From tamasgunda@tigris.klte.hu Thu Aug 31 04:11:39 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id DAA03242; Thu, 31 Aug 1995 03:57:29 -0400 Message-Id: <199508310757.DAA03242@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Thu, 31 Aug 1995 09:56:41 EDT Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Thu, 31 Aug 1995 09:56:40 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: principal conponents summary Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Some days ago I sent the following summary to CCL, but somehow only a small part has arrived. Here is it again and hopefully without problems. --------------------------------------------------------------- Here is the summary of my question concerning the calculation of principal components and plane fitting to points: The original question was: I am looking for algorithm/numerical methods for the determining of the principal components of a data set. In the words of geo- metry, I have a number of points determined by y1, y2 and y3, and I am looking for the best fitting plane to the points, i.e. the plane determined by the two greatest principal components. Do not refer, please, to programs like Mathcad etc. I need it in a numerical method form, as I'd like to use it as a procedure in a program. *************************************************************** ** That looks like a rather straightforward least-squares problem. You want the parameters a,b,c in the equation for a plane y3 = a y1 + b y2 + c. So you make up a matrix X: y1(1) y2(1) 1 y1(2) y2(2) 1 ... y1(n) y2(n) 1 and a vector Z = (y3(1), y3(2), ..., y3(n)), plus a 3-component vector of unknowns A = (a,b,c). Then A = X^+ Z gives you the best values for the parameters, where X^+ is the generalized inverse of X. 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: gordonh@chem.QueensU.CA (Heather Gordon) To: tamasgunda@tigris.klte.hu Subject: pca There are listings for FORTRAN programs pertaining to all aspects of factor analyses, including pca in "Factor Analysis of Data Matrices", P. Horst, Holt, Rinehart and Winston, New York, 1965. I also have written my own code, using the routines TRED2 and TQLI >from "Numerical Recipes in Fortran" to diagonalize the covariance matrix and locate the eigenvalues and eigenvectors. Heather Gordon Department of Chemistry Queen's University Kingston, Ontario *************************************************************** ** What you say you want sounds a lot like the transformation of a molecule to the coordinate system in which the moment-of-inertia tensor is diagonal. If your (y1, y2, y3) components are *orthogonal*, you ought to be able a similar approach. This kind of code is buried in all sorts of programs It should be a simple matter to adapt a suitable code fragment to you use. ++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com *************************************************************** ** Tamas, A friend sent me your e-mail on the subject of an algorithm for calculating the first two PC's from a dataset. I have written PCA (NIPALS) routines in BASIC and C and will be happy to send them to you, if required. I also have a book (Numerical Recipes) which details PCA (Singular VDecomposition) which does a similar thing. If you still need some help, send me an e-mail Steve Gurden, Bristol Chemometrics Group, School of Chemistry, University of Bristol, Cantock's Close, BRISTOL BS8 1TS Tel: +44 (0)117 9289000 extn. 4421 e-mail: S.P.Gurden@bris.ac.uk *************************************************************** ** Dear Dr. Gunda, One of the most simple and elegant method to perform Principal Component Analysis is that of the NIPALS algorithm. It can be formulated in a few lines of programming and it works really fine. You can find it in the following references: * Analytica Chimica Acta, vol. 185, p. 1-17 (1986) * Chemometrics and Intelligent Laboratory Systems, vol. 2, p. 37-52 (1987) I hope this helps you. Sincerely. Jose I. Garcia -- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-350475 Departamento de Quimica Organica Fax : 34-(9)76-567920 Instituto de Ciencia de Materiales de Aragon e-mail: jig@qorg.unizar.es C.S.I.jig@msf.unizar.es E-50009 ZARAGOZA (SPAIN) *************************************************************** ** I thought the principle (no pun intended) was quite simple; just calculate the variance/covariance