials box if attached. The resulting image may be saved at any point in PostScript, GIF, PPM, Sun rasterfile or Microsoft BMP formats. For more details see the RasMol user reference. The current version of the program has been tested on sun3, sun4, hp9000, sequent and mips (dec,sgi and E&S) machines compiled under both gcc and the native compiler. The version for Microsoft Windows requires version 7 of the Microsoft Optimizing C Compiler and the SDK. Binaries for the IBM PC and compatibles will be made available if there is sufficient interest. The source code is public domain and available under the terms of the GNU public license agreement. Any comments, suggestions or questions about the package may be directed to "rasmol@dcs.ed.ac.uk". -- Roger Sayle JANET: ros@uk.ac.ed.dcs Department of Computer Science UUCP: ..!mcsun!uknet!dcs!ros University of Edinburgh ARPA: ros%dcs.ed.ac.uk@nsfnet-relay.ac.uk Edinburgh EH9 3JZ, UK. Tel: (+44) 031 650 5163 (direct line) From cmao771@charon.chpc.utexas.edu Tue Jan 11 15:49:16 1994 Received: from hermes.chpc.utexas.edu for cmao771@charon.chpc.utexas.edu by www.ccl.net (8.6.4/930601.1506) id PAA28278; Tue, 11 Jan 1994 15:26:26 -0500 Received: from charon.chpc.utexas.edu by hermes.chpc.utexas.edu (5.64/SMI-3.2) id AA24249; Tue, 11 Jan 94 14:26:25 -0600 Received: by charon.chpc.utexas.edu (5.61/SMI-3.2) id AA72891; Tue, 11 Jan 94 14:26:24 -0600 From: cmao771@charon.chpc.utexas.edu (Bersuker) Message-Id: <9401112026.AA72891@charon.chpc.utexas.edu> Subject: MM for transition metal cpds To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 11 Jan 94 14:26:22 CST Cc: cmao771@charon.chpc.utexas.edu X-Mailer: ELM [version 2.3 PL11] Dear Dr. Szilagyi: I agree that problems should be solved with as small as possible efforts. If your problem is solvable with the simple Hooke law, you are justified to do that provided you proved that the results are reliable. But to my knowledge in many (maybe most) cases, even if you are interested just in the nuclear configuration it is impossible to avoid at least qualitative consideration of the electronic structure (see for example the effects of vibronic coupling in my book by Plenum, 1984, or Springer, 1989). You mention the practical difficulties of ab initio calculations for these systems (I agree with your reasoning), but there is a variety of semiempirical methods which are much more reasonable and adequate to the real physical and chemical problems. I am now working on a relatively simple (practically acceptable) method of modeling TM systems that includes the d-electron effects I suggested earlier. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Isaac B. Bersuker | E-mail: Dept. of Chemsitry | cmao771@charon.chpc.utexas.edu Univeristy of Texas at Austin | Vox: (512) 471-4671 Austin, TX 78712 | Fax: (512) 471-8696 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From elewars@alchemy.chem.utoronto.ca Tue Jan 11 16:49:17 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id QAA28928; Tue, 11 Jan 1994 16:38:47 -0500 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id QAA16163 for chemistry@ccl.net; Tue, 11 Jan 1994 16:38:53 -0500 Date: Tue, 11 Jan 1994 16:38:53 -0500 From: "E. Lewars" Message-Id: <199401112138.QAA16163@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: MMX parameters for organometallics There was some discussion recently on the net about whether MMx could treat organometallics. There is a paper on MMX parameters for the allyl/palladium moiety in JACS 1993 115 4859. ============================================= From cmao771@charon.chpc.utexas.edu Tue Jan 11 16:52:18 1994 Received: from hermes.chpc.utexas.edu for cmao771@charon.chpc.utexas.edu by www.ccl.net (8.6.4/930601.1506) id PAA28584; Tue, 11 Jan 1994 15:59:29 -0500 Received: from charon.chpc.utexas.edu by hermes.chpc.utexas.edu (5.64/SMI-3.2) id AA26340; Tue, 11 Jan 94 14:59:28 -0600 Received: by charon.chpc.utexas.edu (5.61/SMI-3.2) id AA77349; Tue, 11 Jan 94 14:59:27 -0600 From: cmao771@charon.chpc.utexas.edu (Bersuker) Message-Id: <9401112059.AA77349@charon.chpc.utexas.edu> Subject: MM for Transition Metal Cpds To: cundarit@suvx1.memst.edu Date: Tue, 11 Jan 94 14:59:25 CST Cc: chemistry@ccl.net (Computational Chemistry List) X-Mailer: ELM [version 2.3 PL11] Dear Dr. Cundari: d**0 is not much easier than d**n in TM