matrix of the variables (or better the correlation matrix) and diagonalize that. You can get the correlation matrix by autoscaling the data and calculating the covariance matrix then. Next, select the number of principal components that you want by calculating the cumulative sum of the eigenvalues divided by the sum of all the eigenvalues (the eigenvalues, eigenvectors need to be sorted by their size by the diagonalization procedure or afterwards) I mean: T = \sum_i \labda_i suppose, as an example: \labda_1 / T = 90 % (\labda_1 + \labda_2) / T = 98 % ... (\labda_1 + \labda_2 + ...) /T = .. if this is sufficiently accurate for you, use the subspace spanned by the first two eigenvectors as your new space, and project all datapoints onto it. otherwise, use more eigenvectors until (\sum_j \labda_j) / T is sufficiently near 100 % (1.00), and project the datapoints on the subspace (unfortunately it is no longer a 2-D plane, which would be most easy for viewing) Hopefully you can use this information, I can't think of any references off-hand.. There is a book by Box (and Hunter?) which describes these multivariate techniques in great detail. Sorry I can't help you better, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-274505 *************************************************************** ** Check the NIST CD for handwritten characters -- there is a principal component algorithm coded there (may be in C, but you could then recode it in FORTRAN). There are several sites that catalog algorithms, too -- here are a few: http://gams.nist.gov/, http://netlib.att.com/netlib/att/cs/home/1127.ht, http://www.netlib.org/. Good luck. Joe McDaniel joe@psiint.com Dear Dr. Gunda, There are many references to Principal Component Analysis.It is actually a straightforward problem in matrix diagonalization. However, if your real goal is to simply fit a plane to a set of points (minimizing the sum of squares of the distances of the points to the plane) or a line to a set of points (minimizing the sum of squares of the distances of the points to the line), then this is also a simple matrix diagonalization problem whose solution is given and discussed in the following references: "To Fit a Plane or Line to a Set of Points by Least Squares", V. Schomaker, J. Waser, R.E. Marsh, and G. Bergman, Acta Cryst., vol. 12, pp. 600-604 (1959). and "To fit a plane to a set of points by least squares", D.M. Blow, Acta Cryst., vol. 13, p. 168 (1960). Regards, Marvin Waldman, Ph.D. Director, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com *************************************************************** ** Dear Dr. Gunda, There are two ways to do what you want (as I understand it). One is to use a statistical analysis package which supports principal components analysis as statisticians define it. The plane you are looking for is the one defined by the first two principal components. The other is to perform the equivalent of a moment of inertia calculation with all masses set to 1. First find the mean value of each of the three coordinates (call them x, y, z). This is equivlant to your center of mass. Build the symmetric 3x3 tensor with the following elements, summed over all points (distances are relative to the centroid): y*y + z*z -x*y -x*z -x*y x*x + z*z -y*z -x*z -y*z x*x + y*y Diagonalize the tensor (the Jacobi method works well here - see any of the "Numerical Recipes" series by Press et all.) The transformation matrix gives you your three principal coordinates. Hope this helps, Paul Soper ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-8412 *************************************************************** ** According to the math of the normal least square procedure, as far as I know, NOT the distances of the points and the line are minimized (i.e. a perdendicular from a point to the line), but the difference of the measured and the calculated y values,which is represented graphically by a line between the point and the regression line and it is parallel with the y axis: That depends on the error criterion that you use. The one sent yesterday (and probably some others too) does indeed minimize the error along one coordinate axis (and in fact works only if that axis does not lie in the plane that you want to fit). If you want to minimize the distances of the points >from the plane, use the normal form for the plane: n x - d = 0, where n is the normalized normal vector, x is the coordinate vector, and d the distance of the origin from the plane. The distance of any point y >from this plane is simply given by n y - d, so you must minimize __ \ | | 2 / | n y_i - d | -- i with the constraint that n is normalized, so you need a least-squaresminimizer that can handle constraints (e.g. via Lagrange multipliers). Or use a "dirty hack": if you know (or assume) that d will never be zero (i.e. the plane will not contain the coordinate origin), set d = 1 and use an unnormalized normal vector, whose length then is the inverse of the distance from the origin. ------------------------------------------------------------------------------ - 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) ------------------------------------------------------------------------------ *************************************************************** ** What you say you want sounds a lot like the transformation of a molecule to the coordinate system in which the moment-of-inertia tensor is diagonal. If your (y1, y2, y3) components are *orthogonal*, you ought to be able a similar approach. This kind of code is buried in all sorts of programs. It should be a simple matter to adapt a suitable code fragment to you use. FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com Tamas, I think I have solved a problem fairly similar to the one you are interested in. My problem was less general and involved finding thebest-fit plane to a group of four points centred around a fifth point and arose because I am looking at compression strain in tetracoordinate carbon systems. For example the molecule [4.4.4.4]fenestrane C9H12 H H2C__C__CH2 | | | HC-----CH | | | H2C--C--CH2 H contains a central "flattened" tetracoordinate carbon atom. One way to determine the flattening at any C(C)4 moiety is to find the best-fit plane for the four alpha-C atoms passing through the central C atom. This can be done simply by finding the eigenvectors of what we have termed the Geometry Tensor. The Geometry Tensor is constructed by multiplying the matrix D (the vectors to your points -- in this case the 4 alpha-C atoms) by its transpose to give a 3x3 Real Symmetric Matrix (routines to find the eigenvectors/values of any RSM can be found in eispak and similar sets of routines). The eigenvectors of this matrix will correspond to the minimum (Best-Fit) -- this will have the smallest eigenvalue, maximum and one other extremum (i.e. they will form a set of cartesian axes -- x,y and z -- one of which will be the normal to your best-fit plane. The mathematics behind this is actually quite simple and involes setting up the equations to minimise d' = (sum of squared distances of your points to an orbitrary plane). After which the need to form and find the eigenvectors of the "Geometry Tensor" becomes obvious. Naturally this can be readily extended to any number of atoms and any origin. I have used this method to re-orient molecules that were optimised in C1 symmetry (in cartesians) which exhibit higher symmetry but where the axes/planes of symmetry do not lie on the x,y or z axes of my final cartesians. I might be able to send you my fortran code (it is very simple) if you think this would help but I will need to check the origin of the eigenvector solving routines that I use (to make sure we do not break anyone's intellectual property rights as I did not write these routines myself -- I think they came from eispak). Cheers, Danne Danne R Rasmussen, PhD Student phone: +61 6 249-3771 Research School of Chemistry fax: +61 6 249-0750 Australian National University Canberra ACT 0200 e-mail: danne@rsc.anu.edu.au ***************************************************************** Hi, Your assumption about the fitting of the least squares of perpendicular distances is correct .. this is what is done by linear regression. A side note, linear regression is used in teaching software, but programs are always built around the matrix formulation. The way that you can fit perpendicular distances, as well as do non-linear fits (constants other than linear coeficients) is using optimization methods, such as steepest descent, Newton-Rhapson, etc. This is just like doing geometry optimization, only you are minimizing on your perpendicular distances instead of energy. The other possibility is spline methods (cube splines are most commonly used). A spline method is not a least square fit, it is an exact fit. However, if there is noise in the data you fit exactly to the noise. Hope this helps. Dave Young young@slater.cem.msu.edu *************************************************************** ** Dear Tamas, I also am a chemist, a chemometrician in fact, and am interested in chemistry , statistics and computing all mixed togoether. Whenever I have a mathematical problem like yours, I often find an answer in the excellent book "Numerical Recipes in C: The Art of Scientific Computing" by W. H.Press, S.A.Teukolsky, W.T.Vetterling and B.P.Flannery (Cambridge University Press). There are also version for FORTRAN and, I think, BASIC. PCA is also described in various multivariate statistics and chemometrics books, such as "Multivariate Calibration" by H.Martens and T.Naes (Wiley) and "Multivariate pattern recognition in chemometrics" edited by R.G.Brereton (Elsevier). The source code is actually written in Visual Basic, but conversion to Basic, Fortran or C should be quite straightforward PCA: ijX = ikT * kjP where X is an i by j datamatrix, T is an i by k scores matrix and P is a k by j loadings matrix. In your case, the number of components to extract ("kmax" in the source code) will be 2. For this listing, "evals" are the eigenvalues, one for each PC, which I have defined as the sum of squares of the scores. NIPALS calculates the PC's in order of importance (i.e. PC's with the biggest eigenvalues come first). The loadings will be 2 vectors of unit length, which represent the two new PC axis, and the scores matrix gives the coordinates of the points on these new PC axis. Think about whether you wish to mean-centre the data prior to the PCA or not - this will give different results! Maybe you have the answer to your problem anyway, by the time I write this, but best of luck anyway! ****************************************************** Sub NIPALS (X!(), kmax%, mc%, T!(), P!(), evals!()) Dim i%, imax%, j%, jmax%, k%, maxcol% imax = UBound(Xmat, 1) jmax = UBound(Xmat, 2) Dim sm#, ss#, cmaxss#, rmaxss#, smaxss# Dim cmax#(), rmax#(), smax#() ReDim cmax(1 To imax) ReDim rmax(1 To jmax) ReDim smax(1 To imax) ReDim T(1 To imax, 1 To kmax) ReDim P(1 To kmax, 1 To jmax) ReDim evals(1 To kmax) k = 1 ' Mean-centre matrix if required If mc = 1 Then For j = 1 To jmax sm = 0 For i = 1 To imax sm = sm + X(i, j) Next i sm = sm / imax Next j For j = 1 To jmax For i = 1 To imax X(i, j) = X(i, j) - sm Next i Next j End If START1: ' Find column with greatest sum of squares cmaxss = 0# For j = 1 To jmax ss = 0# For i = 1 To imax ss = ss + X(i, j) ^ 2 Next i If ss > cmaxss Then cmaxss = ss maxcol = j End If Next j For i = 1 To imax cmax(i) = X(i, maxcol) Next i START2: ' Calculate row vector and its sum of squares rmaxss = 0# For j = 1 To jmax rmax(j) = 0# For i = 1 To imax rmax(j) = rmax(j) + (cmax(i) * X(i, j)) Next i rmaxss = rmaxss + rmax(j) ^ 2 Next j ' Scale this row vector to unit length, after checking that it is not a ' zero vector If rmaxss = 0# Then MsgBox ("Nipals( ): Exited before all PC's found") Exit Sub End If For j = 1 To jmax rmax(j) = rmax(j) / Sqr(rmaxss) Next j ' Calculate a new estimate of the PC scores smaxss = 0# For i = 1 To imax smax(i) = 0# For j = 1 To jmax smax(i) = smax(i) + (X(i, j) * rmax(j)) Next j smaxss = smaxss + smax(i) ^ 2 Next i ' Test to see if PC has converged. If so, store scores and loadings, ' adjust matrix, and look for next PC. If not, use last scores estimate ' to put back into the algorithm. The convergence criterion can be ' adjusted (i.e. 1e-6 used for single precision). If Abs(smaxss - cmaxss) / cmaxss < .000000000001 Then evals(k) = smaxss For i = 1 To imax T(i, k) = smax(i) Next i For j = 1 To jmax P(k, j) = rmax(j) Next j For i = 1 To imax For j = 1 To jmax X(i, j) = X(i, j) - (smax(i) * rmax(j)) Next j Next i If k = kmax Then Exit Sub End If k = k + 1 GoTo START1 Else For i = 1 To imax cmax(i) = smax(i) Next i cmaxss = smaxss Go End If End Sub ================ Steve Gurden, Bristol Chemometrics Group, School of Chemistry, University of Bristol, Cantock's Close, BRISTOL BS8 1TS Tel: +44 (0)117 9289000 extn. 4421 e-mail: S.P.Gurden@bris.ac.uk *************************************************************** ** From: g80@chm.uri.edu Hi Dr. Tamas Gunda, I too have been interested in the question of fitting a plane to a set of points(3D). As you correctly pointed out this is a problem in total least squares, not simple least squares. This problem as been approached many times using a variety of algorithims(its' fundamental to crystallography). I have written a simple FORTRAN program based on the method of D. M. Blow, Acta. Cryst.