cpds. In particular, there may be a strong pseudo Jahn-Teller and other vibronic effects; in BaTiO3,for instance, they result in ferroelectricity (see my book by Plenum, 1984, or Springer, 1989)I worked out a method of molecular modeling for TM systems; it might be interesting to discuss this problem in more detail Regards -- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Isaac B. Bersuker | E-mail: Dept. of Chemsitry | cmao771@charon.chpc.utexas.edu Univeristy of Texas at Austin | Vox: (512) 471-4671 Austin, TX 78712 | Fax: (512) 471-8696 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From hcj@gull.uncc.edu Tue Jan 11 17:49:24 1994 Received: from mail.uncc.edu for hcj@gull.uncc.edu by www.ccl.net (8.6.4/930601.1506) id RAA29728; Tue, 11 Jan 1994 17:36:33 -0500 Received: from gull.uncc.edu (gull.uncc.edu [152.15.52.2]) by mail.uncc.edu (8.6.4/8.6.4) with SMTP id RAA16046; Tue, 11 Jan 1994 17:36:09 -0500 Received: by gull.uncc.edu (920330.SGI/890607.SGI) (for chemistry@ccl.net) id AA13231; Tue, 11 Jan 94 16:00:53 -0500 Date: Tue, 11 Jan 94 16:00:53 -0500 From: hcj@gull.uncc.edu (Harry C. Johnson) Message-Id: <9401112100.AA13231@gull.uncc.edu> To: dqujfm0@PS.UIB.ES Cc: chemistry@ccl.net In-Reply-To: <90*dqujfm0@PS.UIB.ES> (message from Juan Frau on Tue, 11 Jan 1994 17:15:55 UTC+0200) Subject: Re: Compilation Problem with Interchem Warnings should not prevent the program from compiling. Check to see if there are any lines that start out Error instead of Warning. If not, it probably compiled. -Harry From bkarlak@ren.onyx-pharm.com Tue Jan 11 16:52:16 1994 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.4/930601.1506) id QAA28830; Tue, 11 Jan 1994 16:24:08 -0500 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (5.67/1.37) id AA16535; Tue, 11 Jan 94 13:24:07 -0800 Received: by ren.onyx-pharm.com (920330.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:CHEMISTRY@ccl.net id AA00315; Tue, 11 Jan 94 13:24:31 -0800 Date: Tue, 11 Jan 94 13:24:31 -0800 From: bkarlak@ren.onyx-pharm.com (Brian Karlak) Message-Id: <9401112124.AA00315@ren.onyx-pharm.com> To: CHEMISTRY@ccl.net Subject: Old R4000 uses This may not be the correct forum for this, but I thought I'd ask: We just upgraded our SGI Indigo2 with the new R4400 chip. Does anyone know any potential uses for the old R4000 chip that we removed? SGI will give us a small amount of cash for it, but we'd rather use it. Any ideas? Thanks, Brian Karlak This signature file intentionally left blank. From CBAS25@VAXE.STRATHCLYDE.AC.UK Tue Jan 11 20:49:22 1994 Received: from sun2.nsfnet-relay.ac.uk for CBAS25@VAXE.STRATHCLYDE.AC.UK by www.ccl.net (8.6.4/930601.1506) id UAA01214; Tue, 11 Jan 1994 20:13:24 -0500 Message-Id: <199401120113.UAA01214@www.ccl.net> Via: uk.ac.strathclyde.vaxe; Wed, 12 Jan 1994 01:13:00 +0000 Date: Wed, 12 Jan 94 1:15 GMT From: "CBAS25 ::P_BLADON ::CBAS25" To: CHEMISTRY Subject: Warning messages when compiling INTERCHEM Compiling INTERCHEM on SGI machines Since the introduction of the 3.5.1 version of the fortran compiler, there has been a problem in that certain parts of the library have been offered twice over at the linkin stage, first as /usrlib/libX11_s.a and then as /usr/lib/libmpc.a, thus causing the second type of warning message reported by Dr. Juan Frau. The messages are warnings only and the compiled code should be there and work correctly (as pointed out by Harry). The warnings can be avoided if the following script is used for compilation:- mkf2c message.c message.s; f77 -Nc40 -col120 -o inter \ sysmain57.f sysmenu57.f sysgeom57.f sysdisp57.f\ sysbuld57.f sysener57.f sysprot57.f syssurf57.f\ sysmerg57.f syspred57.f sysdriv57.f sysconn57.f\ syschir57.f syschem57.f syscrys57.f syswind57.f\ sysseri57.f \ -lmpc -lsphere -lm -lfgl -lgl_s\ <<<<< note addition of -lmpc message.s message.c -lfm_s -lgl_s (Substitute "56" for "57" if you have the earlier version of source code). I am not sure whether the first type of warning message is cured by this, because I have not encountered it. The same sort of problems arose in other fortran programs which used the graphics library, and these were cured in a similar manner. I hope that this helps anyone else who has this problem; it does highlight the perennial trouble that occurs when SGI comes out with new versions of software. (Sorry SGI folks) Peter Bladon