(1960),13,168. One fundamental paper is V. Schomaker, J. Waser, R. E. Marsh and ?. Bergman, Acta Cryst(1959),12,60. There are many other papers on this subject. I hope this helps and good luck. Brian Schmitz Univ. of Rhode Island *************************************************************** ** end summary ***************************************************************************** Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ***************************************************************************** From jkl@ccl.net Thu Aug 31 06:11:40 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA04657; Thu, 31 Aug 1995 06:00:30 -0400 Received: from uivt1.uivt.cas.cz for HRUSAK@JH-INST.CAS.CZ by bedrock.ccl.net (8.6.10/950822.1) id GAA19304; Thu, 31 Aug 1995 06:00:02 -0400 Received: from bob.jh-inst.cas.cz (bob.jh-inst.cas.cz [147.231.28.65]) by uivt1.uivt.cas.cz (8.6.12/8.6.12) with ESMTP id LAA29648 for ; Thu, 31 Aug 1995 11:53:33 +0200 Received: from BOB/MAILQUEUE by bob.jh-inst.cas.cz (Mercury 1.21); 31 Aug 95 11:57:47 GMT+1 Received: from MAILQUEUE by BOB (Mercury 1.21); 31 Aug 95 11:57:34 GMT+1 From: "Dr. Jan Hrusak" Organization: Institute of Physical Chemistry To: chemistry@ccl.net Date: Thu, 31 Aug 1995 11:57:25 +0100 Subject: S-T gap in phenyl cation Priority: normal X-mailer: Pegasus Mail for Windows (v2.01) Message-ID: <3D0A2B2451@bob.jh-inst.cas.cz> Dear Netters, does somebody know anything about the singlet/triplet gap in the phenyl cation? Any information (regardless whether old or new, experiment or theory) would be appreciated. Jan Hrusak ---------------------------------------------------------------------------- Dr. Jan Hrusak ############################### J. Heyrovsky Institute of Physical Chemistry ## MEMOR ESTO CONGREGATIONIS ## Academy of Sciences of the Czech Republic ## TVAE QVAM POSSEDISTI ## Dolejskova 3, CZ-182 23 Prague 8 ## AB INITIO ## Czech Republic ############################### ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Phone: (0042 2) 66 05 3436 FAX: (0042 2) 858 2307 E-Mail: hrusak@jh-inst.cas.cz ---------------------------------------------------------------------------- From chessyx@gsusgi1.Gsu.EDU Thu Aug 31 10:13:00 1995 Received: from gsusgi1.Gsu.EDU for chessyx@gsusgi1.Gsu.EDU by www.ccl.net (8.6.10/950822.1) id KAA08463; Thu, 31 Aug 1995 10:09:41 -0400 Received: (from chessyx@localhost) by gsusgi1.Gsu.EDU (8.6.10/8.6.10) id KAA21868 for chemistry@www.ccl.net; Thu, 31 Aug 1995 10:09:41 -0400 Date: Thu, 31 Aug 1995 10:09:41 -0400 From: Shijie Yao Message-Id: <199508311409.KAA21868@gsusgi1.Gsu.EDU> To: chemistry@www.ccl.net Subject: Stability comparison of two products by QM Dear netters, We have a couple of reactions like A + B = C A + B'= C' Can we calculate the relative stability of C' vs C using quantum mechanical calculations? Thank you very much for your help. Shijie Yao From Jeffrey.Gosper@brunel.ac.uk Thu Aug 31 10:26:46 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950822.1) id KAA08338; Thu, 31 Aug 1995 10:06:06 -0400 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <26561-0@monge.brunel.ac.uk>; Thu, 31 Aug 1995 15:04:41 +0100 Date: Thu, 31 Aug 1995 15:04:34 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: SUMMARY: MOPAC reaction path publications To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII A short while ago I posted the following question: I am trying to locate computational studies that make use of the reaction path calculation offered by MOPAC (i.e. use of the -1 optimization flag). I would therefore appreciate any pointers to published work on this matter. I'll summarize any responses as usual. *********************************** Thanks to those who responded however very few pointers were provided (I'm sure there must be more out there). *********************************** From: Stanislaw Oldziej Subject: Re: CCL:MOPAC reaction path calculations To: Jeffrey J Gosper Hi Jeffrey, I have to you two works with using this option -1 in MOPAC to locate transition states. Both this works are from my lab: 1. M.Tarnowska, St.Oldziej, A.Liwo, P.Kania, F.Kasprzykowski, Z.Grzonka. MNDO study of the mechanism of the inhibition of cysteine proteinases by diazomethyl ketones. Eur. Biophys. J., 21, 217-222 (1992) 2. A.Tempczyk, M.Tarnowska, A.Liwo, E.Borowski. A theoretical study of glucosamine synthase. II. Combined quantum and molecular mechanics simulation of sulfhydryl attack on the carboxyamide group. Eur. Biophys. J., 21, 137-145 (1992) You also may look at the work of Kolllman's group: 3. E.H.Alison, P.A.Kollman. OH- versus SH- nucleophilic attack on amides: Dramatically different gas-phase and solvation energetics. J.Am.Chem.Soc., 110, 7195-7200 (1988) Stanislaw Oldziej Faculty of Chemistry University of Gdansk Sobieskiego 18, 80-952 Gdansk POLAND *************************************************** I have published one such article, and another has been submitted recently. Here is the reference for the published paper: Martin, N.H.; Allen, D.B.; Taylor, K.N. "Semi-Empirical Molecular Orbital Calculations on the Reaction of Singlet Oxygen with Vinylamine; Examination of a Charge-Transfer Mechanism," J. Elisha Mitchell Sci. Soc. 1991, 107, 89-96. Good luck. Ned H. Martin ******************************************************************** Ned H. Martin, Chair Department of Chemistry University of North Carolina at Wilmington Voice: 910-395-3453 601 S. College Rd Fax: 910-395-3013 Wilmington, NC 28403-3297 martinn@vxc.uncwil.edu ******************************************************************** /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From oreola@chem.QueensU.CA Thu Aug 31 10:56:48 1995 Received: from QUCDN.QueensU.CA for oreola@chem.QueensU.CA by www.ccl.net (8.6.10/950822.1) id KAA09463; Thu, 31 Aug 1995 10:45:17 -0400 Received: from quchem.chem.QueensU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with TCP; Thu, 31 Aug 95 10:45:22 EDT Received: by quchem.chem.QueensU.CA (4.1/SMI-4.0) id AA04875; Thu, 31 Aug 95 10:52:29 EDT Date: Thu, 31 Aug 95 10:52:29 EDT From: oreola@chem.QueensU.CA (Oreola Donini) Message-Id: <9508311452.AA04875@quchem.chem.QueensU.CA> To: chemistry@www.ccl.net Subject: DMol module on Insight II Hi, I should be getting access to the DMol module in the Insight II package and I was wondering if someone could list for me the density functionals available within the package. I will not get actual documentation for a while, but I need to chose a functional for another part of a project which should be consistent with DMol. Thank-you for your help, Oreola Donini From toukie@zui.unizh.ch Thu Aug 31 11:11:47 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id LAA09967; Thu, 31 Aug 1995 11:04:05 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA10366; Thu, 31 Aug 95 17:03:51 +0200 X-Nupop-Charset: Swiss Date: Thu, 31 Aug 1995 17:03:59 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <61439.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Seeking molecular mechanics force fields Dear Colleagues; I am seeking the source codes for some molecular mechanics force fields, especially AMBER, MMP2, and MM2. If anyone has knowledge of an FTP site >from which the source codes for these or possibly other) MM FFs can be found, please contact me. Alternatively, if you would be willing to donate a source code for any of the above MM FFs, I would also very much appreciate hearing from you. Sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 Zuerich 7 Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From POLLARD@CCIT.ARIZONA.EDU Thu Aug 31 12:41:58 1995 Received: from Madder.CCIT.Arizona.EDU for POLLARD@CCIT.ARIZONA.EDU by www.ccl.net (8.6.10/950822.1) id MAA12036; Thu, 31 Aug 1995 12:40:21 -0400 From: Received: from CCIT.ARIZONA.EDU by CCIT.ARIZONA.EDU (PMDF V5.0-5 #2381) id <01HUPVGMOK408Y56M9@CCIT.ARIZONA.EDU> for chemistry@www.ccl.net; Thu, 31 Aug 1995 09:40:10 -0700 (MST) Date: Thu, 31 Aug 1995 09:40:10 -0700 (MST) Subject: Matrix elements in G9X To: chemistry@www.ccl.net Message-id: <01HUPVGMU6NM8Y56M9@CCIT.ARIZONA.EDU> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT I was wondering if anyone could tell me how to include the Fock and overlap matrix elements in the output from G92. I have e-mailed gaussian, but they are not responding. Thanks, John Pollard, University of Arizona. From jstewart@fujitsuI.fujitsu.com Thu Aug 31 13:26:46 1995 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.10/950822.1) id NAA13373; Thu, 31 Aug 1995 13:14:40 -0400 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [133.164.254.1]) by mail.barrnet.net (8.6.10/MAIL-RELAY-LEN) with SMTP id KAA07867 for ; Thu, 31 Aug 1995 10:14:34 -0700 Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA29809; Thu, 31 Aug 95 10:15:53 PDT Date: Thu, 31 Aug 95 10:15:53 PDT From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9508311715.AA29809@fujitsu1.fujitsu.com> To: CHEMISTRY@www.ccl.net Subject: normal vibrations Ferenc Molnar writes: > The eigenvalue number k correspond to (w_k)^2, where the w_ks > are the vibrational frequencies, this means: > > (w_k)^2=K_k/M_k > > K_k: force constant of the kth normal mode > M_k: reduced mass of the k_th normal mode > > Now my question is, if (w_k)^2 determines only the ratio > of K_k and M_k, then how are the reduced masses, reported > in the "vibrational analysis" section of the MOPAC output > file, calculated? Is there a convention, which "fraction" of > (w_k)^2 to use for K_k and which for M_k? The reduced mass is like atomic charges, in that it is not an observable, however, for specific systems - mainly homonuclear diatomics - the reduced mass does have meaning. The reduced mass definition used in MOPAC can be understood as follows: Each vibration can be modelled by a mass, M_k, at the end of a spring of force constant K_k, attached to an infinite mass. Inf | K_k M_k Mass | |^^^^^^^^^^^^^^^^^^O | | The contribution to the mass is proportional to the amount each atom contributes to the normal mode, and is proportional to the fraction of the atomic mass contributed by each atom. Put in more formal terms, the contribution of each atom to the effective mass of a vibration is proportional to the product of the intensity on that atom times the mass-weighted intensity. rho = sum_A = sum_A (c_A_x**2+c_A_y**2+c_A_z**2)**2*M_A where c_A are the coefficients of the normal modes. Consider H2: c_1 = 0.7071*H_1+0.7071*H_2 rho_1 = 0.7071**4*1 + 0.7071**4*1 =0.5 Consider M-H, M being an atom of very large mass, say 1000: c_1 = 0.0316*M+0.9995*H rho_1 = 0.0316**4*1000 + 0.9995**4*1 = 0.9990 [0.0316 ~ sqrt(1/1000); 0.9995 ~sqrt(1-1/1000)] Consider N2: c_1 = 0.7071*N_1+0.7071*N_2 rho_1 = 0.7071**4*14+0.7071**4*14 = 7.0 Jimmy Stewart From mrigank@imtech.ernet.in Thu Aug 31 13:41:47 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/950822.1) id NAA13650; Thu, 31 Aug 1995 13:31:52 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id XAA04478 for chemistry@www.ccl.net; Thu, 31 Aug 1995 23:02:27 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA22769; Thu, 31 Aug 95 22:52:31+050 Message-Id: <9508311752.AA22769@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Thu, 31 Aug 95 14:01:50 +0530 Date: Thu, 31 Aug 95 14:01:50 +0530 From: Mrigank To: chemistry@www.ccl.net Subject: Workshop Announcement: X-Vms-Mail-To: CHEM,NMR,WATOC,AMBER NATIONAL WORKSHOP ON COMPUTER AIDED PROTEIN DESIGN ================================================== (November 6-10, 1995) Organized by Bioinformatics Centre, Institute of Microbial Technology Chandigarh. 160 014 THE THEME --------- Protein engineering, though originally conceived as a realm of molecular biology is now as multidisclipinary approach to the study of biological systems. Structural Biology and Molecular Biophysics are some of them. Though there is a many fold increase in the pace at which 3-D structures of proteins are now available, the protein sequences far outnumber it. Although the ultimate goal of all "protein engineers" is the prediction of 3-D structure from a given sequence, present day aims are somewhat more modest, like to find out what if a residue is replaced or deleted in a protein. This necessitates the usage of tools of Compu tational Chemistry, a field that has seen very rapid growth of late. The idea of this workshop is to familiarize the participants with the state of art in this area and to make them appreciate as to what information can one glean out from the information available with molecular biologists or biophysicists and with what degree of confidence and caution should it be used. What information does one get from just the protein sequence? How well can one predict the effect of mutations on proteins with known structure ? How and what kind of ideas can one get from structure to introduce desired properties into a protein? These will be the some of the questions the workshop will attempt to enlighten. Topics to be covered: -------------------- o Sequence Analysis o Protein Secondary/Supersecondary Structure o Homology Based Protein Modeling o Molecular Dynamics/Simulated Annealing o Genetic Algorithms o Graphic Representation of Protein Structure o Conformational Analysis Who Should Apply? ---------------- Biotechnologists, Molecular Biophysicists, Molecular Pharmacologists, Structural Biologists actively involved in R & D in the area of protein engineering/protein modeling. The workshop will be useful from research scholars to senior scientists working in academic institutions or industries. How To Apply? ------------ Applicants should send their application along, brief resume, and a statement of purpose briefly describing how this workshop will be useful to their research work. REGISTRATION ------------ Registration Fee: Academic: Faculty Rs. 500/- Students Rs. 300/- Industry: Rs. 3000/- Last Date: Applications must reach before September 20, 1995. Accommodation: Applicants needing accommodation must send request along with registration form. Travel Assistance: No travel assistance will be provided to the participants. TA/DA must be met by the participants' own sources. Number of Participants: There will be maximum of twenty(20) participants. ORGANIZING COMMITTEE -------------------- Dr. C. M. Gupta Chairman Dr. Amit Ghosh Co - chairman Dr. Naresh Kumar Member Dr. G. Sahn Member Dr. R. M. Vohra Member Mr. C. R. Suri Member Mr. G. P. S. Raghava Secretary Mr. Bijay Singh Member Dr. Mrigank Member REGISTRATION FORM ----------------- NATIONAL WORKSHOP ON COMPUTER AIDED PROTEIN DESIGN 1. Name (Mr./Ms).................................... 2. Designation ......................................... 3. Department/Institute........................... ...................................................................... 4. Address for communication............... ...................................................................... ...................................................................... 5. Telephone No. & Fax No...................... 6. Whether accommodation required ..... Date............... Signature of the candidate N.B. Please include your resume and statement of purpose with this form. Please do not send registration fee with this form. Registration fee would be procured from applicants selected for workshop after selection. THE CENTRE ---------- Bioinformatics Centre(BIC) at IMTECH was established in 1987 by Department of Biotechnology, Govt. of India. The objectives of the Centre is to create the infrastructure in the field of protein engineering and protein modeling. The resources available at the Centre includes : Hardware: DEC Alpha workstations (one DEC 3000/600 and seven DEC 3000/300LX) , PCs (Two 486, one 386, two 286) and one MicroVax II system. Software: AMBER , RasMol, MidasPlus, X-plor, MicroGenie, GMAP, DNAOPT, Cang, Hpat, DNASIZE, CPSSD, CONFang, GAMESS, BOSS, Modeller, etc. Databases: PDB, ATLAS (PIR,NRL_3D,ALN), CODONtab, RESTseq, Cang, Hpat, PROSITE, Rotamer Library(Dunbruck and Karplus), DSSP etc. Communication and other facilities: All the systems in the Centre are networked using TCP/IP on a ethernet. E-mail, access to internet, literature search etc. THE CITY -------- Chandigarh offers a rich fare of places of tourist interest such as the Rock Garden, Pinjore Garden, Botanical Garden and Sukhna Lake. The weather here in November is very pleasant (temperature 15o-25oC). Chandigarh is well connected by bus/Train/Air from Delhi. Many trains pass Via Ambala which is about 45 Km away from Chandigarh. There is frequent bus service between Ambala and Chandigarh. CORRESPONDANCE -------------- G. P. S. Raghava, Coordinator Bioinformatics Centre. Institute of Microbial Technology Sector 39 A, Chandigarh-160 014. Phones: 0172-690004, 0172-690908, Telex: 0395-7369-IMT-IN Gram : IMTECH Fax : 0172-690585, 0172-690632 ______________________________________________________________________________ There will be opportunity of venders to advertize and demonstrate their product. Intereseted people can ask for details Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// Science does not have a country, But Scientist has one -L. Pastuer